bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Solar Photospheric Nitrogen Abundance: Determination with 3D and 1D Model Atmospheres
Authors: Maiorca E. , Caffau E. , Bonifacio P. , Busso M. , Faraggiana R. , Steffen M. , Ludwig H.-G. , Kamp I. 
Published: September 2009

AbstractWe present a new determination of the solar nitrogen abundance making use of 3D hydrodynamical modelling of the solar photosphere, which is more physically motivated than traditional static 1D models. We selected suitable atomic spectral lines, relying on equivalent width measurements already existing in the literature. For atmospheric modelling we used the co5bold 3D radiation hydrodynamics code. We investigated the influence of both deviations from local thermodynamic equilibrium (non-LTE effects) and photospheric inhomogeneities (granulation effects) on the resulting abundance. We also compared several atlases of solar flux and centre-disc intensity presently available. As a result of our analysis, the photospheric solar nitrogen abundance is A(N) = 7.86 ± 0.12.
Chemical Evolution of the Juvenile Universe
Authors: Wasserburg G. J. , Qian Y.-Z. 
Published: September 2009

AbstractModels of average Galactic chemical abundances are in good general agreement with observations for [Fe/H] > –1.5, but there are gross discrepancies at lower metallicities. Only massive stars contribute to the chemical evolution of the ‘juvenile universe’ corresponding to [Fe/H] ≲ –1.5. If Type II supernovae (SNe II) are the only relevant sources, then the abundances in the interstellar medium of the juvenile epoch are simply the sum of different SN II contributions. Both low-mass (∼8–11 M⊙) and normal (∼12–25 M⊙) SNe II produce neutron stars, which have intense neutrino-driven winds in their nascent stages. These winds produce elements such as Sr, Y and Zr through charged-particle reactions (CPR). Such elements are often called the ‘light r-process elements’, but are considered here as products of CPR and not the r process. The observed absence of production of the low-A elements (Na through Zn including Fe) when the true r-process elements (Ba and above) are produced requires that only low-mass SNe II be the site if the r process occurs in SNe II. Normal SNe II produce the CPR elements in addition to the low-A elements. This results in a two-component model that is quantitatively successful in explaining the abundances of all elements relative to hydrogen for –3 ≲ [Fe/H] ≲ –1.5. This model explicitly predicts that [Sr/Fe] ≥ –0.32. Recent observations show that there are stars with [Sr/Fe] ≲ –2 and [Fe/H] < –3. This proves that the two-component model is not correct and that a third component is necessary to explain the observations. The production of CPR elements associated with the formation of neutron stars requires that the third component must be massive stars ending as black holes. It is concluded that stars of ∼25–50 M⊙ (possibly up to ∼100 M⊙) are the appropriate candidates. These produce hypernovae (HNe) that have very high Fe yields and are observed today. Stars of ∼140–260 M⊙ are completely disrupted upon explosion. However, they produce an abundance pattern greatly deficient in elements of odd atomic numbers, which is not observed, and therefore they are not considered as a source here. Using a Salpeter initial mass function, it is shown that HNe are a source of Fe that far outweighs normal SNe II, with the former and the latter contributing ∼24% and ∼9% of the solar Fe abundance, respectively. It follows that the usual assignment of ∼⅓ of the solar Fe abundance to normal SNe II is not correct. This leads to a simple three-component model including low-mass and normal SNe II and HNe, which gives a good description of essentially all the data for stars with [Fe/H] ≲ –1.5. We conclude that HNe are more important than normal SNe II in the chemical evolution of the low-A elements from Na through Zn (including Fe), in sharp distinction to earlier models.
Binary Populations of Carbon-Enhanced Metal-Poor Stars
Authors: Izzard Robert G. , Glebbeek Evert , Stancliffe Richard J. , Pols Onno 
Published: September 2009

AbstractWe construct binary-star population nucleosynthesis models of carbon-enhanced metal-poor (CEMP) stars. We compare the CEMP to extremely metal-poor (EMP) ratio of our models to the observed ratio and find it is an order of magnitude too small. Through an increase in the efficiency of third dredge-up in low-mass, low-metallicity, thermally-pulsing Asymptotic Giant Branch (TP-AGB) stars our models better match the observations.
The Mystery of CEMPs+r Stars and the Dual Core-Flash Neutron Superburst
Authors: Lugaro M. , Campbell S. W. , de Mink S. E. 
Published: September 2009

AbstractCarbon-enhanced metal-poor (CEMPs+r) stars show large enhancements of elements produced both by the slow and the rapid neutron capture processes (the s and r process, respectively) and represent a relatively large fraction, 30% to 50%, of the CEMP population. Many scenarios have been proposed to explain this peculiar chemical composition and most of them involve a binary companion producing the s-process elements during its Asymptotic Giant Branch (AGB) phase. The problem is that none of the proposed explanations appears to be able to account for all observational constraints, hence, alternatives are needed to be put forward and investigated. In this spirit, we propose a new scenario for the formation of CEMPs+r stars based on S. W. Campbell's finding that during the ‘dual core flash’ in low-mass stars of extremely low metallicity, when protons are ingested in the He-flash convective zone, a ‘neutron superburst’ is produced. Further calculations are needed to verify if this neutron superburst could make the r-process component observed in CEMPs+r, as well as their Fe abundances. The s-process component would then be produced during the following AGB phase.
The Effect of Aqueous Alteration and Metamorphism in the Survival of Presolar Silicate Grains in Chondrites
Authors: Trigo-Rodriguez Josep M. , Blum Jürgen 
Published: September 2009

AbstractRelatively small amounts (typically between 2 and 200 ppm) of presolar grains have been preserved in the matrices of chondritic meteorites. The measured abundances of the different types of grains are highly variable from one chondrite to another, but are higher in unequilibrated chondrites that have experienced little or no aqueous alteration and/or metamorphic heating than in processed meteorites. A general overview of the abundances measured in presolar grains (particularly the recently identified presolar silicates) contained in primitive chondrites is presented. Here we will focus on the most primitive chondrite groups, as typically the highest measured abundances of presolar grains occur in primitive chondrites that have experienced little thermal metamorphism. Looking at the most aqueously altered chondrite groups, we find a clear pattern of decreasing abundance of presolar silicate grains with increasing levels of aqueous alteration. We conclude that measured abundances of presolar grains in altered chondrites are strongly biased by their peculiar histories. Scales quantifying the intensity of aqueous alteration and shock metamorphism in chondrites could correlate with the content of presolar silicates. To do this it would be required to infer the degree of destruction or homogenization of presolar grains in the matrices of primitive meteorites. To get an unbiased picture of the relative abundance of presolar grains in the different regions of the protoplanetary disk where first meteorites consolidated, future dedicated studies of primitive meteorites, IDPs, and collected materials from sample-return missions (like e.g. the planned Marco Polo) are urgently required.
The Puzzling Frequencies of CEMP and NEMP Stars
Authors: Pols O. R. , Izzard R. G. , Glebbeek E. , Stancliffe R. J. 
Published: September 2009

AbstractWe present the results of binary population simulations of carbon- and nitrogen-enhanced metal-poor (CEMP and NEMP) stars. We show that the observed paucity of very nitrogen-rich stars puts strong constraints on possible modifications of the initial mass function at low metallicity.
A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean
Authors: David Perrine , Chen Nicolas W.G. , Pedrosa-Harand Andrea , Thareau Vincent , Sévignac Mireille , Cannon Steven B. , Debouck Daniel , Langin Thierry , Geffroy Valérie 
Published: September 2009

AbstractThe B4 resistance (R) gene cluster is one of the largest clusters known in common bean (Phaseolus vulgaris [Pv]). It is located in a peculiar genomic environment in the subtelomeric region of the short arm of chromosome 4, adjacent to two heterochromatic blocks (knobs). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-Coil-Nucleotide-Binding-Site-Leucine-Rich-Repeat (CNL). Conserved microsynteny was observed between the Pv B4 locus and corresponding regions of Medicago truncatula and Lotus japonicus in chromosomes Mt6 and Lj2, respectively. The notable exception was the CNL sequences, which were completely absent in these regions. The origin of the Pv B4-CNL sequences was investigated through phylogenetic analysis, which reveals that, in the Pv genome, paralogous CNL genes are shared among nonhomologous chromosomes (4 and 11). Together, our results suggest that Pv B4-CNL was derived from CNL sequences from another cluster, the Co-2 cluster, through an ectopic recombination event. Integration of the soybean (Glycine max) genome data enables us to date more precisely this event and also to infer that a single CNL moved from the Co-2 to the B4 cluster. Moreover, we identified a new 528-bp satellite repeat, referred to as khipu, specific to the Phaseolus genus, present both between B4-CNL sequences and in the two knobs identified at the B4 R gene cluster. The khipu repeat is present on most chromosomal termini, indicating the existence of frequent ectopic recombination events in Pv subtelomeric regions. Our results highlight the importance of ectopic recombination in R gene evolution.
Multiple origins of symbioses between ascomycetes and bryophytes suggested by a five‐gene phylogeny
Authors: Stenroos Soili , Laukka Tomi , Huhtinen Seppo , Döbbeler Peter , Myllys Leena , Syrjänen Kimmo , Hyvönen Jaakko 
Published: September 2009

AbstractNumerous species of microscopic fungi inhabit mosses and hepatics. They are severely overlooked and their identity and nutritional strategies are mostly unknown. Most of these bryosymbiotic fungi belong to the Ascomycota. Their fruit‐bodies are extremely small, often reduced and simply structured, which is why they cannot be reliably identified and classified by their morphological and anatomical characters. A phylogenetic hypothesis of bryosymbiotic ascomycetes is presented. New sequences of 78 samples, including 61 bryosymbionts, were produced, the total amount of terminals being 206. Of these, 202 are Ascomycetes. Sequences from the following five gene loci were used: rDNA SSU, rDNA LSU, RPB2, mitochondrial rDNA SSU, and rDNA 5.8S. The program TNT was used for tree search and support value estimation. We show that bryosymbiotic fungi occur in numerous lineages, one of which represents a newly discovered lineage among the Ascomycota and exhibits a tripartite association with cyanobacteria and sphagna. A new genus Trizodia is proposed for this basal clade. Our results demonstrate that even highly specialized life strategies can be adopted multiple times during evolution, and that in many cases bryosymbionts appear to have evolved from saprobic ancestors. © The Willi Hennig Society 2009.
Prevalence of hepatitis B virus DNA polymerase mutations in treatment‐naïve patients with chronic hepatitis B
Authors: NGUYEN M. H. , GARCIA R. T. , TRINH H. N. , NGUYEN H. A. , NGUYEN K. K. , NGUYEN L. H. , LEVITT B. 
Published: September 2009

SummaryBackground  One of the most important factors in treatment failure using nucleos(t)ide analogues in chronic hepatitis B is anti‐viral resistance. Primary drug resistance refers to amino acid changes in the hepatitis B virus polymerase/reverse transcriptase (rt) that result in reduced susceptibility to anti‐viral agents. Pre‐existing drug resistance mutations may occur in untreated patients and may affect their treatment outcomes.Aim  To determine the prevalence of hepatitis B DNA polymerase mutations in treatment‐naïve patients.Methods  We used a direct PCR sequencing test to detect DNA polymerase mutations in 472 consecutive treatment‐naïve patients at two community gastroenterology clinics in Northern California.Results  A majority of patients were Asians (>95%), had either genotype B or C (95%) and had no evidence of cirrhosis or liver cancer (94%). Mean age was 45 ± 13 and mean hepatitis B virus DNA was 5.3 ± 1.8 log10 IU/mL. Most patients did not have any detectable mutations (82.4%). Some (16.7%) had mutations of unknown clinical significance (rtV207M/L/I) and only 4 patients had rtA181A/S, rtA194S or M250I.Conclusions  No rtM204V/I or rtN236T mutations were observed in our study. Less than 1% of our patients had mutations that can be associated with primary resistance to existing anti‐viral therapies for hepatitis B virus.
Identification of a 3.7‐Mb region for a marbling QTL on bovine chromosome 4 by identical‐by‐descent and association analysis
Authors: Yokouchi K. , Mizoguchi Y. , Watanabe T. , Iwamoto E. , Sugimoto Y. , Takasuga A. 
Published: September 2009

SummaryQTL mapping for growth and carcass traits was performed using a paternal half‐sib family composed of 325 Japanese Black cattle offspring. Nine QTL were detected at the 1% chromosome‐wise significance level at a false discovery rate of less than 0.1. These included two QTL for marbling on BTA 4 and 18, two QTL for carcass weight on BTA 14 and 24, two QTL for longissimus muscle area on BTA 1 and 4, two QTL for subcutaneous fat thickness on BTA 1 and 15 and one QTL for rib thickness on BTA 6. Although the marbling QTL on BTA 4 has been replicated with significant linkages in two Japanese Black cattle sires, the three Q (more marbling) haplotypes, each inherited maternally, were apparently different. To compare the three Q haplotypes in more detail, high‐density microsatellite markers for the overlapping regions were developed within the 95% CIs (65 markers in 44–78 cM). A detailed haplotype comparison indicated that a small region (<3.7 Mb) around 46 cM was shared between the Qs of the two sires, whose dams were related. An association of this region with marbling was shown by a regression analysis using the local population, in which the two sires were produced and this was confirmed by an association study using a population collected throughout Japan. These results strongly suggest that the marbling QTL on BTA 4 is located in the 3.7‐Mb region at around 46 cM.
Postnatal transcription profile and polymorphism of the ADIPOR1 gene in five pig breeds
Authors: Stachowiak M. , Flisikowski K. , Szydlowski M. , Fries R. , Switonski M. 
Published: September 2009

SummaryAs a result of its role in energy homeostasis regulation, the ADIPOR1 gene is a candidate for fat deposition, an important production trait, in the pig. The aim of the study was to conduct a comparative analysis of the ADIPOR1 postnatal transcript level, in order to establish its promoter and 5′UTR sequences and to search the gene for polymorphisms. The transcription level was examined in longissimus dorsi and semimembranosus muscles collected from 180 pigs at 60–210 days of age, representing five pig breeds: Duroc, Polish Large White, Polish Landrace, Pietrain and Pulawska. We calculated highly significant breed by age by muscle interaction (P < 0.0001) and breed by muscle interactions (P < 0.01). The 5′UTR and promoter region of the porcine ADIPOR1 gene were amplified for the first time and their sequences were deposited in the GenBank database. In total, 21 novel and two previously described polymorphisms were found in the ADIPOR1 promoter, coding, intronic, 5′ and 3′ untranslated regions. The only SNP detected in the coding region was a synonymous substitution. Two polymorphisms in 3′UTR (c.*129A>C and c.*536A>G) showed no significant effect on the transcript level. Our results showed a high polymorphism of the ADIPOR1 and a complexity in its transcription level in the studied muscles. This complexity indicates that conclusions based on such studies should be carefully gradated.
Across‐line SNP association study of innate and adaptive immune response in laying hens
Authors: Biscarini F. , Bovenhuis H. , Van Arendonk J. A. M. , Parmentier H. K. , Jungerius A. P. , Van Der Poel J. J. 
Published: September 2009

SummaryThe aim of the present study was to detect quantitative trait loci (QTL) for innate and adaptive immunity in laying hens. For this purpose, the associations between 1022 single nucleotide polymorphism (SNP) markers and immune traits were studied in 583 hens from nine different layer lines. Immune traits were natural antibodies for keyhole limpet haemocyanin (KLH) and lipopolysaccharide (LPS) at 20, 40 and 65 weeks, acquired antibodies to the vaccinal virus of Newcastle disease at 20 weeks, and complement activity measured on sheep and bovine red blood cells at 20, 40 and 65 weeks. We adopted a novel approach based on across‐line analysis and testing of the SNP‐by‐line interaction. Among lines, linkage disequilibrium is conserved at shorter distances than in individual lines; therefore, SNPs significantly associated with immune traits across lines are expected to be near the functional mutations. In the analysis, the SNPs that had a significant across‐line effect but did not show significant SNP‐by‐line interaction were identified to test whether the association was consistent in the individual lines. Ultimately, 59 significant associations between SNPs and immune traits were detected. Our results confirmed some previously identified QTL and identified new QTL potentially involved in the immune function. We found evidence for a role of IL17A (chromosome 3) in natural and acquired antibody titres and in the classical and alternative pathways of complement activation. The major histocompatibility genes on chromosome 16 showed significant association with natural and acquired antibody titres and classical complement activity. The IL12B gene on chromosome 13 was associated with natural antibody titres.
Spatial and temporal variability of fires in relation to ecosystems, land tenure and rainfall in savannas of northern South America
Authors: ROMERO‐RUIZ M. , ETTER A. , SARMIENTO A. , TANSEY K. 
Published: September 2009

AbstractFire is a predominant factor forcing global terrestrial biomass dynamics, with more than 30% of the land surface showing frequent burning, particularly in the tropics, where it mostly affects savannas ecosystems annually. Savannas, which cover approximately 269 million ha in South America, play a major role in the global carbon cycle. They are affected by increasing human pressures and global climate change. Using satellite data, this study quantifies vegetation burning in the Colombian Llanos savannas for the period 2000–2008, and analyzes how fire spatial pattern, frequency and extent vary with ecosystem type, land tenure and rainfall. On average 2.75±0.5 million ha (24±4.2%) of the savannas burn each year. Burned area is highly variable, with 3.4 million ha burned in 2002–2003 and <1.9 million ha in 2005–2006. However, during the 2000–2008 period near of 3.7 million ha (33.5%) of the savannas never burned. Compared with the average 8–10 years of fire return time for the tropics and subtropics, these savannas burn twice as often. In addition, the average burn size figure for tropical and subtropical grassland savannas (with <5% trees) of 7000 ha (median 5000 ha), is about seven times the average burned patch size we found in our study. Fires predominate in the well‐drained high plain savannas, lowest figures occurring along the Andean foothills, in forested areas and in pasture and croplands. Annual proportion burned varies with land tenure, being highest in National Parks. This study is the first complete regional map of fire disturbance in a South American savanna. This detailed regional data provides a unique opportunity for increasing the accuracy of global carbon emission calculations.
Turnover of labile and recalcitrant soil carbon differ in response to nitrate and ammonium deposition in an ombrotrophic peatland
Authors: CURREY PAULINE M. , JOHNSON DAVID , SHEPPARD LUCY J. , LEITH IAN D. , TOBERMAN HANNAH , Van Der WAL RENÉ , DAWSON LORNA A. , ARTZ REBEKKA R. E. 
Published: September 2009

AbstractThe effects of 4 years of simulated nitrogen deposition, as nitrate (NO3−) and ammonium (NH4+), on microbial carbon turnover were studied in an ombrotrophic peatland. We investigated the mineralization of simple forms of carbon using MicroResp™ measurements (a multiple substrate induced respiration technique) and the activities of four soil enzymes involved in the decomposition of more complex forms of carbon or in nutrient acquisition: N‐acetyl‐glucosaminidase (NAG), cellobiohydrolase (CBH), acid phosphatase (AP), and phenol oxidase (PO). The potential mineralization of labile forms of carbon was significantly enhanced at the higher N additions, especially with NH4+ amendments, while potential enzyme activities involved in breakdown of more complex forms of carbon or nutrient acquisition decreased slightly (NAG and CBH) or remained unchanged (AP and PO) with N amendments. This study also showed the importance of distinguishing between NO3− and NH4+ amendments, as their impact often differed. It is possible that the limited response on potential extracellular enzyme activity is due to other factors, such as limited exposure to the added N in the deeper soil or continued suboptimal functioning of the enzymes due to the low pH, possibly via the inhibitory effect of low phenol oxidase activity.