bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome Comparison of Susceptible and Resistant Wheat in Response to Powdery Mildew Infection
Authors: Xin Mingming , Wang Xiangfeng , Peng Huiru , Yao Yingyin , Xie Chaojie , Han Yao , Ni Zhongfu , Sun Qixin 
Published: June 2012

Abstract
Powdery mildew (Pm) caused by the infection of Blumeria graminis f. sp. tritici (Bgt) is a worldwide crop disease resulting in significant loss of wheat yield. To profile the genes and pathways responding to the Bgt infection, here, using Affymetrix wheat microarrays, we compared the leaf transcriptomes before and after Bgt inoculation in two wheat genotypes, a Pm-susceptible cultivar Jingdong 8 (S) and its near-isogenic line (R) carrying a single Pm resistant gene Pm30. Our analysis showed that the original gene expression status in the S and R genotypes of wheat was almost identical before Bgt inoculation, since only 60 genes exhibited differential expression by P  = 0.01 cutoff. However, 12 h after Bgt inoculation, 3014 and 2800 genes in the S and R genotype, respectively, responded to infection. A wide range of pathways were involved, including cell wall fortification, flavonoid biosynthesis and metabolic processes. Furthermore, for the first time, we show that sense-antisense pair genes might be participants in wheat-powdery mildew interaction. In addition, the results of qRT-PCR analysis on several candidate genes were consistent with the microarray data in their expression patterns. In summary, this study reveals leaf transcriptome changes before and after powdery mildew infection in wheat near-isogenic lines, suggesting that powdery mildew resistance is a highly complex systematic response involving a large amount of gene regulation.
Searching for Non-Coding RNAs in Genomic Sequences Using ncRNAscout
Authors: Bao Michael , Cervantes Cervantes Miguel , Zhong Ling , Wang Jason T.L. 
Published: June 2012

Abstract
Recently non-coding RNA (ncRNA) genes have been found to serve many important functions in the cell such as regulation of gene expression at the transcriptional level. Potentially there are more ncRNA molecules yet to be found and their possible functions are to be revealed. The discovery of ncRNAs is a difficult task because they lack sequence indicators such as the start and stop codons displayed by protein-coding RNAs. Current methods utilize either sequence motifs or structural parameters to detect novel ncRNAs within genomes. Here, we present an ab initio ncRNA finder, named ncRNAscout, by utilizing both sequence motifs and structural parameters. Specifically, our method has three components: (i) a measure of the frequency of a sequence, (ii) a measure of the structural stability of a sequence contained in a t-score, and (iii) a measure of the frequency of certain patterns within a sequence that may indicate the presence of ncRNA. Experimental results show that, given a genome and a set of known ncRNAs, our method is able to accurately identify and locate a significant number of ncRNA sequences in the genome. The ncRNAscout tool is available for downloading at http://bioinformatics.njit.edu/ncRNAscout.
Comparative Analyses of H3K4 and H3K27 Trimethylations Between the Mouse Cerebrum and Testis
Authors: Cui Peng , Liu Wanfei , Zhao Yuhui , Lin Qiang , Zhang Daoyong , Ding Feng , Xin Chengqi , Zhang Zhang , Song Shuhui , Sun Fanglin , Yu Jun , Hu Songnian 
Published: June 2012

Abstract
The global features of H3K4 and H3K27 trimethylations (H3K4me3 and H3K27me3) have been well studied in recent years, but most of these studies were performed in mammalian cell lines. In this work, we generated the genome-wide maps of H3K4me3 and H3K27me3 of mouse cerebrum and testis using ChIP-seq and their high-coverage transcriptomes using ribominus RNA-seq with SOLiD technology. We examined the global patterns of H3K4me3 and H3K27me3 in both tissues and found that modifications are closely-associated with tissue-specific expression, function and development. Moreover, we revealed that H3K4me3 and H3K27me3 rarely occur in silent genes, which contradicts the findings in previous studies. Finally, we observed that bivalent domains, with both H3K4me3 and H3K27me3, existed ubiquitously in both tissues and demonstrated an invariable preference for the regulation of developmentally-related genes. However, the bivalent domains tend towards a “winner-takes-all” approach to regulate the expression of associated genes. We also verified the above results in mouse ES cells. As expected, the results in ES cells are consistent with those in cerebrum and testis. In conclusion, we present two very important findings. One is that H3K4me3 and H3K27me3 rarely occur in silent genes. The other is that bivalent domains may adopt a “winner-takes-all” principle to regulate gene expression.
Diatom-inferred total phosphorus from dystrophic Lake Arapisto, Finland, in relation to Holocene paleoclimate
Authors: Luoto Tomi P. , Nevalainen Liisa , Kauppila Tommi , Tammelin Mira , Sarmaja-Korjonen Kaarina 
Published: June 2012

AbstractA sediment core from Lake Arapisto, Finland, was examined for fossil diatom assemblages to reconstruct changes in Holocene nutrient availability. Our aim was to investigate the long-term relationship between lake trophic status and climate by comparing the diatom-based phosphorus reconstruction with paleoclimatic proxies. Our results showed that the cold early Holocene was characterized by elevated nutrient conditions concurrent with newly exposed fertile ground. As the climate rapidly warmed and ice sheet further retreated, the catchment vegetation developed, which resulted in decreased nutrient flux into the lake. The Holocene Thermal Maximum (HTM), between ~ 8000 and 4000 cal yr BP, was characterized by oligotrophic conditions, which may have been caused by low effective precipitation and stable watershed vegetation. After the HTM, the lake became more productive. There was no particular increase in the trophic state that could be connected to more recent human influence. Although lake productivity has been shown to be affected by temperature, our record indicated that the nutrient dynamics were driven by complex interactions between changes in temperature, precipitation, catchment, and in-lake processes. Understanding of long-term nutrient dynamics and the associated processes can help in resolving relationships between lake productivity and climate during past and present climate changes.
Constraining the onset of the Holocene “Neoglacial” over the central Italy using tephra layers
Authors: Zanchetta Giovanni , Giraudi Carlo , Sulpizio Roberto , Magny Michel , Drysdale Russell N. , Sadori Laura 
Published: June 2012

AbstractA study of six tephra layers discovered in different deposits between 1600 and 2700 m a.s.l. in the Apennine chain in central Italy allowed precise stratigraphic constraints on environmental and climatic changes between ca. 4.5 and 3.8 cal ka BP. Chemical analyses allowed the correlation of these tephra layers with the eruptions of Agnano Mt Spina (AMST) from Phlegrean Field and Avellino (AVT) from Somma–Vesuvius. Major environmental changes in the high mountains of the Central Apennines occurred just after the deposition of the AMST and predate the deposition of the AVT. At this time, renewed growth of the Calderone Glacier occurred, marking the onset of the Apennine “Neoglacial”. The presence of the AMST and AVT enabled us to make a precise, physical correlation with other archives in central Italy. Synchronization of records between sites showed that the period intervening the deposition of the AMST and AVT layers coincided with environmental changes that were not always exactly in phase. This highlights the fact that stratigraphic correlations using only radiocarbon chronologies (the most common method used for dating archives during the Holocene) could produce erroneous correlation of events, giving rise to oversimplified paleoclimatic reconstructions.
Acidic ionic liquid/water solution as both medium and proton source for electrocatalytic H
2
evolution by [Ni(P
2
N
2
)
2
]
2+
complexes
Authors: Pool Douglas H. , Stewart Michael P. , O’Hagan Molly , Shaw Wendy J. , Roberts John A. S. , Bullock R. Morris , DuBois Daniel L. 
Published: June 2012

The electrocatalytic reduction of protons to H
2
by

(where

in the highly acidic ionic liquid dibutylformamidium bis(trifluoromethanesulfonyl)amide shows a strong dependence on added water. A turnover frequency of 43,000–53,000 s
-1
has been measured for hydrogen production at 25 °C when the mole fraction of water (
χ

H
2
O

) is 0.72. The same catalyst in acetonitrile with added dimethylformamidium trifluoromethanesulfonate and water has a turnover frequency of 720 s
-1
. Thus, the use of an ionic liquid/aqueous solution enhances the observed catalytic rate by more than a factor of 50, compared to a similar acid in a traditional organic solvent. Complexes

(X = H, OMe,CH
2
P(O)(OEt)
2
, Br) are also catalysts in the ionic liquid/water mixture, and the observed catalytic rates correlate with the hydrophobicity of
X
.
Splitting CO
2
into CO and O
2
by a single catalyst
Authors: Chen Zuofeng , Concepcion Javier J. , Brennaman M. Kyle , Kang Peng , Norris Michael R. , Hoertz Paul G. , Meyer Thomas J. 
Published: June 2012

The metal complex [(tpy)(Mebim-py)Ru
II
(S)]
2+
(tpy = 2,2
′
: 6
′
,2
′′
-terpyridine; Mebim-py = 3-methyl-1-pyridylbenzimidazol-2-ylidene; S = solvent) is a robust, reactive electrocatalyst toward both water oxidation to oxygen and carbon dioxide reduction to carbon monoxide. Here we describe its use as a single electrocatalyst for CO
2
splitting, CO
2
→ CO + 1/2 O
2
, in a two-compartment electrochemical cell.
Electron transfer-based combination therapy of cisplatin with tetramethyl-
p
-phenylenediamine for ovarian, cervical, and lung cancers
Authors: Luo Ting , Yu Jianqing , Nguyen Jenny , Wang Chun-Rong , Bristow Robert G. , Jaffray David A. , Zhou Xiao Zhen , Lu Kun Ping , Lu Qing-Bin 
Published: June 2012

The platinum-based chemotherapy is the standard treatment for several types of cancer. However, cancer cells often become refractory with time and most patients with serious cancers die of drug resistance. Recently, we have discovered a unique dissociative electron-transfer mechanism of action of cisplatin, the first and most widely used platinum-based anticancer drug. Here, we show that the combination of cisplatin with an exemplary biological electron donor,
N
,
N
,
N
′,
N
′-tetramethyl-
p
-phenylenediamine (TMPD), may overcome the resistance of cancer cells to cisplatin. Our steady-state absorption and fluorescence spectroscopic measurements confirm the effective dissociative electron-transfer reaction between TMPD and cisplatin. More significantly, we found that the combination of 100 μM TMPD with cisplatin enhances double-strand breaks of plasmid DNA by a factor of approximately 3.5 and dramatically reduces the viability of cisplatin-sensitive human cervical (HeLa) cancer cells and highly cisplatin-resistant human ovarian (NIH:OVCAR-3) and lung (A549) cancer cells. Furthermore, this combination enhances apoptosis and DNA fragmentation by factors of 2–5 compared with cisplatin alone. These results demonstrate that this combination treatment not only results in a strong synergetic effect, but also makes resistant cancer cells sensitive to cisplatin. Because cisplatin is the cornerstone agent for the treatment of a variety of human cancers (including testicular, ovarian, cervical, bladder, head/neck, and lung cancers), our results show both the potential to improve platinum-based chemotherapy of various human cancers and the promise of femtomedicine as an emerging frontier in advancing cancer therapy.
Evidence for a spontaneous gapped state in ultraclean bilayer graphene
Authors: Bao Wenzhong , Velasco Jairo , Zhang Fan , Jing Lei , Standley Brian , Smirnov Dmitry , Bockrath Marc , MacDonald Allan H. , Lau Chun Ning 
Published: June 2012

At the charge neutrality point, bilayer graphene (BLG) is strongly susceptible to electronic interactions and is expected to undergo a phase transition to a state with spontaneously broken symmetries. By systematically investigating a large number of single-and double-gated BLG devices, we observe a bimodal distribution of minimum conductivities at the charge neutrality point. Although
σ
min
is often approximately 2–3
e
2
/
h
(where
e
is the electron charge and
h
is Planck’s constant), it is several orders of magnitude smaller in BLG devices that have both high mobility and low extrinsic doping. The insulating state in the latter samples appears below a transition temperature
T

c

of approximately 5 K and has a
T
= 0 energy gap of approximately 3 meV. Transitions between these different states can be tuned by adjusting disorder or carrier density.
A Reappraisal of Investing in Commodity Futures Markets
Authors: Sanders Dwight R. , Irwin Scott H. 
Published: June 2012

AbstractInvestments into commodity‐linked products have grown considerably in recent years. Unlike investments in equities, commodity futures markets produce no earnings; the source of returns is thus unclear. This paper examines returns to static long‐only U.S. commodity futures investments over five decades and finds that returns to individual futures markets are zero, and the returns to futures market portfolios depend critically on portfolio weighting schemes. Historical portfolio returns are not statistically different from zero and are driven by price episodes such as that of 1972‐1974. In other periods, portfolio returns are zero or negative. Overall, the case for long‐only investment in commodities may not be as strong as that implied in some studies (e.g., Gorton and Rouwenhorst, 2006a). If so, the growth in long‐only commodity investments may naturally subside and ease the policy debate regarding speculative position limits.
The effect of decreasing seasonal sea-ice cover on the winter Bering Sea pollock fishery
Authors: Pfeiffer Lisa , Haynie Alan C. 
Published: June 2012

Abstract
Pfeiffer, L., and Haynie, A. C. 2012. The effect of decreasing seasonal sea-ice cover on the winter Bering Sea pollock fishery. – ICES Journal of Marine Science, 69: . The winter fishing season for eastern Bering Sea pollock (Theragra chalcogramma) is during the period of maximum seasonal sea-ice extent, but harvesters avoid fishing in ice-covered waters. Global climate models predict a 40% reduction in winter ice cover by 2050, with potential implications for the costs incurred by vessels travelling to and around their fishing grounds and the value of their catch. Additionally, it may open entirely new areas to fishing. Using retrospective data from 1999 to 2009, a period of extensive annual climate variation, the variation in important characteristics of the fishery is analysed. When ice is present, it restricts a portion of the fishing grounds, but in general, ice-restricted areas have lower expected profits at the time of restriction than the areas left open. Some areas show a change in effort in warm years relative to cold, but the global redistribution of effort attributable to ice cover is small. This is largely because the winter fishery is driven by the pursuit of roe-bearing fish whose spawning location is stable in the southern part of the fishing grounds.
Does predation by grey seals (Halichoerus grypus) affect Bothnian Sea herring stock estimates?
Authors: Gårdmark Anna , Östman Örjan , Nielsen Anders , Lundström Karl , Karlsson Olle , Pönni Jukka , Aho Teija 
Published: June 2012

Abstract
Gårdmark, A., Östman, Ö., Nielsen, A., Lundström K., Karlsson O., Pönni, J., and Aho, T. 2012. Does predation by grey seals (Halichoerus grypus) affect Bothnian Sea herring stock estimates? – ICES Journal of Marine Science, 69: . Mortality of small pelagic fish due to marine mammals is generally considered to be low compared with other sources of mortality. With recent recoveries of marine mammal predators worldwide, this may no longer hold. The grey seal (Halichoerus grypus) population in the Bothnian Sea has increased fivefold since 1985. Its main prey, herring (Clupea harrengus), is a key species for fisheries in the region. Yet, current stock assessments assume constant natural mortality, leading to a risk of biased stock estimates with increasing predation and misleading analyses of herring population dynamics. We estimated grey seal predation from diet data and reanalysed herring spawning stock biomass (SSB) during 1973–2009. Accounting for predation increased the herring SSB 16% (maximum 19%), but this was within the confidence intervals when ignoring predation. Although mortality in older individuals was inflated when accounting for seal predation, this did not change the conclusions about drivers of herring dynamics. Accounting for grey seal predation is important for abundance estimates of old herring, but currently not for SSB estimates, given the great uncertainties in the standard assessment. The grey seal impact on Bothnian Sea herring will need to be reassessed if stock age composition, grey seal feeding preferences, or total stock development change.
Modelling the abundance of grey seals (Halichoerus grypus) along the Norwegian coast
Authors: Øigård Tor Arne , Frie Anne Kirstine , Nilssen Kjell Tormod , Hammill Mike Osborne 
Published: June 2012

Abstract
Øigård, T. A., Frie, A. K., Nilssen, K. T., and Hammill, M. O. 2012. Modelling the abundance of grey seals (Halichoerus grypus) along the Norwegian coast. – ICES Journal of Marine Science, 69: . An age-structured population dynamics model of the Norwegian grey seal (Halichoerus grypus) population has been developed. The model is of a Bayesian character in the sense that priors for various parameters were used. Model runs indicated an increase in the abundance of the total Norwegian grey seal population during the last 30 years, suggesting a total of 8740 (95% confidence interval: 7320–10 170) animals in 2011. A total catch of 707 (95% confidence interval: 532–882) grey seals would maintain the population size at the 2011 level. Model runs suggest that current catch levels will likely result in a reduction in the population size in Sør-Trøndelag and Nord-Trøndelag counties, and an increase in the population size in Rogaland, Nordland, Troms, and Finnmark counties. The model runs assumed that 80% of the seals taken in Rogaland came from the UK and that 50 and 55% of the catches in Troms and Finnmark, respectively, were immigrants from Russia.
Influence of asymmetrical mating patterns and male reproductive success on the maintenance of sexual polymorphism inAcer pictumsubsp.mono(Aceraceae)
Authors: SHANG HUI , LUO YI‐BO , BAI WEI‐NING 
Published: June 2012

AbstractPopulations ofAcerspecies often contain more than three sex phenotypes with complex sexual polymorphism including duodichogamy, protandry and protogyny. We identified the mechanisms that maintain sexual polymorphism inAcer pictumsubsp.mono, a temperate tree from northern China, by investigating maternal mating patterns and male reproductive success. We used paternity analyses to estimate rates of outcrossing and disassortative mating, as well as male outcrossed siring success, in a population ofA. pictumsubsp.monowith uneven sex phenotype ratios (duodichogamous 69.1%, protandrous 19.6%, protogynous 11.3%). We used a pollen‐transfer model to investigate whether the unequal ratios of sex phenotypes could be explained by the observed patterns of mating. Most progeny resulted from outcrossing, particularly disassortative among the sex phenotypes. Although the duodichogamous phenotype showed a significant amount of intraphenotypic mating, the frequency did not exceed that of disassortative mating. We detected no significant differences in male outcrossed siring success among the sex phenotypes. The pollen‐transfer model demonstrated that sex phenotype ratios could be maintained by the observed mating pattern in the population. Our results indicate that disassortative mating among the sex phenotypes can maintain sexual polymorphism inA. pictumsubsp.monoand that ratios biased towards duodichogamy can result from frequent intraphenotypic mating in this phenotype.
Limited gene flow among brown bear populations in far Northern Europe? Genetic analysis of the east–west border population in the Pasvik Valley
Authors: SCHREGEL JULIA , KOPATZ ALEXANDER , HAGEN SNORRE B. , BRØSETH HENRIK , SMITH MARTIN E. , WIKAN STEINAR , WARTIAINEN INGVILD , ASPHOLM PAUL E. , ASPI JOUNI , SWENSON JON E. , MAKAROVA OLGA , POLIKARPOVA NATALIA , SCHNEIDER MICHAEL , KNAPPSKOG PER M. , RUOKONEN MINNA , KOJOLA ILPO , TIRRONEN KONSTANTIN F. , DANILOV PJOTR I. , EIKEN HANS GEIR 
Published: June 2012

AbstractNoninvasively collected genetic data can be used to analyse large‐scale connectivity patterns among populations of large predators without disturbing them, which may contribute to unravel the species’ roles in natural ecosystems and their requirements for long‐term survival. The demographic history of brown bears (Ursus arctos) in Northern Europe indicates several extinction and recolonization events, but little is known about present gene flow between populations of the east and west. We used 12 validated microsatellite markers to analyse 1580 hair and faecal samples collected during six consecutive years (2005–2010) in the Pasvik Valley at 70°N on the border of Norway, Finland and Russia. Our results showed an overall high correlation between the annual estimates of population size (Nc), density (D), effective size (Ne) andNe/Ncratio. Furthermore, we observed a genetic heterogeneity of ∼0.8 and highNe/Ncratios of ∼0.6, which suggests gene flow from the east. Thus, we expanded the population genetic study to include Karelia (Russia, Finland), Västerbotten (Sweden) and Troms (Norway) (477 individuals in total) and detected four distinct genetic clusters with low migration rates among the regions. More specifically, we found that differentiation was relatively low from the Pasvik Valley towards the south and east, whereas, in contrast, moderately high pairwiseFSTvalues (0.91–0.12) were detected between the east and the west. Our results indicate ongoing limits to gene flow towards the west, and the existence of barriers to migration between eastern and western brown bear populations in Northern Europe.
Is Sperm Freezability Related to the Post‐Thaw Lipid Peroxidation and the Formation of Reactive Oxygen Species in Boars?
Authors: Gómez‐Fernández J , Gómez‐Izquierdo E , Tomás C , Mocé E , de Mercado E 
Published: June 2012

ContentsThe aim of the present study was to determine whether the levels of reactive oxygen species (ROS) substances production and the levels of lipid peroxidation of the sperm membrane were related to the quality that the ejaculates exhibited after cryopreservation in boars. Ejaculates from 42 healthy boars were used in this study and they were cryopreserved with the lactose‐egg yolk extender (LEY). Several sperm quality parameters were assessed by flow cytometry in samples incubated for 30 and 150 min at 37°C after thawing: the percentage of sperm with intact plasma membrane (SIPM), intracellular reactive oxygen substances production through mean of DCF fluorescence intensity of total sperm (mean‐DCF) and the percentage of viable and non‐viable sperm containing oxidized BODIPY (VSOB and NVSOB). In addition, the percentages of total motile (TMS) and progressively motile sperm (PMS) were assessed at the same incubation times with a computer‐assisted sperm analysis system. The classification of the ejaculates into good or bad freezers was performed through hierarchical cluster analysis from SIPM and TMS at 150 min post‐thawing. The ejaculates of those males classified as good freezers exhibited higher (p < 0.05) SPIM, TMS and PMS than the bad freezers, although both groups presented similar (p > 0.05) VSOB, NVSOB and mean‐DCF. Therefore, these results show that lipid peroxidation and the amount of reactive oxygen substances in the sperm after cryopreservation are similar between boars classified as good or bad freezers.