bluuebunny/crossref_metadata_2025_split huggingface dataset:
CO2 Emissions Determined by HadGEM2-ES to be Compatible with the Representative Concentration Pathway Scenarios and Their Extensions
Authors: Liddicoat Spencer , Jones Chris , Robertson Eddy 
Published: January 2013

Abstract
This paper presents the fossil fuel–derived CO2 emissions simulated by the Hadley Centre Global Environmental Model, version 2, Earth System (HadGEM2-ES) to be compatible with four representative concentration pathways (RCPs) from 2006 to 2100. For three of the four RCPs, the analysis is extended to 2300. The compatible emissions compare well with those generated by integrated assessment models from which the RCPs were constructed. Historical compatible emissions are also presented, which closely match observation-based estimates from 1860 to 2005 (cumulatively 330 and 319 GtC, respectively). Simulated land and ocean carbon uptake, which determines the compatible emissions, is examined, with an emphasis on changes in vegetation carbon. In addition, historical land and ocean carbon uptake is compared with observations. The influences of climate change and the carbon cycle on compatible emissions are investigated individually through two additional experiments in which either aspect is decoupled from the CO2 pathway. Exposure of the biogeochemical components of the Earth system to increasing CO2 is found to be responsible for 68% of the compatible emissions of the fully coupled simulation, while increased radiative forcing from the CO2 pathway reduces its compatible emissions by 11%. The importance of dynamic vegetation to compatible emissions is investigated and discussed. Two different methods of determining emissions from land use and land-use change are compared; differencing the land–atmosphere CO2 exchange of two experiments, one with fixed land use and the other variable, results in historical land-use emissions within the uncertainty range of observed estimates, while those simulated directly by the model are well below the lower limit of the observations.
Cloud and Water Vapor Feedbacks to the El Niño Warming: Are They Still Biased in CMIP5 Models?
Authors: Chen Lin , Yu Yongqiang , Sun De-Zheng 
Published: January 2013

Abstract
Previous evaluations of model simulations of the cloud and water vapor feedbacks in response to El Niño warming have singled out two common biases in models from phase 3 of the Coupled Model Intercomparison Project (CMIP3): an underestimate of the negative feedback from the shortwave cloud radiative forcing (SWCRF) and an overestimate of the positive feedback from the greenhouse effect of water vapor. Here, the authors check whether these two biases are alleviated in the CMIP5 models. While encouraging improvements are found, particularly in the simulation of the negative SWCRF feedback, the biases in the simulation of these two feedbacks remain prevalent and significant. It is shown that bias in the SWCRF feedback correlates well with biases in the corresponding feedbacks from precipitation, large-scale circulation, and longwave radiative forcing of clouds (LWCRF). By dividing CMIP5 models into two categories—high score models (HSM) and low score models (LSM)—based on their individual skills of simulating the SWCRF feedback, the authors further find that ocean–atmosphere coupling generally lowers the score of the simulated feedbacks of water vapor and clouds but that the LSM is more affected by the coupling than the HSM. They also find that the SWCRF feedback is simulated better in the models that have a more realistic zonal extent of the equatorial cold tongue, suggesting that the continuing existence of an excessive cold tongue is a key factor behind the persistence of the feedback biases in models.
CFSv2-Based Seasonal Hydroclimatic Forecasts over the Conterminous United States
Authors: Yuan Xing , Wood Eric F. , Roundy Joshua K. , Pan Ming 
Published: January 2013

AbstractThere is a long history of debate on the usefulness of climate model–based seasonal hydroclimatic forecasts as compared to ensemble streamflow prediction (ESP). In this study, the authors use NCEP's operational forecast system, the Climate Forecast System version 2 (CFSv2), and its previous version, CFSv1, to investigate the value of climate models by conducting a set of 27-yr seasonal hydroclimatic hindcasts over the conterminous United States (CONUS). Through Bayesian downscaling, climate models have higher squared correlation R2 and smaller error than ESP for monthly precipitation, and the forecasts conditional on ENSO have further improvements over southern basins out to 4 months. Verification of streamflow forecasts over 1734 U.S. Geological Survey (USGS) gauges shows that CFSv2 has moderately smaller error than ESP, but all three approaches have limited added skill against climatology beyond 1 month because of overforecasting or underdispersion errors. Using a postprocessor, 60%–70% of probabilistic streamflow forecasts are more skillful than climatology. All three approaches have plausible predictions of soil moisture drought frequency over the central United States out to 6 months, and climate models provide better results over the central and eastern United States. The R2 of drought extent is higher for arid basins and for the forecasts initiated during dry seasons, but significant improvements from CFSv2 occur in different seasons for different basins. The R2 of drought severity accumulated over CONUS is higher during winter, and climate models present added value, especially at long leads. This study indicates that climate models can provide better seasonal hydroclimatic forecasts than ESP through appropriate downscaling procedures, but significant improvements are dependent on the variables, seasons, and regions.
Bias Correction, Quantile Mapping, and Downscaling: Revisiting the Inflation Issue
Authors: Maraun Douglas 
Published: January 2013

AbstractQuantile mapping is routinely applied to correct biases of regional climate model simulations compared to observational data. If the observations are of similar resolution as the regional climate model, quantile mapping is a feasible approach. However, if the observations are of much higher resolution, quantile mapping also attempts to bridge this scale mismatch. Here, it is shown for daily precipitation that such quantile mapping–based downscaling is not feasible but introduces similar problems as inflation of perfect prognosis (“prog”) downscaling: the spatial and temporal structure of the corrected time series is misrepresented, the drizzle effect for area means is overcorrected, area-mean extremes are overestimated, and trends are affected. To overcome these problems, stochastic bias correction is required.
Sudden Tropical Cyclone Track Changes over the Western North Pacific: A Composite Study
Authors: Wu Liguang , Ni Zhongping , Duan Jingjing , Zong Huijun 
Published: January 2013

Abstract
Tropical cyclones (TCs) over the western North Pacific (WNP) are usually embedded in the multitime-scale summer monsoon circulation and occasionally experience sudden track changes, which are currently a challenge in TC forecasting. A composite analysis of 15 sudden north-turning cases and 14 west-turning cases that occurred during the period 2000–10 was conducted with a focus on influences of low-frequency monsoon circulations. It is found that TCs in the two specific categories of track changes are embedded in a monsoon gyre of about 2500 km in diameter on the quasi-biweekly oscillation (QBW) time scale, which is also embedded in a larger-scale cyclonic gyre or monsoon trough on the Madden–Julian oscillation (MJO) time scale. The two types of track changes are closely associated with interaction between low-frequency and synoptic flows. Two different types of asymmetric flow patterns are identified on the synoptic time scale in the vicinity of these TCs. In the north-turning case, enhanced winds lie mainly on the southeast side of TCs due to strong ridging associated with interactions between low-frequency and synoptic flows. In the west-turning case, the westward extension of the subtropical high leads to ridging on the northwest side of TCs and the enhanced winds can largely offset the steering of enhanced southwesterly winds on the synoptic time scale. Thus the north-turning (west turning) sudden track changes are affected primarily by the synoptic-scale (low frequency) steering. This may be one of the reasons for the larger forecasting errors in the north-turning case than in the west-turning case.
Mechanism of Orographic Precipitation around the Meghalaya Plateau Associated with Intraseasonal Oscillation and the Diurnal Cycle
Authors: Sato Tomonori 
Published: January 2013

Abstract
Mesoscale processes that cause tremendous amounts of precipitation around the Meghalaya Plateau, northeast India, were investigated using a regional atmospheric model, with a particular focus on the possible role of an intraseasonal oscillation (ISO) and the diurnal cycle. A numerical experiment was conducted using the Weather Research and Forecasting Model (WRF) to simulate a prominent submonthly-scale ISO event observed during June–July 2004. A WRF experiment successfully simulated the timing and magnitude of precipitation during the first active period and subsequent inactive period of the ISO, despite large biases in the second active period. The WRF experiment revealed that the magnitude of prevailing southwesterly winds in the lower troposphere differs significantly between active and inactive periods; strong southwesterly flow transports abundant moisture to the southern slope of the Meghalaya Plateau during the active period, which triggers forced lifting and brings orographic precipitation. However, low-level wind during the inactive period is too weak to overcome the vertical stratification barrier; hence, it is unable to reach the condensation level. The WRF experiment suggested that the diurnal cycle of precipitation is enhanced during the active period, exhibiting an evening to early morning maximum, as observed by the Tropical Rainfall Measuring Mission (TRMM). The experiment also indicated a prominent nocturnal low-level jet (LLJ) appearing at 900 hPa. The direction of the LLJ varies clockwise with time, which accelerates the preexisting southwesterly flow during 1800–0600 LT. The diurnal variation of the LLJ is responsible for the evening to early morning maximum of precipitation, thus contributing to the precipitation variability in the ISO.
The Impact of Climate on Atmospheric Emissions: Constructing an Index of Heating Degrees for 21 OECD Countries from 1960 to 2005*
Authors: Jahn Detlef 
Published: January 2013

Abstract
The impact of climate on atmospheric emissions is a highly neglected aspect in research on environmental performance. Cold winters may be a major factor for the increase in heating needs and energy consumption, which may in turn lead to substantial increases in atmospheric emissions, thus contributing to climate change. To measure such an impact, this article develops an index that measures the heating requirements in highly populated regions in 21 Organisation for Economic Co-operation and Development (OECD) countries from 1960 to 2005. Applying this index of heating degree months (HDMs) to atmospheric emissions shows that climate has a significant effect. This is above all true for particular atmospheric emissions that have not been substantially reduced over the last three decades. For atmospheric emissions that have been substantially reduced, climate has no explanatory power, suggesting that other factors such as policies and technological development may explain the reduction. These results remain robust when controlling for various aspects of energy production, economic development, and structural changes.
Gender Violence in Portugal: Discourses, Knowledge and Practices
Authors: Azambuja Mariana , Nogueira Conceição , Neves Sofia , de Oliveira João Manuel 
Published: January 2013

This article discusses the emergence of feminism in Portugal with special emphasis on the actions taken in confronting gender violence. Starting with the history of feminist movements and its implications for the development of the country, it maps public policies, legal measures and victim support institutions/services to better understand the phenomena of violence against women and to identify strategies, adopted in the last decades, to confront it. Presenting a synthesis of some Portuguese studies on women and violence, this article mirrors the increasing interest in the study of violence against women in the academic context and especially in the context of gender studies.
Still Heard: Echoes from a Colonial Past
Authors: Vatsal Tulsi 
Published: January 2013

In the 19th century, Parsi women started wearing elaborately embroidered saris known as garas. What is not generally known is that these beautiful textiles were imported from China. Their arrival in India forms a little known sub-plot in the wider saga of British imperialism and the unique Parsi response to the imperatives of foreign rule. When new marketing opportunities opened up in China for the East India Company in the second half of the 18th century, the Parsis were well-positioned to take advantage of them. By the 1830s, the Parsis had become leading players in the China trade. Clothing, that very visible marker of social status, was part of the wider process through which the Parsis came to identify themselves with the ruling elite. While Parsi women continued to wear saris, they achieved a modern and sophisticated look by adding elements of Western fashion to their clothing. It is reasonable to conjecture that the appeal of Chinese embroidery was a reflection of prevailing fashion trends in Britain. Parsi clients selected designs for their garas from the same generic pattern books used as sources for other Chinese export embroideries, including those that went to Europe and America. Workshops producing ‘Chinese’ embroidery sprang up in Surat and, in time, Parsi housewives, especially in smaller towns, also took up the craft, their embroidery skills providing a welcome source of income. This article traces the history of the gara and its association with imperialism as well as trade with China.
Reverse-Bayes analysis of two common misinterpretations of significance tests
Authors: Held Leonhard 
Published: January 2013

Background Misunderstanding of significance tests and P values is widespread in clinical research and elsewhere. Purpose To assess the implications of two common mistakes in the interpretation of statistical significance tests. The first one is the misinterpretation of the type I error rate as the expected proportion of false-positive results among all those called significant, also known as the false-positive report probability (FPRP). The second is the misinterpretation of a P value as (posterior) probability of the null hypothesis. Methods A reverse-Bayes approach is used to calculate a lower bound on the proportion of truly effective treatments that would ensure the FPRP to be equal or below the type I error rate. A reverse-Bayes approach using minimum Bayes factors (BFs) yields upper bounds on the prior probability of the null hypothesis that would justify the interpretation of the P value as the posterior probability of the null hypothesis. Results In a typical clinical trials setting, more than 50% of the treatments need to be truly effective to justify equality of the type I error rate and the FPRP. To interpret the P value as posterior probability, the difference between the corresponding prior probability and the P value cannot exceed 12.4 percentage points. Limitations The first analysis requires that the (one-sided) type I error rate is smaller than the type II error rate. The second result is valid under different scenarios describing how to transform P values to minimum BFs. Conclusions The two misinterpretations imply strong and often unrealistic assumptions on the prior proportion or probability of truly effective treatments.
Blood cell mRNAs and microRNAs: optimized protocols for extraction and preservation
Authors: Eikmans Michael , Rekers Niels V. , Anholts Jacqueline D. H. , Heidt Sebastiaan , Claas Frans H. J. 
Published: January 2013

Key PointsAn optimized protocol for obtaining and preserving RNA from blood cells is provided. The results serve as guideline for sensitive measurement of mRNA and microRNA expression in clinical material.
Lineage relationships of human interleukin-22–producing CD56+ RORγt+ innate lymphoid cells and conventional natural killer cells
Authors: Ahn Yong-Oon , Blazar Bruce R. , Miller Jeffrey S. , Verneris Michael R. 
Published: January 2013

Key PointsILC22 and cNK cells can be distinguished on the basis of LFA-1 expression. ILC22 and cNK cells have differing requirements for their development from hematopoietic stem cells.
Inflammatory neovascularization during graft-versus-host disease is regulated by αv integrin and miR-100
Authors: Leonhardt Franziska , Grundmann Sebastian , Behe Martin , Bluhm Franziska , Dumont Rebecca A. , Braun Friederike , Fani Melpomeni , Riesner Katarina , Prinz Gabriele , Hechinger Anne-Kathrin , Gerlach Ulrike V. , Dierbach Heide , Penack Olaf , Schmitt-Gräff Annette , Finke Jürgen , Weber Wolfgang A. , Zeiser Robert 
Published: January 2013

Key Points
Our data from the mouse model and patients indicate that inflammatory neovascularization during GvHD is targetable via αv integrin. We identify a negative regulation of GvHD-related neovascularization by miR-100.
Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data
Authors: Gallant Andrew , Leiserson Mark DM , Kachalov Maxim , Cowen Lenore J , Hescott Benjamin J 
Published: January 2013

Abstract

Background
New technology has resulted in high-throughput screens for pairwise genetic interactions in yeast and other model organisms. For each pair in a collection of non-essential genes, an epistasis score is obtained, representing how much sicker (or healthier) the double-knockout organism will be compared to what would be expected from the sickness of the component single knockouts. Recent algorithmic work has identified graph-theoretic patterns in this data that can indicate functional modules, and even sets of genes that may occur in compensatory pathways, such as a BPM-type schema first introduced by Kelley and Ideker. However, to date, any algorithms for finding such patterns in the data were implemented internally, with no software being made publically available.

Results
Genecentric is a new package that implements a parallelized version of the Leiserson et al. algorithm (J Comput Biol 18:1399-1409, 2011) for generating generalized BPMs from high-throughput genetic interaction data. Given a matrix of weighted epistasis values for a set of double knock-outs, Genecentric returns a list of generalized BPMs that may represent compensatory pathways. Genecentric also has an extension, GenecentricGO, to query FuncAssociate (Bioinformatics 25:3043-3044, 2009) to retrieve GO enrichment statistics on generated BPMs. Python is the only dependency, and our web site provides working examples and documentation.

Conclusion
We find that Genecentric can be used to find coherent functional and perhaps compensatory gene sets from high throughput genetic interaction data. Genecentric is made freely available for download under the GPLv2 from http://bcb.cs.tufts.edu/genecentric.
De novotranscriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity
Authors: Venturini Luca , Ferrarini Alberto , Zenoni Sara , Tornielli Giovanni Battista , Fasoli Marianna , Santo Silvia Dal , Minio Andrea , Buson Genny , Tononi Paola , Zago Elisa Debora , Zamperin Gianpiero , Bellin Diana , Pezzotti Mario , Delledonne Massimo 
Published: January 2013

Abstract

Background
Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to disentangle genetic and environmental factors.

Results
We have shown that cDNA sequencing by RNA-seq is a robust approach for the characterization of varietal diversity between a local grapevine cultivar (Corvina) and the PN40024 reference genome. We detected 15,161 known genes including 9463 with novel splice isoforms, and identified 2321 potentially novel protein-coding genes in non-annotated or unassembled regions of the reference genome. We also discovered 180 apparent private genes in the Corvina genome which were missing from the reference genome.

Conclusions
The de novo assembly approach allowed a substantial amount of the Corvina transcriptome to be reconstructed, improving known gene annotations by robustly defining gene structures, annotating splice isoforms and detecting genes without annotations. The private genes we discovered are likely to be nonessential but could influence certain cultivar-specific characteristics. Therefore, the application of de novo transcriptome assembly should not be restricted to species lacking a reference genome because it can also improve existing reference genome annotations and identify novel, cultivar-specific genes.
Characterization of a newly identified rice chitinase-like protein (OsCLP) homologous to xylanase inhibitor
Authors: Wu Jingni , Wang Yiming , Kim Sun Tae , Kim Sang Gon , Kang Kyu Young 
Published: January 2013

Abstract

Background
During rice blast fungal attack, plant xylanase inhibitor proteins (XIPs) that inhibit fungal xylanase activity are believed to act as a defensive barrier against fungal pathogens. To understand the role of XIPs in rice, a xylanase inhibitor was cloned from rice. The expression of this gene was examined at the transcriptional/translational levels during compatible and incompatible interactions, and the biochemical activity of this protein was also examined.

Results
Sequence alignment revealed that the deduced amino acid sequence of OsCLP shares a high degree of similarity with that of other plant TAXI-type XIPs. However, recombinant OsCLP did not display inhibitory activity against endo-1,4-β-xylanase enzymes from Aureobasidium pullulans (A. pullulans) or Trichoderma viride (T. viride). Instead, an in-gel activity assay revealed strong chitinase activity. The transcription and translation of OsCLP were highly induced when rice was exposed to pathogens in an incompatible interaction. In addition, exogenous treatment with OsCLP affected the growth of the basidiomycete fungus Rhizoctonia solani through degradation of the hyphal cell wall. These data suggest that OsCLP, which has chitinase activity, may play an important role in plant defenses against pathogens.

Conclusions
Taken together, our results demonstrate that OsCLP may have antifungal activity. This protein may directly inhibit pathogen growth by degrading fungal cell wall components through chitinase activity.
Optical absorption and photoluminescence studies of gold nanoparticles deposited on porous silicon
Authors: Amran Tengku Sarah Tengku , Hashim Md Roslan , Al-Obaidi Nihad K Ali , Yazid Hanani , Adnan Rohana 
Published: January 2013

Abstract
We present an investigation on a coupled system consists of gold nanoparticles and silicon nanocrystals. Gold nanoparticles (AuNPs) embedded into porous silicon (PSi) were prepared using the electrochemical deposition method. Scanning electron microscope images and energy-dispersive X-ray results indicated that the growth of AuNPs on PSi varies with current density. X-ray diffraction analysis showed the presence of cubic gold phases with crystallite sizes around 40 to 58 nm. Size dependence on the plasmon absorption was studied from nanoparticles with various sizes. Comparison with the reference sample, PSi without AuNP deposition, showed a significant blueshift with decreasing AuNP size which was explained in terms of optical coupling between PSi and AuNPs within the pores featuring localized plasmon resonances.