bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autoantibodies to IgG/HLA class II complexes are associated with rheumatoid arthritis susceptibility
Authors: Jin Hui , Arase Noriko , Hirayasu Kouyuki , Kohyama Masako , Suenaga Tadahiro , Saito Fumiji , Tanimura Kenji , Matsuoka Sumiko , Ebina Kosuke , Shi Kenrin , Toyama-Sorimachi Noriko , Yasuda Shinsuke , Horita Tetsuya , Hiwa Ryosuke , Takasugi Kiyoshi , Ohmura Koichiro , Yoshikawa Hideki , Saito Takashi , Atsumi Tatsuya , Sasazuki Takehiko , Katayama Ichiro , Lanier Lewis L. , Arase Hisashi 
Published: February 2014

SignificanceCellular misfolded proteins are transported to the cell surface by MHC class II molecules via association with the peptide-binding groove without processing to peptides. We found that IgG heavy chain is transported to the cell surface by MHC class II molecules. Furthermore, IgG heavy chain associated with MHC class II molecules is recognized by autoantibodies in rheumatoid arthritis patients. Autoantibody binding to IgG heavy chain complexed with different MHC class II alleles was strongly associated with rheumatoid arthritis susceptibility conferred by certain MHC class II alleles. These findings suggest that misfolded proteins complexed with MHC class II molecules could be targets for autoantibodies in autoimmune diseases, which might be involved in autoimmune disease susceptibility.
Eukaryotic algal phytochromes span the visible spectrum
Authors: Rockwell Nathan C. , Duanmu Deqiang , Martin Shelley S. , Bachy Charles , Price Dana C. , Bhattacharya Debashish , Worden Alexandra Z. , Lagarias J. Clark 
Published: February 2014

Significance
Photosynthetic organisms exploit photosensory proteins to respond to changing light conditions. In land plants, phytochromes use the ratio of red to far-red light to detect shading by neighboring plants, leading to changes in growth and development. Light conditions can be more variable for algae because of the wavelength-dependent attenuation of light by water and because of ocean mixing. We studied phytochromes from taxonomically diverse eukaryotic algae from groups considered important for coastal ecosystems and the global carbon cycle. These proteins detect light throughout the visible spectrum (blue, green, orange, red, and far-red). Extensive spectral tuning has evolved within these algae, presumably reflecting aquatic light environments. These studies should ultimately facilitate engineering of crop plant species for diverse light environments.
Negatives and positives in the language of politics
Authors: Chen Lily 
Published: February 2014

An analytic model based on MAK Halliday’s System of Transitivity provides a powerful tool for decoding a journalist’s attitude to the events or individuals being written about. Chen (2005) showed how in the UK Times use of certain verbal processes rather than others to introduce direct or indirect speech could be an indicator that the journalist’s attitude towards the person being quoted was either negative or positive.
In this study, using a model for the linguistic comparison of the British and Chinese press developed by Chen (2004), verbal process use in the UK Times and the English-language China Daily is contrasted for evidence of differences in the attitude of British and Chinese journalists towards political figures.
The evidence is clear. Times journalists frequently use ‘negative’ verbal processes which indicate doubt or scepticism towards the person being quoted. China Daily journalists, meanwhile, more often use ‘positive’ verbal processes which enhance the authority of the speaker.
Responsive Justice?
Authors: Nelson Michael J. 
Published: February 2014

AbstractDo elected judges and prosecutors change their behavior to reflect public opinion after they receive information about constituent preferences? In this article I use a unique measure of public opinion—votes on an initiative to legalize marijuana—to examine the responsiveness of prosecutors and trial court judges to a strong, issue-specific, constituency-level opinion signal. I find that, at least in recent drug cases in Colorado, both prosecutors and judges changed their sentencing behavior after receiving that signal. Prosecutors responded only to local-level opinion, while judges responded to both local and statewide opinion.
Judges and Their Allies
Authors: Trochev Alexei , Ellett Rachel 
Published: February 2014

AbstractThe social construction of judicial power is a complicated process, especially in hybrid political regimes. We argue that off-bench resistance against blatant interference supported by vibrant social networks is an important manifestation of judicial autonomy. By drawing on evidence from field research, media coverage, and the existing scholarly literature, we clarify the logic of off-bench judicial resistance against external interference, outline a taxonomy of five strategies of resistance in hybrid regimes, and explain the political implications of off-bench judicial behavior.
iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array
Authors: Zhou Jin , Tantoso Erwin , Wong Lai-Ping , Ong Rick Twee-Hee , Bei Jin-Xin , Li Yi , Liu Jianjun , Khor Chiea-Chuen , Teo Yik-Ying 
Published: February 2014

Abstract
Motivation: Next-generation genotyping microarrays have been designed with insights from 1000 Genomes Project and whole-exome sequencing studies. These arrays additionally include variants that are typically present at lower frequencies. Determining the genotypes of these variants from hybridization intensities is challenging because there is less support to locate the presence of the minor alleles when the allele counts are low. Existing algorithms are mainly designed for calling common variants and are notorious for failing to generate accurate calls for low-frequency and rare variants. Here, we introduce a new calling algorithm, iCall, to call genotypes for variants across the whole spectrum of allele frequencies.
Results: We benchmarked iCall against four of the most commonly used algorithms, GenCall, optiCall, illuminus and GenoSNP, as well as a post-processing caller zCall that adopted a two-stage calling design. Normalized hybridization intensities for 12 370 individuals genotyped on the Illumina HumanExome BeadChip were considered, of which 81 individuals were also whole-genome sequenced. The sequence calls were used to benchmark the accuracy of the genotype calling, and our comparisons indicated that iCall outperforms all four single-stage calling algorithms in terms of call rates and concordance, particularly in the calling accuracy of minor alleles, which is the principal concern for rare and low-frequency variants. The application of zCall to post-process the output from iCall also produced marginally improved performance to the combination of zCall and GenCall.
Availability and implementation: iCall is implemented in C++ for use on Linux operating systems and is available for download at http://www.statgen.nus.edu.sg/∼software/icall.html.
Contact: statyy@nus.edu.sg, zhoujin@nus.edu.sg
Evaluation of a fishing captain's ability to predict species composition, sizes, and quantities of tunas associated with drifting fish-aggregating devices in the eastern Pacific Ocean
Authors: Fuller Daniel W. , Schaefer Kurt M. 
Published: February 2014

Abstract
Experiments were conducted to evaluate a fishing captain's ability to predict species composition, sizes, and quantities of tunas associated with drifting fish-aggregating devices (FADs), before encirclement with a purse-seine net. Operating in the equatorial eastern Pacific Ocean, during 11 May–23 July 2011, Captain Ricardo Diaz detected small quantities of bigeye (Thunnus obesus) and yellowfin (Thunnus albacares) tunas within large FAD-associated aggregations dominated by skipjack tuna (Katsuwonus pelamis). The captain's predictions were significantly related to the actual total catch and catch by species, but not to size categories by species. His predictions of species composition were most accurate when estimates of bigeye and yellowfin tuna were combined. If purse-seine captains are able to make accurate predictions of the proportion of bigeye and yellowfin tunas present in mixed-species aggregations associated with FADs, managers may wish to consider incentives to fishers to reduce the fishing mortality on those species.
Determination of the masses of the components of the HDE 226868/Cyg X-1 binary system
Authors: Ziółkowski J. 
Published: February 2014

Abstract
A recent determination of the distance to the HDE 226868/Cyg X-1 binary system and a more precise determination of the effective temperature of HDE 226868 allow for a more accurate estimate of the masses of both components. Using up-to-date evolutionary models, I obtain a mass range of between 25 and 35 M⊙ for the mass of the supergiant and between 13 and 23 M⊙ for the mass of the black hole. By accepting more liberal estimates of uncertainties in both the distance and the effective temperature, it is possible to extend these ranges to 21–35 and 10–23 M⊙ for both masses, respectively. The most likely values within these ranges are 27 and 16 M⊙, respectively. The mass obtained for the black hole agrees with the value of 15 ± 1 M⊙ suggested by Orosz et al. However, their value of 19 ± 2 M⊙ suggested for the mass of the supergiant should not be used because such a star violates the mass–luminosity relation for the massive core hydrogen-burning stars. This consideration was not incorporated into the iterative process of Orosz et al. To resolve this violation, I consider the possibility that the hydrogen content of HDE 226868 might be lowered as a result of the mass transfer and the induced fast rotation of the mass gainer. I have analysed the evolutionary effects of such a situation and have found that, while important, these do not invalidate the conclusions listed above. If, as a result of the rotation-induced mixing, the present hydrogen content of HDE 226868 is equal to about 0.6 (as suggested by some observational data), then its present mass might be lower: ∼24 M⊙ rather than ∼27 M⊙.
Linking functional traits and demographic rates in a subtropical tree community: the importance of size dependency
Authors: Iida Yoshiko , Kohyama Takashi S. , Swenson Nathan G. , Su Sheng‐Hsin , Chen Chien‐Teh , Chiang Jyh‐Min , Sun I‐Fang 
Published: February 2014

Summary

An important goal in plant community ecology is to understand how species traits determine demographic performance. Several functional traits have been shown to correlate with growth and mortality rates in trees, but less is known about how the relationships between functional traits and demographic rates change with tree size.

We examined the associations of functional traits with growth and mortality across 43 tree species in the Fushan 25‐ha subtropical rain forest plot in northern Taiwan. We estimated the 95th percentile maximum stem diameter, wood density and six leaf functional traits (leaf area, specific leaf area, thickness, succulence, and mass‐based nitrogen and phosphorus contents) obtained from leaves on juvenile and adult individuals of each species.

To quantify size‐dependent changes in growth and mortality, relative growth rate (RGR) and mortality were estimated as a function of stem diameter using hierarchical Bayesian models. These rate estimates were then correlated with functional traits at a range of stem diameter classes.

Relationships between functional traits and demographic rates varied with tree size. Maximum size was positively correlated with RGR across a wide range of tree sizes. Wood density was negatively correlated with RGR and mortality for small‐sized trees. Leaf traits such as leaf area and specific leaf area at juvenile and adult stages were associated more strongly with demographic rates for corresponding sizes than from other sizes.

Synthesis. The observed size‐dependent changes in the trait–demography relationships are possibly due to the effects of developmental and environmental changes with increasing tree size. The underlying effects of functional traits on demographic performance vary with tree size, and this should influence dynamics in a tree community.
Variability in seed cone production and functional response of seed predators to seed cone availability: support for the predator satiation hypothesis
Authors: Linhart Yan B. , Moreira Xoaquín , Snyder Marc A. , Mooney Kailen A. 
Published: February 2014

SummaryMast seeding is a reproductive strategy in some perennial plants defined as synchronous production of large seed crops at irregular intervals. One widely accepted theory to explain this behaviour is the predator satiation hypothesis, which states that the synchronous and variable production of seeds within a population will maximize the probability of seed survival through satiation of seed predators.Although some short‐term studies have documented the influence of variable and synchronized production of seeds on herbivore attack rate during one or few mast years, long‐term data including multiple mast seeding years and patterns of cone production and herbivore attack on individual trees are needed to assess (i) how cone production, variability and synchrony affect individual plant fitness and (ii) the functional responses of seed predators to mast seeding events.We tested these objectives, collecting long‐term (29 years) data on female seed cone production and rates of seed predator attack from 217 individual contiguous trees within aPinus ponderosapopulation.Our results support the predator satiation hypothesis. First, we found high interannual synchrony and variability in seed cone production and a typeIIfunctional response of seed predators to available cones. Secondly, years with high cone production (mast years) had markedly lower rates of seed predator attack than years of low production (i.e. a population‐level satiation effect). Thirdly, within mast years, individuals with high cone production had markedly lower rates of attack than individuals with low cone production (i.e. an individual‐level satiation effect). Finally, individual trees with greater synchrony and more variable cone production suffered lower rates of attack.Synthesis: Our long‐term data on individual trees lend strong support to the hypothesis that mast seeding inPinus ponderosahas evolved in response to natural selection from insect seed predators.
Climate drivers, host identity and fungal endophyte infection determine virus prevalence in a grassland ecosystem
Authors: Rúa Megan A. , McCulley Rebecca L. , Mitchell Charles E. 
Published: February 2014

Summary

Under climate change, alterations to precipitation and temperature regimes are expected to impact ecosystem structure and function. These impacts may in part be determined by feedbacks between plants and associated microbes, including both endophytic fungal symbionts and viral pathogens.

To test potential key components of these feedbacks in a grassland system, we conducted a field experiment that factorially manipulated temperature regime, precipitation regime and endophyte infection of a dominant species, Schedonorus arundinaceus. After one growing season, we evaluated the four most frequently occurring grass species for infection by three species of barley and cereal yellow dwarf viruses (B/CYDVs). For S. arundinaceus, we also tracked changes in viral prevalence over an additional two growing seasons, for a total of three growing seasons.

Plant species identity played a strong role in determining virus prevalence; Poa pratensis and Paspalum dilatatum were more frequently infected than either S. arundinaceus (endophyte infected or endophyte free) or Eleusine indica. Both elevated temperature and elevated precipitation impacted virus prevalence, but effects varied among years and interacted with fungal endophyte symbiosis for S. arundinaceus.

In the final year of data collection, elevated precipitation increased virus prevalence in endophyte‐infected, but not endophyte‐free, S. arundinaceus. In the same year, but regardless of endophyte infection, elevated temperature by itself increased virus prevalence for S. arundinaceus. This effect of temperature on virus prevalence may have been driven by vector abundance because the viruses are obligately aphid‐transmitted, and aphids were found more frequently in heated plots.

Synthesis. Overall, our investigation experimentally demonstrates strong combined impacts of biotic and abiotic factors on disease dynamics in a grassland system. Impacts of climate change on virus prevalence in grasslands may depend on the responses of aphid vectors and the presence of endophytic fungal symbionts.
Incorporating dominant species as proxies for biotic interactions strengthens plant community models
Authors: le Roux Peter C. , Pellissier Loïc , Wisz Mary S. , Luoto Miska 
Published: February 2014

Summary

Biotic interactions exert considerable influence on the distribution of individual species and should, thus, strongly impact communities. Implementing biotic interactions in spatial models of community assembly is therefore essential for accurately modelling assemblage properties. However, this remains a challenge due to the difficulty of detecting the role of species interactions and because accurate paired community and environment data sets are required to disentangle biotic influences from abiotic effects.

Here, we incorporate data from three dominant species into community‐level models as a proxy for the frequency and intensity of their interactions with other species and predict emergent assemblage properties for the co‐occurring subdominant species. By analysing plant community and field‐quantified environmental data from specially designed and spatially replicated monitoring grids, we provide a robust in vivo test of community models.

Considering this well‐defined and easily quantified surrogate for biotic interactions consistently improved realism in all aspects of community models (community composition, species richness and functional structure), irrespective of modelling methodology.

Dominant species reduced community richness locally and favoured species with similar leaf dry matter content. This effect was most pronounced under conditions of high plant biomass and cover, where stronger competitive impacts are expected. Analysis of leaf dry matter content suggests that this effect may occur through efficient resource sequestration.

Synthesis. We demonstrate the strong role of dominant species in shaping multiple plant community attributes, and thus the need to explicitly include interspecific interactions to achieve robust predictions of assemblage properties. Incorporating information on biotic interactions strengthens our capacity not only to predict the richness and composition of communities, but also how their structure and function will be modified in the face of global change.
Russian Pioneers of Therapeutic Hemapheresis and Extracorporeal Hemocorrection: 100‐Year Anniversary of the World's First Successful Plasmapheresis
Authors: Sokolov Alexey A , Solovyev Andrey G 
Published: February 2014

AbstractOn 15 February 2013 (2 February on the Julian Calendar) we celebrated the 100‐year anniversary of the world's first successful experimental plasmapheresis. Scientific research projects in this field were carried out by the Department of Infectious Disease, Russian Imperial Medical Surgical Academy located in Saint‐Petersburg. Doctor of Medical Sciences and Professor Vadim A. Yurevich was a Principal Investigator for this research, which in 1913 resulted in the discovery of a new way of treatment. The results were published in Russki Vratch (Russian Physician) Journal no. 18 (1914) – V.A. Yurevich and N.K. Rosenberg “For the Question Regarding Washing of Blood Outside of the Body and the Vitality of Red Blood Cells”. There was no terminology offered for this medical innovation at that time. Plasma removal was performed not solely, but in combination with washing of blood cells returned to the patient. Nowadays this combination is still considered to be more effective than separate plasmapheresis. According to the published experimental protocols this new treatment was done on 15 February (2 February on the Julian Calendar or “old style”). One year later in 1914 a famous researcher, John Abel and coauthors, repeated a separate plasma removal treatment with retransfusion of the blood cells and suggested the term “plasmapheresis”, which is now official. The article entitled “Plasma Removal With Return of Corpuscles (Plasmapheresis)”, written by Abel was published 3 months later than the article by Professor Yurevich. In 1924, Dr Ivan P. Mikhailovskiy repeated experiments by Yurevich and Rosenberg in vivo on a dog model, confirmed the clinical efficiency and developed the methodology in his article “Washing of Blood In Vivo, the Methodology, Problems, and Importance for the Treatment of Toxic Conditions.”
Low Hemoglobin Levels and Hypo‐Responsiveness to Erythropoiesis‐Stimulating Agent Associated With Poor Survival in Incident Japanese Hemodialysis Patients
Authors: Akizawa Tadao , Saito Akira , Gejyo Fumitake , Suzuki Masashi , Nishizawa Yoshiki , Tomino Yasuhiko , Tsubakihara Yoshiharu , Akiba Takashi , Hirakata Hideki , Watanabe Yuzo , Kawanishi Hideki , Bessho Masami , Udagawa Yukio , Aoki Kotonari , Uemura Yukari , Ohashi Yasuo ,   JET Study Group
Published: February 2014

AbstractAlthough erythropoiesis‐stimulating agents (ESAs) are effective at treating anemia, the association between hemoglobin (Hb) levels and survival is still unclear, especially for the incident Japanese hemodialysis (HD) population. The Japan Erythropoietin Treatment (JET) Study is an open multi‐center, prospective, observational study designed to evaluate the relationship between the maintenance of Hb levels and new HD patient prognosis after the first administration of epoetin beta. Landmark analyses were performed to examine the relationship between Hb levels at 6 months and survival. Among a total of 10 310 patients, 6631 completed the initial 6 months of epoetin beta treatment (induction phase) and were followed up for a further 2.5 years (maintenance phase). Three‐year survival rate of patients with <9 g/dL Hb levels after 6 months was 74.1%, which was significantly lower than 89.3% for patients with Hb levels 10 to 11 g/dL; the adjusted hazard ratio (HR) was 2.08 (95% CI, 1.57–2.77; P < 0.0001). Moreover, the 3‐year survival rate for poor responders defined by Hb levels <10 g/dL and weekly epoetin beta doses ≥9000 IU during the induction phase was 71.6%, which was significantly lower than 89.4% for the group, which had Hb levels 10 to 11 g/dL excluding poor responders and those with excursion; the HR was 1.71 (95% CI, 1.13–2.60; P = 0.0118). Adverse events related to the treatment were reported in 71 of 10 310 patients (0.69%). These findings suggest that the achieved low Hb levels and poor response to ESA therapy are significantly associated with high mortality.