bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanodiamonds do not provide unique evidence for a Younger Dryas impact
Authors: Tian H. , Schryvers D. , Claeys Ph. 
Published: December 2010

Microstructural,
δ
13
C isotope and C/N ratio investigations were conducted on excavated material from the black Younger Dryas boundary in Lommel, Belgium, aiming for a characterisation of the carbon content and structures. Cubic diamond nanoparticles are found in large numbers. The larger ones with diameters around or above 10 nm often exhibit single or multiple twins. The smaller ones around 5 nm in diameter are mostly defect-free. Also larger flake-like particles, around 100 nm in lateral dimension, with a cubic diamond structure are observed as well as large carbon onion structures. The combination of these characteristics does not yield unique evidence for an exogenic impact related to the investigated layer.
Functional integration of a metabolic network model and expression data without arbitrary thresholding
Authors: Jensen Paul A. , Papin Jason A. 
Published: December 2010

Abstract
Motivation: Flux balance analysis (FBA) has been used extensively to analyze genome-scale, constraint-based models of metabolism in a variety of organisms. The predictive accuracy of such models has recently been improved through the integration of high-throughput expression profiles of metabolic genes and proteins. However, extensions of FBA often require that such data be discretized a priori into sets of genes or proteins that are either ‘on’ or ‘off’. This procedure requires selecting relatively subjective expression thresholds, often requiring several iterations and refinements to capture the expression dynamics and retain model functionality.
Results: We present a method for mapping expression data from a set of environmental, genetic or temporal conditions onto a metabolic network model without the need for arbitrary expression thresholds. Metabolic Adjustment by Differential Expression (MADE) uses the statistical significance of changes in gene or protein expression to create a functional metabolic model that most accurately recapitulates the expression dynamics. MADE was used to generate a series of models that reflect the metabolic adjustments seen in the transition from fermentative- to glycerol-based respiration in Saccharomyces cerevisiae. The calculated gene states match 98.7% of possible changes in expression, and the resulting models capture functional characteristics of the metabolic shift.
Availability: MADE is implemented in Matlab and requires a mixed-integer linear program solver. Source code is freely available at http://www.bme.virginia.edu/csbl/downloads/.
Contact: papin@virginia.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Statistical analysis of the cancer cell's molecular entropy using high-throughput data
Authors: van Wieringen Wessel N. , van der Vaart Aad W. 
Published: December 2010

Abstract
Motivation: As cancer progresses, DNA copy number aberrations accumulate and the genomic entropy (chromosomal disorganization) increases. For this surge to have any oncogenetic effect, it should (to some extent) be reflected at other molecular levels of the cancer cell, in particular that of the transcriptome. Such a coincidence of cancer progression and the propagation of an entropy increase through the molecular levels of the cancer cell would enhance the understanding of cancer evolution.
Results: A statistical argument reveals that (under some assumptions) an entropy increase in one random variable (DNA copy number) leads to an entropy increase in another (gene expression). Statistical methodology is provided to investigate the relation between the genomic and transcriptomic entropy using high-throughput data. Analyses of multiple high-throughput datasets using this methodology show a close, concordant relation among the genomic and transcriptomic entropy. Hence, as cancer evolves, and the genomic entropy increases, the transcriptomic entropy is also expected to surge.
Contact: wvanwie@few.vu.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
Occurrence of Chilli veinal mottle virus in Nicotiana tabacum in Yunnan, China
Authors: Ding M. , Yang C. , Zhang L. , Jiang Z.-L. , Fang Q. , Qin X.-Y. , Zhang Z.-K. 
Published: December 2010

Flue-cured tobacco (Nicotiana tabacum) is an important crop in Yunnan Province, China. During a survey in July 2010, tobacco plants (N. tabacum cv. Yunyan 85) in the fields near Dali County in the northwest Yunnan Province of China had symptoms of chlorosis along leaf veins and later showed symptoms of white or brown necrosis along the veins. In 10 surveyed fields in Baizhishu Village in the city of Weishan, a commercial tobacco field (10 ha) developed virus-like disease symptoms; the incidence of affected plants ranged from 0.5 to 3%, which caused obvious economic losses. An isolate (YN75) was collected at random from five symptomatic leaves sampled from five plants. Negative staining of crude extracts of the infected leaves and subsequent electron microscopy revealed flexuous rods of 12 to 13 × 750 nm. Pinwheel-like inclusion bodies were abundant in thin sections of infected leaves. The particle size suggested a species of Potyviridae. Thus, the isolate was assayed in double antibody sandwich-ELISA (Agdia, Elkhart, IN) for the presence of Potato virus Y, Tobacco etch virus, and Tobacco vein mottling virus. All antigens gave negative results. Total RNA was extracted from leaves and tested by reverse transcription (RT)-PCR. The primer M4-T (5′-GTT TTC CCA GTC ACG ACT TTT TTT TTT TTT TT-3′) was employed for cDNA synthesis described by Chen et al (1). The primer set ChiVMV-F (5′-TAG TTG YGC ATA C (C/G) C AGG AGA GAG-3′)/M4 (5′-GTT TTC CCA GTC ACG AC-3′) is complimentary to the region of coat protein and 3′-untranslated region of Chilli veinal mottle virus (ChiVMV), respectively. The expected 1,189-bp fragments were amplified from RNA templates and the amplicon was cloned and sequenced (GenBank Accession No. HQ218936). Comparisons of amplicons with the amino acid sequence available in the NCBI database using BLAST showed 91.4% identity with ChiVMV from India (GenBank Accession No. EF213688) and 90.7% with ChiVMV from Taiwan (Accession No. DQ854950). The virus particle size, RT-PCR results, and sequence data revealed that these tobacco plants were infected by ChiVMV. To our knowledge, this is the first report of ChiVMV infecting N. tabacum in China. Reference: (1) J. Chen et al. Arch. Virol. 146:757, 2001.
First Report of Orange Rust of Sugarcane Caused by Puccinia kuehnii in Ivory Coast and Cameroon
Authors: Saumtally A. S. , Viremouneix T. R. , Ahondokpê B. , Girard J-C. R. , Castlebury L. A. , Dixon L. , Glynn N. C. , Comstock J. C. 
Published: December 2010

Orange rust of sugarcane caused by Puccinia kuehnii was detected in Florida in 2007 (1). It was hypothesized that the pathogen originated from Africa because brown rust of sugarcane (synonym common rust) was introduced to the Western Hemisphere from Africa (3). Requests for rust-infected sugarcane samples were made to several western and central African countries to investigate if orange rust of sugarcane was present but as yet undetected. Orange rust had not previously been reported from western or central Africa. At Zuénoula, Ivory Coast in July 2009, symptoms of sugarcane rust were observed on cvs. SP 71-6180 and Co 997 and appeared distinct to those of brown rust of sugarcane. A year later (May 2010), rust-infected specimens of SP 71-6180 and Co 997 from the same location and also from Borotou in Ivory Coast were sent to the USDA-ARS Systematic Mycology and Microbiology Laboratory in Beltsville, MD for identification. Also in May 2010, sugarcane rust was observed at Mbandjock and Nkoteng in Cameroon on cvs. D 88172, FR 87482, and RB 72-454 and on breeding clones RCmr 08/319 and RCmr 08/1121. All specimens had orange uredinial lesions that ranged from 0.6 to 6.5 mm × 200 to 300 μm and were ellipsoidal to elongate. Urediniospores were consistent with P. kuehnii E.J. Butler observed on specimens from Florida (1). DNA isolated from all samples was successfully amplified with P. kuehnii specific primers targeting ITS1 of rDNA (2). The nuclear large subunit region of rDNA of the rust specimens from Ivory Coast (BPI 881015–881017, GenBank Accession No. HQ666888) and Cameroon (BPI 881010–881014, GenBank Accession Nos. HQ666889–HQ666891) were sequenced. DNA sequences for all were identical to sequences of P. kuehnii and distinct from known sequences of P. melanocephala available in GenBank. To our knowledge, this is the first confirmed report of orange rust of sugarcane in western and central Africa. There is evidence that brown rust of sugarcane was introduced to the Western Hemisphere from this region of Africa (3) making it also the likely source of introduction of orange rust. Further experimentation is required to confirm this hypothesis. References: (1) J. C. Comstock et al. Plant Dis. 92:175, 2008. (2) N. C. Glynn et al. Plant Pathol. 59:703. 2010. (3) H. L. Purdy et al. Plant Dis. 69:689, 1985.
First Report of Anthracnose Caused by Glomerella acutata on Chili Pepper in China
Authors: Xia H. , Wang X.-L. , Zhu H.-J. , Gao B.-D. 
Published: December 2010

A new anthracnose disease on chili pepper (cayenne pepper cv. Hongxiu 2003, fruiting type pepper) was found in Zhijiang County, Hunan, China in 2009. The disease was observed only on the fruits. Lesions were generally elongated, on which dark acervuli were arranged concentrically. Later, cracking of older lesions was observed. With a microscope, fungal conidia were observed to be 15.8 × 4.1 μm, fusiform or oval with one end acute, and single celled with two to seven oil globules. No setae were found on the acervuli. Eight isolates (HNZJ001–HNZJ008) showed no difference in colony feature when cultured on potato dextrose agar. All the isolates showed white growth at the early stages, but colonies turned pink when they produced powdery spores and then finally became red gray. The average colony diameter was 68.5 to 72.3 mm after 7 days with obvious gray black concentric rings because of the development of aerial and substrate mycelia. After a needle-prick inoculation with a suspension of 1 × 106 spores per ml of HNZJ001 on 30 chili pepper fruits with three repeats, the same symptoms were observed and the same fungus was recovered. In bioassays, HNZJ001 caused lesions on both mature and immature fruits, while Glomerella cingulata strain LSQ1 (GenBank Accession No. HQ607386) used as a control did not infect immature fruits. PCR amplification was carried out by utilizing universal rDNA-ITS primer pair ITS4/ITS5. Sequencing of the PCR products of HNZJ001 (GenBank Accession No. GU059863) showed 100% identity to G. acutata (GenBank Accession No. EU008863) and Colletotrichum acutatum (GenBank Accession No. AF207794) after a BLAST search. The pathogen was identified as G. acutata (asexual stage: C. acutatum) on the basis of morphological characters and rDNA-ITS sequence analysis. Worldwide, it has been reported that pepper anthracnose might be caused by up to five species of Glomerella (Colletotrichum): G. cingulata, C. coccodes, C. capsici, C. dematium, and G. acutata (2), among which only the first three were previously reported in China. In recent years, G. acutata was reported on such plants as apple (3) and strawberry (1) in China, but not on pepper. To our knowledge, this is the first report of G. acutata on chili pepper in China. References: (1) X.-J. Ren et al. Acta Phytopathol. Sin. 38:325, 2008. (2) P. P. Than et al. Zhejiang Univ. Sci. B 9:764, 2008. (3) R. Zhang et al. Plant Dis. 92:1474, 2008.
The Role of Arabidopsis Rubisco Activase in Jasmonate-Induced Leaf Senescence
Authors: Shan Xiaoyi , Wang Junxia , Chua Lingling , Jiang Dean , Peng Wen , Xie Daoxin 
Published: December 2010

Abstract
Leaf senescence, as the last stage of leaf development, is regulated by diverse developmental and environmental factors. Jasmonates (JAs) have been shown to induce leaf senescence in several plant species; however, the molecular mechanism for JA-induced leaf senescence remains unknown. In this study, proteomic, genetic, and physiological approaches were used to reveal the molecular basis of JA-induced leaf senescence in Arabidopsis (Arabidopsis thaliana). We identified 35 coronatine-insensitive 1 (COI1)-dependent JA-regulated proteins using two-dimensional difference gel electrophoresis in Arabidopsis. Among these 35 proteins, Rubisco activase (RCA) was a COI1-dependent JA-repressed protein. We found that RCA was down-regulated at the levels of transcript and protein abundance by JA in a COI1-dependent manner. We further found that loss of RCA led to typical senescence-associated features and that the COI1-dependent JA repression of RCA played an important role in JA-induced leaf senescence.
Arabidopsis Homologs of thePetunia HAIRY MERISTEMGene Are Required for Maintenance of Shoot and Root Indeterminacy
Authors: Engstrom Eric M. , Andersen Carl M. , Gumulak-Smith Juliann , Hu John , Orlova Evguenia , Sozzani Rosangela , Bowman John L. 
Published: December 2010

AbstractMaintenance of indeterminacy is fundamental to the generation of plant architecture and a central component of the plant life strategy. Indeterminacy in plants is a characteristic of shoot and root meristems, which must balance maintenance of indeterminacy with organogenesis. The Petunia hybrida HAIRY MERISTEM (HAM) gene, a member of the GRAS family of transcriptional regulators, promotes shoot indeterminacy by an undefined non-cell-autonomous signaling mechanism(s). Here, we report that Arabidopsis (Arabidopsis thaliana) mutants triply homozygous for knockout alleles in three Arabidopsis HAM orthologs (Atham1,2,3 mutants) exhibit loss of indeterminacy in both the shoot and root. In the shoot, the degree of penetrance of the loss-of-indeterminacy phenotype of Atham1,2,3 mutants varies among shoot systems, with arrest of the primary vegetative shoot meristem occurring rarely or never, secondary shoot meristems typically arresting prior to initiating organogenesis, and inflorescence and flower meristems exhibiting a phenotypic range extending from wild type (flowers) to meristem arrest preempting organogenesis (flowers and inflorescence). Atham1,2,3 mutants also exhibit aberrant shoot phyllotaxis, lateral organ abnormalities, and altered meristem morphology in functioning meristems of both rosette and inflorescence. Root meristems of Atham1,2,3 mutants are significantly smaller than in the wild type in both longitudinal and radial axes, a consequence of reduced rates of meristem cell division that culminate in root meristem arrest. Atham1,2,3 phenotypes are unlikely to reflect complete loss of HAM function, as a fourth, more distantly related Arabidopsis HAM homolog, AtHAM4, exhibits overlapping function with AtHAM1 and AtHAM2 in promoting shoot indeterminacy.
iTRAQ Protein Profile Analysis of Arabidopsis Roots Reveals New Aspects Critical for Iron Homeostasis
Authors: Lan Ping , Li Wenfeng , Wen Tuan-Nan , Shiau Jeng-Yuan , Wu Yu-Ching , Lin Wendar , Schmidt Wolfgang 
Published: December 2010

Abstract
Iron (Fe) deficiency is a major constraint for plant growth and affects the quality of edible plant parts. To investigate the mechanisms underlying Fe homeostasis in plants, Fe deficiency-induced changes in the protein profile of Arabidopsis (Arabidopsis thaliana) roots were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification) differential liquid chromatography-tandem mass spectrometry on a LTQ-Orbitrap with high-energy collision dissociation. A total of 4,454 proteins were identified with a false discovery rate of less than 1.1%, and 2,882 were reliably quantified. A subset of 101 proteins was differentially expressed upon Fe deficiency. The changes in protein profiles upon Fe deficiency show low congruency with previously reported alterations in transcript levels, indicating posttranscriptional changes, and provide complementary information on Fe deficiency-induced processes. The abundance of proteins involved in the synthesis/regeneration of S-adenosylmethionine, the phenylpropanoid pathway, the response to oxidative stress, and respiration was highly increased by Fe deficiency. Using Fe-responsive proteins as bait, genome-wide fishing for partners with predictable or confirmed interologs revealed that RNA processing and ribonucleoprotein complex assembly may represent critical processes that contribute to the regulation of root responses to Fe deficiency, possibly by biasing translation efficiency.
Computational Analysis of Downcomer Boiling Phenomena Using a Component Thermal Hydraulic Analysis Code, CUPID
Authors: Cho Hyoung Kyu , Yun Byong Jo , Park Ik Kyu , Jeong Jae Jun 
Published: December 2010

Abstract
For the analysis of transient two-phase flows in nuclear reactor components such as a reactor vessel, a steam generator, and a containment, KAERI has developed a three-dimensional thermal hydraulic code, CUPID. It adopts a three-dimensional, transient, two-phase and three-field model and includes various physical models and correlations of the interfacial mass, momentum, and energy transfer for the closure. In the present paper, the CUPID code and its two-phase flow models were assessed against the downcomer boiling experiment, which was performed to simulate the downcomer boiling phenomena. They may happen in the downcomer of a nuclear reactor vessel during the reflood phase of a postulated loss of coolant accident. The stored energy release from the reactor vessel to the liquid inside the downcomer causes the boiling on the wall, and it can reduce the hydraulic head of the accumulated water, which is the driving force of water reflooding to the core. The computational analysis using the CUPID code showed that it can appropriately predict the multidimensional boiling phenomena under a low pressure and low flow rate condition with modification of the bubble size model.
Transfer Function Modeling of Zero-Power Dynamics of Circulating Fuel Reactors
Authors: Cammi A. , Di Marcello V. , Guerrieri C. , Luzzi L. 
Published: December 2010

Abstract
In this paper, the zero-power behavior of circulating fuel reactors (CFRs) has been investigated by means of a zero-dimensional neutron kinetics model that provides a simplified but useful approach to the simulation of the dynamics of this class of nuclear reactors. Among CFRs, the most promising is the molten salt reactor (MSR), which is one of the six innovative concepts of reactor proposed by the “Generation IV International Forum” for future nuclear energy supply. One of the key features of CFRs is represented by the fission material, which is dissolved in a liquid mixture that serves both as fuel and coolant. This causes a relevant coupling between neutronics and thermo-hydrodynamics, so that fuel velocity plays a relevant role in determining the dynamic performance of such systems. In the present study, a preliminary model has been developed that is based on the zero-power kinetics equations (i.e., reactivity feedbacks due to temperature change are neglected), modified in order to take into account the effects of the molten salt circulation on the drift of delayed neutron precursors. The system dynamic behavior has been analyzed using the theory of linear systems, and the transfer functions of the neutron density with respect to both reactivity and fuel velocity have been calculated. The developed model has been assessed on the basis of the available experimental data from the molten salt reactor experiment (MSRE) provided by the Oak Ridge National Laboratory. The results of the present work show that the developed simplified theoretical model is well descriptive of the MSRE zero-power dynamics, allowing a preliminary evaluation of the effects due to the circulation of the fuel salt on the neutronics of the system. Moreover, the model is of general validity for any kind of CFRs, and hence is applicable to study other MSR concepts in order to have some indications on the control strategy to be adopted in the MSR development envisaged by Generation IV.
Concentrations of Tenofovir and Emtricitabine in Breast Milk of HIV-1-Infected Women in Abidjan, Côte d'Ivoire, in the ANRS 12109 TEmAA Study, Step 2
Authors: Benaboud Sihem , Pruvost Alain , Coffie Patrick A. , Ekouévi Didier K. , Urien Saïk , Arrivé Elise , Blanche Stéphane , Théodoro Frédéric , Avit Divine , Dabis François , Tréluyer Jean-Marc , Hirt Déborah 
Published: December 2010

ABSTRACT
The aim was to evaluate emtricitabine (FTC) and tenofovir (TFV) neonatal ingestion through breast milk. Median TFV and FTC breast milk doses represented 0.03% and 2%, respectively, of the proposed oral infant doses. Neonatal simulated plasma concentrations were extremely low for TFV but between the half-maximal inhibitory concentration and the adult minimal expected concentration for FTC. The rare children who will acquire HIV despite TDF-FTC therapy will need to be monitored for viral resistance acquisition.
Nonoptimal DNA Topoisomerases Allow Maintenance of Supercoiling Levels and Improve Fitness of
Streptococcus pneumoniae
Authors: Balsalobre Luz , Ferrándiz María José , de Alba Gabriela , de la Campa Adela G. 
Published: December 2010

ABSTRACT

Fluoroquinolones, which target gyrase and topoisomerase IV, are used for treating
Streptococcus pneumoniae
infections. Fluoroquinolone resistance in this bacterium can arise via point mutation or interspecific recombination with genetically related streptococci. Our previous study on the fitness cost of resistance mutations and recombinant topoisomerases identified GyrAE85K as a high-cost change. However, this cost was compensated for by the presence of a recombinant topoisomerase IV (
parC
and
parE
recombinant genes) in strain T14. In this study, we purified wild-type and mutant topoisomerases and compared their enzymatic activities. In strain T14, both gyrase carrying GyrAE85K and recombinant topoisomerase IV showed lower activities (from 2.0- to 3.7-fold) than the wild-type enzymes. These variations of
in vitro
activity corresponded to changes of
in vivo
supercoiling levels that were analyzed by two-dimensional electrophoresis of an internal plasmid. Strains carrying GyrAE85K and nonrecombinant topoisomerases had lower (11.1% to 14.3%) supercoiling density (σ) values than the wild type. Those carrying GyrAE85K and recombinant topoisomerases showed either partial or total supercoiling level restoration, with σ values being 7.9% (recombinant ParC) and 1.6% (recombinant ParC and recombinant ParE) lower than those for the wild type. These data suggested that changes acquired by interspecific recombination might be selected because they reduce the fitness cost associated with fluoroquinolone resistance mutations. An increase in the incidence of fluoroquinolone resistance, even in the absence of further antibiotic exposure, is envisaged.