bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arabidopsis thaliana ggt1 photorespiratory mutants maintain leaf carbon/nitrogen balance by reducing RuBisCO content and plant growth
Authors: Dellero Younès , Lamothe‐Sibold Marlène , Jossier Mathieu , Hodges Michael 
Published: July 2015

SummaryMetabolic and physiological analyses of glutamate:glyoxylate aminotransferase 1 (GGT1) mutants were performed at the global leaf scale to elucidate the mechanisms involved in their photorespiratory growth phenotype. Air‐grown ggt1 mutants showed retarded growth and development, that was not observed at high CO2 (3000 μL L−1). When compared to wild‐type (WT) plants, air‐grown ggt1 plants exhibited glyoxylate accumulation, global changes in amino acid amounts including a decrease in serine content, lower organic acid levels, and modified ATP/ADP and NADP+/NADPH ratios. When compared to WT plants, their net CO2 assimilation rates (An) were 50% lower and this mirrored decreases in ribulose‐1,5‐bisphosphate carboxylase/oxygenase (RuBisCO) contents. High CO2‐grown ggt1 plants transferred to air revealed a rapid decrease of An and photosynthetic electron transfer rate while maintaining a high energetic state. Short‐term (a night period and 4 h of light) transferred ggt1 leaves accumulated glyoxylate and exhibited low serine contents, while other amino acid levels were not modified. RuBisCO content, activity and activation state were not altered after a short‐term transfer while the ATP/ADP ratio was lowered in ggt1 rosettes. However, plant growth and RuBisCO levels were both reduced in ggt1 leaves after a long‐term (12 days) acclimation to air from high CO2 when compared to WT plants. The data are discussed with respect to a reduced photorespiratory carbon recycling in the mutants. It is proposed that the low An limits nitrogen‐assimilation, this decreases leaf RuBisCO content until plants attain a new homeostatic state that maintains a constant C/N balance and leads to smaller, slower growing plants.
Arabidopsis Elongator subunit 2 positively contributes to resistance to the necrotrophic fungal pathogens Botrytis cinerea and Alternaria brassicicola
Authors: Wang Chenggang , Ding Yezhang , Yao Jin , Zhang Yanping , Sun Yijun , Colee James , Mou Zhonglin 
Published: July 2015

SummaryThe evolutionarily conserved Elongator complex functions in diverse biological processes including salicylic acid‐mediated immune response. However, how Elongator functions in jasmonic acid (JA)/ethylene (ET)‐mediated defense is unknown. Here, we show that Elongator is required for full induction of the JA/ET defense pathway marker gene PLANT DEFENSIN1.2 (PDF1.2) and for resistance to the necrotrophic fungal pathogens Botrytis cinerea and Alternaria brassicicola. A loss‐of‐function mutation in the Arabidopsis Elongator subunit 2 (ELP2) alters B. cinerea‐induced transcriptome reprogramming. Interestingly, in elp2, expression of WRKY33, OCTADECANOID‐RESPONSIVE ARABIDOPSIS AP2/ERF59 (ORA59), and PDF1.2 is inhibited, whereas transcription of MYC2 and its target genes is enhanced. However, overexpression of WRKY33 or ORA59 and mutation of MYC2 fail to restore PDF1.2 expression and B. cinerea resistance in elp2, suggesting that ELP2 is required for induction of not only WRKY33 and ORA59 but also PDF1.2. Moreover, elp2 is as susceptible as coronatine‐insensitive1 (coi1) and ethylene‐insensitive2 (ein2) to B. cinerea, indicating that ELP2 is an important player in B. cinerea resistance. Further analysis of the lesion sizes on the double mutants elp2 coi1 and elp2 ein2 and the corresponding single mutants revealed that the function of ELP2 overlaps with COI1 and is additive to EIN2 for B. cinerea resistance. Finally, basal histone acetylation levels in the coding regions of WRKY33, ORA59, and PDF1.2 are reduced in elp2 and a functional ELP2‐GFP fusion protein binds to the chromatin of these genes, suggesting that constitutive ELP2‐mediated histone acetylation may be required for full activation of the WRKY33/ORA59/PDF1.2 transcriptional cascade.
Molecular Dissection of the Essential Features of the Origin of Replication of the Second Vibrio cholerae Chromosome
Authors: Gerding Matthew A. , Chao Michael C. , Davis Brigid M. , Waldor Matthew K. 
Published: July 2015

ABSTRACT

Vibrionaceae
family members are interesting models for studying DNA replication initiation, as they contain two circular chromosomes. Chromosome II (chrII) replication is governed by two evolutionarily unique yet highly conserved elements, the origin DNA sequence
oriCII
and the initiator protein RctB. The minimum functional region of
oriCII
,
oriCII-min
, contains multiple elements that are bound by RctB
in vitro
, but little is known about the specific requirements for individual elements during
oriCII
initiation. We utilized undirected and site-specific mutagenesis to investigate the functionality of mutant forms of
oriCII-min
and assessed binding to various mutant forms by RctB. Our analyses showed that deletions, point mutations, and changes in RctB target site spacing or methylation all impaired
oriCII-min
-based replication. RctB displayed a reduced affinity for most of the low-efficacy origins tested, although its characteristic cooperative binding was generally maintained. Mutations that removed or altered the relative positions of origin components other than RctB binding sites (e.g., AT-rich sequence, DnaA target site) also abolished replicative capacity. Comprehensive mutagenesis and deep-sequencing-based screening (OriSeq) allowed the identification of a previously uncharacterized methylated domain in
oriCII
that is required for origin function. Together, our results reveal the remarkable evolutionary honing of
oriCII
and provide new insight into the complex interplay between RctB and
oriCII
.

IMPORTANCE
The genome of the enteric pathogen
Vibrio cholerae
consists of two chromosomes. While the chromosome I replication origin and its cognate replication initiator protein resemble those of
Escherichia coli
, the factors responsible for chromosome II replication initiation display no similarity to any other known initiation systems. Here, to enhance our understanding of how this DNA sequence,
oriCII
, and its initiator protein, RctB, function, we used both targeted mutagenesis and a new random-mutagenesis approach (OriSeq) to finely map the
oriCII
structural features and sequences required for RctB-mediated DNA replication. Collectively, our findings reveal the extraordinary evolutionary honing of the architecture and motifs that constitute
oriCII
and reveal a new role for methylation in
oriCII
-based replication. Finally, our findings suggest that the OriSeq approach is likely to be widely applicable for defining critical bases in
cis
-acting sequences.
Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System
Authors: Pecora Nicole D. , Li Ning , Allard Marc , Li Cong , Albano Esperanza , Delaney Mary , Dubois Andrea , Onderdonk Andrew B. , Bry Lynn 
Published: July 2015

ABSTRACT

Carbapenem-resistant
Enterobacteriaceae
(CRE) are an urgent public health concern. Rapid identification of the resistance genes, their mobilization capacity, and strains carrying them is essential to direct hospital resources to prevent spread and improve patient outcomes. Whole-genome sequencing allows refined tracking of both chromosomal traits and associated mobile genetic elements that harbor resistance genes. To enhance surveillance of CREs, clinical isolates with phenotypic resistance to carbapenem antibiotics underwent whole-genome sequencing. Analysis of 41 isolates of
Klebsiella pneumoniae
and
Enterobacter cloacae
, collected over a 3-year period, identified
K. pneumoniae
carbapenemase (KPC) genes encoding KPC-2, −3, and −4 and OXA-48 carbapenemases. All occurred within transposons, including multiple Tn
4401
transposon isoforms, embedded within more than 10 distinct plasmids representing incompatibility (Inc) groups IncR, -N, -A/C, -H, and -X. Using short-read sequencing, draft maps were generated of new KPC-carrying vectors, several of which were derivatives of the IncN plasmid pBK31551. Two strains also had Tn
4401
chromosomal insertions. Integrated analyses of plasmid profiles and chromosomal single-nucleotide polymorphism (SNP) profiles refined the strain patterns and provided a baseline hospital mobilome to facilitate analysis of new isolates. When incorporated with patient epidemiological data, the findings identified limited outbreaks against a broader 3-year period of sporadic external entry of many different strains and resistance vectors into the hospital. These findings highlight the utility of genomic analyses in internal and external surveillance efforts to stem the transmission of drug-resistant strains within and across health care institutions.

IMPORTANCE
We demonstrate how detection of resistance genes within mobile elements and resistance-carrying strains furthers active surveillance efforts for drug resistance. Whole-genome sequencing is increasingly available in hospital laboratories and provides a powerful and nuanced means to define the local landscape of drug resistance. In this study, isolates of
Klebsiella pneumoniae
and
Enterobacter cloacae
with resistance to carbapenem antibiotics were sequenced. Multiple carbapenemase genes were identified that resided in distinct transposons and plasmids. This mobilome, or population of mobile elements capable of mobilizing drug resistance, further highlighted the degree of strain heterogeneity while providing a detailed timeline of carbapenemase entry into the hospital over a 3-year period. These surveillance efforts support effective targeting of infection control resources and the development of institution-specific repositories of resistance genes and the mobile elements that carry them.
Validating prediction scales of type 2 diabetes mellitus in Spain: the SPREDIA-2 population-based prospective cohort study protocol
Authors: Salinero-Fort Miguel Ángel , de Burgos-Lunar Carmen , Mostaza Prieto José , Lahoz Rallo Carlos , Abánades-Herranz Juan Carlos , Gómez-Campelo Paloma , Laguna Cuesta Fernando , Estirado De Cabo Eva , García Iglesias Francisca , González Alegre Teresa , Fernández Puntero Belén , Montesano Sánchez Luis , Vicent López David , Cornejo Del Río Víctor , Fernández García Pedro J , Sabín Rodríguez Concesa , López López Silvia , Patrón Barandío Pedro ,   the SPREDIA-2 Group
Published: July 2015

IntroductionThe incidence of type 2 diabetes mellitus (T2DM) is increasing worldwide. When diagnosed, many patients already have organ damage or advance subclinical atherosclerosis. An early diagnosis could allow the implementation of lifestyle changes and treatment options aimed at delaying the progression of the disease and to avoid cardiovascular complications. Different scores for identifying undiagnosed diabetes have been reported, however, their performance in populations of southern Europe has not been sufficiently evaluated. The main objectives of our study are: to evaluate the screening performance and cut-off points of the main scores that identify the risk of undiagnosed T2DM and prediabetes in a Spanish population, and to develop and validate our own predictive models of undiagnosed T2DM (screening model), and future T2DM (prediction risk model) after 5-year follow-up. As a secondary objective, we will evaluate the atherosclerotic burden of the population with undiagnosed T2DM.Methods and analysisPopulation-based prospective cohort study with baseline screening, to evaluate the performance of the FINDRISC, DANISH, DESIR, ARIC and QDScore, against the gold standard tests: Fasting plasma glucose, oral glucose tolerance and/or HbA1c. The sample size will include 1352 participants between the ages of 45 and 74 years. Analysis: sensitivity, specificity, positive predictive value, negative predictive value, likelihood ratio positive, likelihood ratio negative and receiver operating characteristic curves and area under curve. Binary logistic regression for the first 700 individuals (derivation) and last 652 (validation) will be performed. All analyses will be calculated with their 95% CI; statistical significance will be p<0.05.Ethics and disseminationThe study protocol has been approved by the Research Ethics Committee of the Carlos III Hospital (Madrid). The score performance and predictive model will be presented in medical conferences, workshops, seminars and round table discussions. Furthermore, the predictive model will be published in a peer-reviewed medical journal to further increase the exposure of the scores.
Grading of Regional Apposition after Flow-Diverter Treatment (GRAFT): a comparative evaluation of VasoCT and intravascular OCT
Authors: van der Marel Kajo , Gounis Matthew J , Weaver John P , de Korte Antonius M , King Robert M , Arends Jennifer M , Brooks Olivia W , Wakhloo Ajay K , Puri Ajit S 
Published: July 2015

BackgroundPoor vessel wall apposition of flow diverter (FD) stents poses risks for stroke-related complications when treating intracranial aneurysms, necessitating long-term surveillance imaging. To facilitate quantitative evaluation of deployed devices, a novel algorithm is presented that generates intuitive two-dimensional representations of wall apposition from either high-resolution contrast-enhanced cone-beam CT (VasoCT) or intravascular optical coherence tomography (OCT) images.MethodsVasoCT and OCT images were obtained after FD implant (n=8 aneurysms) in an experimental sidewall aneurysm model in canines. Surface models of the vessel wall and FD device were extracted, and the distance between them was presented on a two-dimensional flattened map. Maps and cross-sections at potential locations of malapposition detected on VasoCT-based maps were compared. The performance of OCT-based apposition detection was evaluated on manually labeled cross-sections using logistic regression against a thresholded (≥0.25 mm) apposition measure.ResultsVasoCT and OCT acquisitions yielded similar Grading of Regional Apposition after Flow-Diverter Treatment (GRAFT) apposition maps. GRAFT maps from VasoCT highlighted 16 potential locations of malapposition, of which two were found to represent malapposed device struts. Logistic regression showed that OCT could detect malapposition with a sensitivity of 98% and a specificity of 81%.ConclusionsGRAFT delivered quantitative and visually convenient representations of potential FD malapposition and occasional acute thrombus formation. A powerful combination for future neuroendovascular applications is foreseen with the superior resolution delivered by intravascular OCT.
FACILE FABRICATION OF GRADIENT SURFACE BASED ON (METH)ACRYLATE COPOLYMER FILMS
Authors: ZHANG Y. , YANG H. , WEN X.-F. , CHENG J. , XIONG J. 
Published: July 2015

This paper describes a simple and economic approach for fabrication of surface wettability gradient on poly(butyl acrylate – methyl methacrylate) [P (BA–MMA)] and poly(butyl acrylate – methyl methacrylate – 2-hydroxyethyl methacrylate) [P (BA–MMA–HEMA)] films. The (meth)acrylate copolymer [including P (BA–MMA) and P (BA–MMA–HEMA)] films are hydrolyzed in an aqueous solution of NaOH and the transformation of surface chemical composition is achieved by hydrolysis in NaOH solution. The gradient wetting properties are generated based on different functional groups on the P (BA–MMA) and P (BA–MMA–HEMA) films. The effects of both the surface chemical and surface topography on wetting of the (meth)acrylate copolymer film are discussed. Surface chemical composition along the materials length is determined by XPS, and surface topography properties of the obtained gradient surfaces are analyzed by FESEM and AFM. Water contact angle system (WCAs) results show that the P (BA–MMA–HEMA) films provide a larger slope of the gradient wetting than P (BA–MMA). Moreover, this work demonstrates that the gradient concentration of chemical composition on the poly(meth) acrylate films is owing to the hydrolysis processes of ester group, and the hydrolysis reactions that have negligible influence on the surface morphology of the poly(meth) acrylate films coated on the glass slide. The gradient wettability surfaces may find broad applications in the field of polymer coating due to the compatibility of (meth) acrylate polymer.
Disparity in Mortality From Rheumatic Heart Disease in Indigenous Australians
Authors: Colquhoun Samantha M. , Condon John R. , Steer Andrew C. , Li Shu Q. , Guthridge Steven , Carapetis Jonathan R. 
Published: July 2015

Background
Recent estimates of the global burden of rheumatic heart disease (RHD) have highlighted the paucity of reliable RHD mortality data from populations most affected by RHD.

Methods and Results
We investigated RHD mortality rates and trends for Indigenous and non‐Indigenous Australians in the Northern Territory (NT) for the period 1977–2005 and seminationally (NT plus 4 other states, covering 89% of Indigenous Australians) from 1997 to 2005 using vital statistics data. All analysis was undertaken by Indigenous status, sex, and age at death. In the NT, 90% of all deaths from RHD were among Indigenous persons; however, the Indigenous population makes up only 30.4% of the NT population. The death rate ratio (Indigenous compared with non‐Indigenous) was 54.80 in the NT and 12.74 in the other 4 states (estimated at the median age of 50 years). Non‐Indigenous death rates were low for all age groups except ≥65 years, indicating RHD deaths in the elderly non‐Indigenous population. Death rates decreased at a more rapid rate for non‐Indigenous than Indigenous persons in the NT between 1997 and 2005. Indigenous persons in other parts of Australia showed lower death rates than their NT counterparts, but the death rates for Indigenous persons in all states were still much higher than rates for non‐Indigenous Australians.

Conclusions
Indigenous Australians are much more likely to die from RHD than other Australians. Among the Indigenous population, RHD mortality is much higher in the NT than elsewhere in Australia, exceeding levels reported in many industrialized countries more than a century ago. With the paucity of data from high‐prevalence areas, these data contribute substantially to understanding the global burden of RHD mortality.
Clinical Implications of Changes in Individual Platelet Reactivity to Aspirin Over Time in Acute Ischemic Stroke
Authors: Kim Joon-Tae , Heo Suk-Hee , Choi Kang-Ho , Nam Tai-Seung , Choi Seong-Min , Lee Seung-Han , Park Man-Seok , Kim Byeong C. , Kim Myeong-Kyu , Saver Jeffrey L. , Cho Ki-Hyun 
Published: July 2015

Background and Purpose—
Time-dependent changes in individual platelet reactivity have been detected in patients with coronary artery disease. Therefore, we sought to evaluate the time-dependent changes in platelet reactivity to aspirin during the acute stage after ischemic stroke and the clinical implications of variable patient responses to aspirin in acute ischemic stroke.

Methods—
We conducted a single-center, prospective, observational study. The acute aspirin reaction unit (ARU) was measured after 3 hours of aspirin loading, with higher values indicating increased platelet reactivity despite aspirin therapy. The follow-up ARU was measured on the fifth day of consecutive aspirin intake. The numeric difference between the follow-up ARU and the acute ARU was defined as ΔARU and was stratified into quartiles. Early neurological deterioration was regarded as an early clinical outcome.

Results—

Both the acute ARU (476±69 IU) and the follow-up ARU (451±68 IU) were measured in 349 patients in this study. Early neurological deterioration was observed in 72 patients (20.6%). Changes in aspirin platelet reactivity over time showed an approximately Gaussian distribution. The highest ΔARU quartile was independently associated with early neurological deterioration (odds ratio, 3.19; 95% confidence interval, 1.43–7.10;
P
=0.005) by multivariate logistic regression analysis.

Conclusions—
The results of our study showed that the increase in platelet reactivity to aspirin over time is independently associated with early neurological deterioration in patients with acute ischemic stroke. In addition, during the acute stage of ischemic stroke, serial platelet reactivity assays may be more useful than a single assay for identifying the clinical implications of aspirin platelet reactivity after ischemic stroke.
A Climatology of the Precipitation over the Southern Ocean as Observed at Macquarie Island
Authors: Wang Zhan , Siems Steven T. , Belusic Danijel , Manton Michael J. , Huang Yi 
Published: July 2015

AbstractMacquarie Island (54.50°S, 158.94°E) is an isolated island with modest orography in the midst of the Southern Ocean with precipitation records dating back to 1948. These records (referred to as MAC) are of particular interest because of the relatively large biases in the energy and water budgets commonly found in climate simulations and reanalysis products over the region. A basic climatology of the surface precipitation P is presented and compared with the ERA-Interim (ERA-I) reanalysis. The annual ERA-I precipitation (953 mm) is found to underestimate the annual MAC precipitation (1023 mm) by 6.8% from 1979 to 2011. The frequency of 3-h surface precipitation at MAC is 36.4% from 2003 to 2011. Light precipitation (0.066 ≤ P < 0.5 mm h−1) dominates this dataset (29.7%), and heavy precipitation (P ≥ 1.5 mm h−1) is rare (1.1%). Drizzle (0 < P < 0.066 mm h−1) is commonly produced by ERA-I (43.9%) but is weaker than the detectable threshold of MAC. Warm rain intensity and frequency from CloudSat products were compared with those from MAC. These CloudSat products also recorded considerable drizzle (16%–30%) but were not significantly different from MAC when P ≥ 0.5 mm h−1. Heavy precipitation events were, in general, more commonly associated with fronts and cyclonic lows. Some heavy precipitation events were found to arise from weaker fronts and lows that were not adequately represented in the reanalysis products. Yet other heavy precipitation events were observed at points/times not associated with either fronts or cyclonic lows. Two case studies are employed to further examine this finding.
Sea Surface Temperature Warming Patterns and Future Vegetation Change
Authors: Rauscher Sara A. , Jiang Xiaoyan , Steiner Allison , Williams A. Park , Cai D. Michael , McDowell Nathan G. 
Published: July 2015

Abstract
Recent modeling studies of future vegetation change suggest the potential for large-scale forest die-off in the tropics. Taken together with observational evidence of increasing tree mortality in numerous ecosystem types, there is clearly a need for projections of vegetation change. To that end, the authors have performed an ensemble of climate–vegetation experiments with the National Science Foundation–DOE Community Atmosphere Model (CAM) coupled to the Community Land Model (CAM–CLM-CN) with its dynamic vegetation model enabled (CAM–CLM-CNDV). To overcome the limitations of using a single model, the authors employ the sea surface temperature (SST) warming patterns simulated by eight different models from the Coupled Model Intercomparison Program phase 3 (CMIP3) as boundary conditions. Since the SST warming pattern in part dictates how precipitation may change in the future, in this way a range of future vegetation–climate trajectories can be produced.
On an annual average basis, this study’s CAM–CLM-CN simulations do not produce as large a spread in projected precipitation as the original CMIP3 archive. These differences are due to the tendency of CAM–CLM-CN to increase tropical precipitation under a global warming scenario, although this response is modulated by the SST warming patterns imposed. However, the CAM–CLM-CN simulations reproduce the enhanced dry season in the tropics simulated by CMIP3. These simulations show longer fire seasons and increases in fractional area burned. In one ensemble member, extreme droughts over tropical South America lead to fires that remove vegetation cover in the eastern Amazon, suggesting that large-scale die-offs are an unlikely but still possible event.