bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stripe-like nanoscale structural phase separation in superconducting BaPb1−xBixO3
Authors: Giraldo-Gallo P. , Zhang Y. , Parra C. , Manoharan H.C. , Beasley M.R. , Geballe T.H. , Kramer M.J. , Fisher I.R. 
Published: September 2015

AbstractThe phase diagram of BaPb1−xBixO3 exhibits a superconducting dome in the proximity of a charge density wave phase. For the superconducting compositions, the material coexists as two structural polymorphs. Here we show, via high-resolution transmission electron microscopy, that the structural dimorphism is accommodated in the form of partially disordered nanoscale stripes. Identification of the morphology of the nanoscale structural phase separation enables determination of the associated length scales, which we compare with the Ginzburg–Landau coherence length. We find that the maximum Tc occurs when the superconducting coherence length matches the width of the partially disordered stripes, implying a connection between the structural phase separation and the shape of the superconducting dome.
Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA
Authors: Izumchenko Evgeny , Chang Xiaofei , Brait Mariana , Fertig Elana , Kagohara Luciane T. , Bedi Atul , Marchionni Luigi , Agrawal Nishant , Ravi Rajani , Jones Sian , Hoque Mohammad O. , Westra William H. , Sidransky David 
Published: September 2015

AbstractLungs resected for adenocarcinomas often harbour minute discrete foci of cytologically atypical pneumocyte proliferations designated as atypical adenomatous hyperplasia (AAH). Evidence suggests that AAH represents an initial step in the progression to adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA) and fully invasive adenocarcinoma. Despite efforts to identify predictive markers of malignant transformation, alterations driving this progression are poorly understood. Here we perform targeted next-generation sequencing on multifocal AAHs and different zones of histologic progression within AISs and MIAs. Multiregion sequencing demonstrated different genetic drivers within the same tumour and reveal that clonal expansion is an early event of tumorigenesis. We find that KRAS, TP53 and EGFR mutations are indicators of malignant transition. Utilizing droplet digital PCR, we find alterations associated with early neoplasms in paired circulating DNA. This study provides insight into the heterogeneity of clonal events in the progression of early lung neoplasia and demonstrates that these events can be detected even before neoplasms have invaded and acquired malignant potential.
Reconstruction of cropland cover changes in the Shandong Province over the past 300 years
Authors: Ye Yu , Wei Xueqiong , Li Fan , Fang Xiuqi 
Published: September 2015

AbstractTo advance global change rssearch, it is essential to reconstruct changes in historical cropland coverage on a regional scale in China. This paper presents data collected from 244 local gazetteers, government statistical records and remote-sensing land cover data from the Shandong Province. The study reconstructed the spatial distribution of the rate of reclaimed land at the county level and compared this map with a map of the current spatial distribution of suitable cropland. The following conclusions were drawn: (i) The rate of cultivated land grew exponentially. The extent of reconstruction in cropland areas during the 17th century, 18th~19th centuries, the beginning of the 20th century, the 1980 s and the beginning of the 20th century are 4.51 mha, 6.51 mha, 7.52 mha, 8.53 mha and 11.80–12.00 mha, respectively. (ii) Several agricultural centers formed during the late 17th century. Until the beginning of the 20th century, the reclamation rate increased rapidly near the four southern lakes, which are located in the Zaozhuang and Linyi regions. (iii) Most reclamation activities before the 19th century occurred in suitable agricultural areas and the cultivated land was already reclaimed by the beginning of the 20th century.
Genomic insights into the taxonomic status of the Bacillus cereus group
Authors: Liu Yang , Lai Qiliang , Göker Markus , Meier-Kolthoff Jan P. , Wang Meng , Sun Yamin , Wang Lei , Shao Zongze 
Published: September 2015

AbstractThe identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clearly separated 224 strains into 30 clusters, representing eleven known, partially merged species and accordingly 19–20 putative novel species. Additionally, 16S rRNA gene analysis, a novel variant of multi-locus sequence analysis (nMLSA) and screening of virulence genes were performed. The 16S rRNA gene sequence was not sufficient to differentiate the bacteria within this group due to its high conservation. The nMLSA results were consistent with GBDP. Moreover, a fast typing method was proposed using the pycA gene and where necessary, the ccpA gene. The pXO plasmids and cry genes were widely distributed, suggesting little correlation with the phylogenetic positions of the host bacteria. This might explain why classifications based on virulence characteristics proved unsatisfactory in the past. In summary, this is the first large-scale and systematic study of the taxonomic status of the bacteria within the B. cereus group using whole-genome sequences and is likely to contribute to further insights into their pathogenicity, phylogeny and adaptation to diverse environments.
Recovery trajectories of kelp forest animals are rapid yet spatially variable across a network of temperate marine protected areas
Authors: Caselle Jennifer E. , Rassweiler Andrew , Hamilton Scott L. , Warner Robert R. 
Published: September 2015

AbstractOceans currently face a variety of threats, requiring ecosystem-based approaches to management such as networks of marine protected areas (MPAs). We evaluated changes in fish biomass on temperate rocky reefs over the decade following implementation of a network of MPAs in the northern Channel Islands, California. We found that the biomass of targeted (i.e. fished) species has increased consistently inside all MPAs in the network, with an effect of geography on the strength of the response. More interesting, biomass of targeted fish species also increased outside MPAs, although only 27% as rapidly as in the protected areas, indicating that redistribution of fishing effort has not severely affected unprotected populations. Whether the increase outside of MPAs is due to changes in fishing pressure, fisheries management actions, adult spillover, favorable environmental conditions, or a combination of all four remains unknown. We evaluated methods of controlling for biogeographic or environmental variation across networks of protected areas and found similar performance of models incorporating empirical sea surface temperature versus a simple geographic blocking term based on assemblage structure. The patterns observed are promising indicators of the success of this network, but more work is needed to understand how ecological and physical contexts affect MPA performance.
Donkey genome and insight into the imprinting of fast karyotype evolution
Authors: Huang Jinlong , Zhao Yiping , Bai Dongyi , Shiraigol Wunierfu , Li Bei , Yang Lihua , Wu Jing , Bao Wuyundalai , Ren Xiujuan , Jin Burenqiqige , Zhao Qinan , Li Anaer , Bao Sarula , Bao Wuyingga , Xing Zhencun , An Aoruga , Gao Yahan , Wei Ruiyuan , Bao Yirugeletu , Bao Taoketao , Han Haige , Bai Haitang , Bao Yanqing , Zhang Yuhong , Daidiikhuu Dorjsuren , Zhao Wenjing , Liu Shuyun , Ding Jinmei , Ye Weixing , Ding Fangmei , Sun Zikui , Shi Yixiang , Zhang Yan , Meng He , Dugarjaviin Manglai 
Published: September 2015

AbstractThe donkey, like the horse, is a promising model for exploring karyotypic instability. We report the de novo whole-genome assemblies of the donkey and the Asiatic wild ass. Our results reflect the distinct characteristics of donkeys, including more effective energy metabolism and better immunity than horses. The donkey shows a steady demographic trajectory. We detected abundant satellite sequences in some inactive centromere regions but not in neocentromere regions, while ribosomal RNAs frequently emerged in neocentromere regions but not in the obsolete centromere regions. Expanded miRNA families and five newly discovered miRNA target genes involved in meiosis may be associated with fast karyotype evolution. APC/C, controlling sister chromatid segregation, cytokinesis and the establishment of the G1 cell cycle phase were identified by analysis of miRNA targets and rapidly evolving genes.
Signatures of new d-wave vortex physics in overdoped Tl2Ba2CuO6+x revealed by TF-µ+SR
Authors: Brewer Jess H. , Stubbs Scott L. , Liang Ruixing , Bonn D. A. , Hardy W. N. , Sonier J. E. , MacFarlane W. Andrew , Peets Darren C. 
Published: September 2015

AbstractThe spontaneous expulsion of applied magnetic field, the Meissner effect, is a defining feature of superconductors; in Type-II superconductors above the lower critical field, this screening takes the form of a lattice of magnetic flux vortices. Using implanted spin-1/2 positive muons, one can measure the vortex lattice field distribution through the spin precession and deduce key parameters of the superconducting ground state and thereby fundamental properties of the superconducting pairing. Muon spin rotation/relaxation (µSR) experiments have indeed revealed much interesting physics in the underdoped cuprates, where superconductivity is closely related to, or coexistent with, disordered or fluctuating magnetic and charge excitations. Such complications should be absent in overdoped cuprates, which are believed to exhibit conventional Fermi liquid behaviour. These first transverse field (TF)-µ+SR experiments on heavily-overdoped single crystals reveal a superfluid density exhibiting a clear inflection point near 0.5Tc , with a striking doping-independent scaling. This reflects hitherto unrecognized physics intrinsic to d-wave vortices, evidently generic to the cuprates and may offer fundamentally new insights into their still-mysterious superconductivity.
Signatures of selection in tilapia revealed by whole genome resequencing
Authors: Hong Xia Jun , Bai Zhiyi , Meng Zining , Zhang Yong , Wang Le , Liu Feng , Jing Wu , Yi Wan Zi , Li Jiale , Lin Haoran , Hua Yue Gen 
Published: September 2015

AbstractNatural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10–100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia.
Polarization dependent photocurrent in the Bi2Te3 topological insulator film for multifunctional photodetection
Authors: Yao J. D. , Shao J. M. , Li S. W. , Bao D. H. , Yang G. W. 
Published: September 2015

AbstractThree dimensional Z2 Topological insulator (TI) is an unconventional phase of quantum matter possessing insulating bulk state as well as time-reversal symmetry-protected Dirac-like surface state, which is demonstrated by extensive experiments based on surface sensitive detection techniques. This intriguing gapless surface state is theoretically predicted to exhibit many exotic phenomena when interacting with light and some of them have been observed. Herein, we report the first experimental observation of novel polarization dependent photocurrent of photodetectors based on the TI Bi2Te3 film under irradiation of linearly polarized light. This photocurrent is linearly dependent on both the light intensity and the applied bias voltage. To pursue the physical origin of the polarization dependent photocurrent, we establish the basic TI surface state model to treat the light irradiation as a perturbation and we adopt the Boltzmann equation to calculate the photocurrent. It turns out that the theoretical results are in nice qualitative agreement with the experiment. These findings show that the polycrystalline TI Bi2Te3 film working as a multifunctional photodetector can not only detect the light intensity, but also measure the polarization state of the incident light, which is remarkably different from conventional photodetectors that usually only detect the light intensity.
Luteinizing hormone induces ovulation via tumor necrosis factor α-dependent increases in prostaglandin F2α in a nonmammalian vertebrate
Authors: Crespo Diego , Goetz Frederick W. , Planas Josep V. 
Published: September 2015

AbstractOvulation is induced by the preovulatory surge of luteinizing hormone (LH) that acts on the ovary and triggers the rupture of the preovulatory ovarian follicle by stimulating proteolysis and apoptosis in the follicle wall, causing the release of the mature oocyte. The pro-inflammatory cytokine tumor necrosis factor α (TNFα) and prostaglandin (PG) F2α (PGF2α) are involved in the control of ovulation but their role mediating the pro-ovulatory actions of LH is not well established. Here we show that Lh induces PGF2α synthesis through its stimulation of Tnfα production in trout, a primitive teleost fish. Recombinant trout Tnfα (rTnfα) and PGF2α recapitulate the stimulatory in vitro effects of salmon Lh (sLh) on contraction, proteolysis and loss of cell viability in the preovulatory follicle wall and, finally, ovulation. Furthermore, all pro-ovulatory actions of sLh are blocked by inhibition of Tnfα secretion or PG synthesis and all actions of rTnfα are blocked by PG synthesis inhibitors. Therefore, we provide evidence that the Tnfα–dependent increase in PGF2α production is necessary for the pro-ovulatory actions of Lh. The results from this study shed light onto the mechanisms underlying the pro-ovulatory actions of LH in vertebrates and may prove important in clinical assessments of female infertility.
Subcellular trafficking of guanylyl cyclase/natriuretic peptide receptor-A with concurrent generation of intracellular cGMP
Authors: Mani Indra , Garg Renu , Tripathi Satyabha , Pandey Kailash N. 
Published: September 2015

Atrial natriuretic peptide (ANP) activates guanylyl cyclase/natriuretic peptide receptor-A (GC-A/NPRA), which lowers blood pressure and blood volume. The objective of the present study was to visualize internalization and trafficking of enhanced GFP (eGFP)-tagged NPRA (eGFP–NPRA) in human embryonic kidney-293 (HEK-293) cells, using immunofluorescence (IF) and co-immunoprecipitation (co-IP) of eGFP–NPRA. Treatment of cells with ANP initiated rapid internalization and co-localization of the receptor with early endosome antigen-1 (EEA-1), which was highest at 5 min and gradually decreased within 30 min. Similarly, co-localization of the receptor was observed with lysosome-associated membrane protein-1 (LAMP-1); however, after treatment with lysosomotropic agents, intracellular accumulation of the receptor gradually increased within 30 min. Co-IP assays confirmed that the localization of internalized receptors occurred with subcellular organelles during the endocytosis of NPRA. Rab 11, which was used as a recycling endosome (Re) marker, indicated that ∼20% of receptors recycled back to the plasma membrane. ANP-treated cells showed a marked increase in the IF of cGMP, whereas receptor was still trafficking into the intracellular compartments. Thus, after ligand binding, NPRA is rapidly internalized and trafficked from the cell surface into endosomes, Res and lysosomes, with concurrent generation of intracellular cGMP.
System flexibility provision using short term grid scale storage
Authors: Devlin Joseph , Li Kang , Higgins Paraic , Foley Aoife 
Published: September 2015

This study presents a novel analysis of the utilisation of grid scale energy storage to mitigate negative system operational impacts due to high penetrations of wind power. This was investigated by artificially lowering the minimum stable generation level of a gas thermal generating unit coupled to a storage device over a five hour storage charging window using a unit commitment and economic dispatch model. The key findings of the analysis were a 0.18% reduction in wind curtailment, a 2.35 MW/min reduction in the ramping rate required to be met by all generators in the test system during a representative period and a total generation cost reduction of €6.5 million.
The myokine irisin increases cortical bone mass
Authors: Colaianni Graziana , Cuscito Concetta , Mongelli Teresa , Pignataro Paolo , Buccoliero Cinzia , Liu Peng , Lu Ping , Sartini Loris , Di Comite Mariasevera , Mori Giorgio , Di Benedetto Adriana , Brunetti Giacomina , Yuen Tony , Sun Li , Reseland Janne E. , Colucci Silvia , New Maria I. , Zaidi Mone , Cinti Saverio , Grano Maria 
Published: September 2015

Significance
Although exercise is a well known and potent stimulus for new bone formation, and weightlessness or muscle loss characteristically cause bone loss, it has remained unclear how muscle talks to bone, despite their close proximity. Here, we show that a molecule irisin derived from skeletal muscle in response to exercise has profound effects in enhancing mass and improving the geometry and strength specifically of cortical bone, the key function of which is to resist bending and torsion. Trabecular bone, which is a reservoir for bodily calcium, is remarkably spared. Irisin may therefore not only be the molecule responsible for muscle–bone connectivity, but could also become a therapy for sarcopenia and osteoporosis, which occur in tandem in the elderly.
Propagation of Hybrid Devils Hole Pupfish × Ash Meadows Amargosa Pupfish
Authors: Feuerbacher Olin G , Mapula Justin A , Bonar Scott A 
Published: September 2015

Abstract
Recent censuses of Devils Hole Pupfish Cyprinodon diabolis revealed that fewer than 100 individuals currently remain in the wild. Captive propagation is among actions being considered to prevent their extinction, but no pure-strain Devils Hole Pupfish were available for broodstock. To help provide emergency information, we investigated techniques to propagate their most closely related relative, hybrid Devils Hole Pupfish C. diabolis × Ash Meadows Amargosa Pupfish C. nevadensis mionectes. We tested various temperatures and larval feeds with respect to egg production, larval survival, and growth. Larval survival and growth were similar from 24°C to 32°C and egg production peaked at static 28°C; however, reducing water temperatures to 23°C and then raising them to 28°C resulted in even higher production. Larvae fed infusoria, Rio Grande Silvery Minnow Chow (RGSM), or Zeigler larval diet (ZLD) had the highest survival (79.4, 71.6, and 73.4%, respectively), and those fed Otohime (OTO) had the lowest survival (60.8%), although OTO provided greatest (14 mm) 30-d growth. Supplementation of RGSM or ZLD with Artemia nauplii increased growth but decreased survival. Larval production was maximized by placing six spawning mops, constructed of yarn and tile, in each of four 437-L parental aquaria, stocked with 24 adult fish each (1:1 sex ratio) for 3 d, to attract adults and provide spawning substrate. A 30% water change conducted on the same day of mop placement lowered water temperature from 28°C to 23°C. Water temperature was raised back to 28°C over 48 h. After 3 d, mops were transferred to hatching aquaria that were held at 28°C and aerated until larval hatch. Although some differences likely exist in effective propagation techniques for hybrid and pure-strain Devils Hole Pupfish, these data help provide initial recommendations to aid recovery.
Tolerance and Avoidance Behavior towards Gas Supersaturation in Rock Carp Procypris rabaudi with a History of Previous Exposure
Authors: Wang Yuanming , Liang Ruifeng , Tuo Youcai , Li Kefeng , Hodges Ben 
Published: September 2015

Abstract
Total dissolved gas (TDG) supersaturation on the upper Yangtze River basin is becoming increasingly serious because of the intense construction of high dams, posing a threat to resident fish. The tolerance and behavior characteristics of Rock Carp Procypris rabaudi preexposed to TDG-supersaturated water were evaluated by placing juveniles (weight 6.4 ± 1.67 g, fork length 7.2 ± 0.7 cm; mean ± SD) in 35-cm-deep tanks at 130% supersaturation for 2.33 h as preexposure. Surviving fish were allowed 5 d of recovery in saturated-equilibrium (100% TDG) water and then examined in an acute lethality experiment at TDG supersaturation values of 120, 125, 130, 135, 140, and 145%. The resulting median lethal times were 10.4, 4.6, 3.2, 2.1, 1.4, and 1.4 h, respectively. The preexposed fish showed a poorer tolerance to TDG-supersaturated water than did a control group that were not preexposed for TDG above 120% supersaturation (P &lt; 0.05 in cases where there was a significant difference between individual groups). Experiments on horizontal behavior and vertical behavior used the same preexposure routine, followed by 5 d of recovery in saturated-equilibrium water. For all behavior experiments, both the preexposed and control groups showed significant avoidance responses to TDG-supersaturated water; however, there were no significant differences between the preexposed and control groups.
Impact of Minimum Daily Dissolved Oxygen Concentration on Production Performance of Hybrid Female Channel Catfish × Male Blue Catfish
Authors: Torrans Les , Ott Brian , Bosworth Brian 
Published: September 2015

Abstract
Hybrid catfish (♀ Channel Catfish Ictalurus punctatus × ♂ Blue Catfish I. furcatus) were reared as single-batch crops during the growing season (June–September) of two years under two different dissolved oxygen (DO) regimes each year: (1) a high-DO (control) treatment with minimum daily DO maintained above 3.8 ppm in both years and (2) a low-DO (test) treatment with minimum DO maintained at 1.6 ppm in the first year and 1.3 ppm in the second year. Fish were fed daily to apparent satiation with a 32% protein commercial feed and harvested each year. In both years, dissolved oxygen concentration significantly impacted gross and net production, final fish weight, and mean fish weight gain due to reduced feed intake. Feed intake was reduced in the low-DO treatment by 26.6% in year 1 and 29.2% in year 2. Food conversion ratios averaged 1.83 overall and were not affected by minimum DO. Fish in high-DO treatments gained an average of 44% more weight (1.50 lb/fish) than fish in low-DO treatments (1.04 lb/fish). Initial weight at stocking also had a significant impact on weight gain: fish stocked at a 0.16-lb average weight (year 2) gained 37% more weight than fish stocked at a 0.11-lb average weight (year 1), even though the stocking rate of the larger fish was 50% higher. Hybrid catfish had less reduction in feed intake at reduced DO compared with reported values for Channel Catfish and Blue Catfish.