bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Predictable AMO-Like Pattern in the GFDL Fully Coupled Ensemble Initialization and Decadal Forecasting System
Authors: Yang Xiaosong , Rosati Anthony , Zhang Shaoqing , Delworth Thomas L. , Gudgel Rich G. , Zhang Rong , Vecchi Gabriel , Anderson Whit , Chang You-Soon , DelSole Timothy , Dixon Keith , Msadek Rym , Stern William F. , Wittenberg Andrew , Zeng Fanrong 
Published: August 2012

Abstract
The decadal predictability of sea surface temperature (SST) and 2-m air temperature (T2m) in the Geophysical Fluid Dynamics Laboratory (GFDL) decadal hindcasts, which are part of the Fifth Coupled Model Intercomparison Project experiments, has been investigated using an average predictability time (APT) analysis. Comparison of retrospective forecasts initialized using the GFDL Ensemble Coupled Data Assimilation system with uninitialized historical forcing simulations using the same model allows identification of the internal multidecadal pattern (IMP) for SST and T2m. The IMP of SST is characterized by an interhemisphere dipole, with warm anomalies centered in the North Atlantic subpolar gyre region and North Pacific subpolar gyre region, and cold anomalies centered in the Antarctic Circumpolar Current region. The IMP of T2m is characterized by a general bipolar seesaw, with warm anomalies centered in Greenland and cold anomalies centered in Antarctica. The retrospective prediction skill of the initialized system, verified against independent observational datasets, indicates that the IMP of SST may be predictable up to 4 (10) yr lead time at 95% (90%) significance level, and the IMP of T2m may be predictable up to 2 (10) yr at the 95% (90%) significance level. The initialization of multidecadal variations of northward oceanic heat transport in the North Atlantic significantly improves the predictive skill of the IMP. The dominant roles of oceanic internal dynamics in decadal prediction are further elucidated by fixed-forcing experiments in which radiative forcing is returned abruptly to 1961 values. These results point toward the possibility of meaningful decadal climate outlooks using dynamical coupled models if they are appropriately initialized from a sustained climate observing system.
Forecasting with Reference to a Specific Climatology
Authors: Wallace Emily , Arribas Alberto 
Published: August 2012

Abstract
Seasonal forecasts are most commonly issued as anomalies with respect to some multiyear reference period. However, different seasonal forecasting centers use different reference periods. This paper shows that for near-surface temperature, precipitation, and mean sea level pressure, over most regions of the world there is evidence that these differences between reference periods should not be ignored, especially when forecasters combine outputs from several prediction systems. Three methods are presented by which reference periods could be adjusted, and it is shown that the differences between the proposed methods are smaller than the errors that result from not correcting for different reference periods.
Precursors of Executive Function in Infants With Sickle Cell Anemia
Authors: Hogan Alexandra M. , Telfer Paul T. , Kirkham Fenella J. , Haan Michelle de 
Published: August 2012

Executive dysfunction occurs in sickle cell anemia, but there are few early data. Infants with sickle cell anemia (n = 14) and controls (n = 14) performed the “A-not-B” and Object Retrieval search tasks, measuring precursors of executive function at 9 and 12 months. Significant group differences were not found. However, for the A-not-B task, 7 of 11 sickle cell anemia infants scored in the lower 2 performance categories at 9 months, but only 1 at 12 months ( P = .024); controls obtained scores at 12 months that were statistically comparable to the scores they had already obtained at 9 months. On the Object Retrieval task, 9- and 12-month controls showed comparable scores, whereas infants with sickle cell anemia continued to improve ( P = .027); at 9 months, those with lower hemoglobin oxygen saturation passed fewer trials ( Rs = 0.670, P = .024) and took longer to obtain the toy ( Rs = –0.664, P = .013). Subtle delays in acquiring developmental skills may underlie abnormal executive function in childhood.
Perioperative management of patients on chronic antithrombotic therapy
Authors: Ortel Thomas L. 
Published: August 2012

AbstractPerioperative management of antithrombotic therapy is a situation that occurs frequently and requires consideration of the patient, the procedure, and an expanding array of anticoagulant and antiplatelet agents. Preoperative assessment must address each patient's risk for thromboembolic events balanced against the risk for perioperative bleeding. Procedures can be separated into those with a low bleeding risk, which generally do not require complete reversal of the antithrombotic therapy, and those associated with an intermediate or high bleeding risk. For patients who are receiving warfarin who need interruption of the anticoagulant, consideration must be given to whether simply withholding the anticoagulant is the optimal approach or whether a perioperative “bridge” with an alternative agent, typically a low-molecular-weight heparin, should be used. The new oral anticoagulants dabigatran and rivaroxaban have shorter effective half-lives, but they introduce other concerns for perioperative management, including prolonged drug effect in patients with renal insufficiency, limited experience with clinical laboratory testing to confirm lack of residual anticoagulant effect, and lack of a reversal agent. Antiplatelet agents must also be considered in the perioperative setting, with particular consideration given to the potential risk for thrombotic complications in patients with coronary artery stents who have antiplatelet therapy withheld.
Vibration response imaging: a novel noninvasive tool for evaluating the initial therapeutic effect of noninvasive positive pressure ventilation in patients with acute exacerbation of chronic obstructive pulmonary disease
Authors: Bing Dai , Jian Kang , Long-feng Sun , Wei Tan , Hong-wen Zhao 
Published: August 2012

Abstract

Background
The popular methods for evaluating the initial therapeutic effect (ITE) of noninvasive positive pressure ventilation (NPPV) can only roughly reflect the therapeutic outcome of a patient’s ventilation because they are subjective, invasive and time-delayed. In contrast, vibration response imaging (VRI) can monitor the function of a patient’s ventilation over the NPPV therapy in a non-invasive manner. This study aimed to investigate the value of VRI in evaluating the ITE of NPPV for patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD).

Methods
Thirty-six AECOPD patients received VRI at three time points: before NPPV treatment (T1), at 15 min of NPPV treatment (T2), and at 15 min after the end of NPPV treatment (T4). Blood gas analysis was also performed at T1 and at 2 hours of NPPV treatment (T3). Thirty-nine healthy volunteers also received VRI at T1 and T2. VRI examination at the time point T2 in either the patients or volunteers did not require any interruption of the on-going NPPV. The clinical indices at each time point were compared between the two groups. Moreover, correlations between the PaCO2 changes (T3 vs T1) and abnormal VRI scores (AVRIS) changes (T2 vs T1) were analyzed.

Results
No significant AVRIS differences were found between T1 and T2 in the healthy controls (8.51 ± 3.36 vs. 8.53 ± 3.57, P > 0.05). The AVRIS, dynamic score, MEF score and EVP score showed a significant decrease in AECOPD patients at T2 compared with T1 (P < 0.05), but a significant increase at T4 compared with T2 (P < 0.05). We also found a positive correlation (R2 = 0.6399) between the PaCO2 changes (T3 vs T1) and AVRIS changes (T2 vs T1).

Conclusions
VRI is a promising noninvasive tool for evaluating the initial therapeutic effects of NPPV in AECOPD patients and predicting the success of NPPV in the early stage.
A web-based multi-genome synteny viewer for customized data
Authors: Revanna Kashi V , Munro Daniel , Gao Alvin , Chiu Chi-Chen , Pathak Anil , Dong Qunfeng 
Published: August 2012

Abstract

Background
Web-based synteny visualization tools are important for sharing data and revealing patterns of complicated genome conservation and rearrangements. Such tools should allow biologists to upload genomic data for their own analysis. This requirement is critical because individual biologists are generating large amounts of genomic sequences that quickly overwhelm any centralized web resources to collect and display all those data. Recently, we published a web-based synteny viewer, GSV, which was designed to satisfy the above requirement. However, GSV can only compare two genomes at a given time. Extending the functionality of GSV to visualize multiple genomes is important to meet the increasing demand of the research community.

Results
We have developed a multi-Genome Synteny Viewer (mGSV). Similar to GSV, mGSV is a web-based tool that allows users to upload their own genomic data files for visualization. Multiple genomes can be presented in a single integrated view with an enhanced user interface. Users can navigate through all the selected genomes in either pairwise or multiple viewing mode to examine conserved genomic regions as well as the accompanying genome annotations. Besides serving users who manually interact with the web server, mGSV also provides Web Services for machine-to-machine communication to accept data sent by other remote resources. The entire mGSV package can also be downloaded for easy local installation.

Conclusions
mGSV significantly enhances the original functionalities of GSV. A web server hosting mGSV is provided at http://cas-bioinfo.cas.unt.edu/mgsv.
Implications of hybridisation and cytotypic differentiation in speciation assessed by AFLP and plastid haplotypes - a case study of Potentilla alpicola La Soie
Authors: Paule Juraj , Scherbantin Antonia , Dobeš Christoph 
Published: August 2012

AbstractBackgroundHybridisation is presumed to be an important mechanism in plant speciation and a creative evolutionary force often accompanied by polyploidisation and in some cases by apomixis. ThePotentilla collinagroup constitutes a particularly suitable model system to study these phenomena as it is morphologically extensively variable, exclusively polyploid and expresses apomixis. In the present study, the alpine taxonPotentilla alpicolahas been chosen in order to study its presumed hybrid origin, identify underlying evolutionary processes and infer the discreteness or taxonomic value of hybrid forms.ResultsCombined analysis of AFLP, cpDNA sequences and ploidy level variation revealed a hybrid origin of theP. alpicolapopulations from South Tyrol (Italy) resulting from crosses betweenP. pusillaand two cytotypes ofP. argentea. Hybrids were locally sympatric with at least one of the parental forms. Three lineages of different evolutionary origin comprising two ploidy levels were identified withinP. alpicola.The lineages differed in parentage and the complexity of the evolutionary process. A geographically wide-spread lineage thus contrasted with locally distributed lineages of different origins. Populations ofP. collinastudied in addition, have been regarded rather as recent derivatives of the hexaploidP. argentea. The observation of clones within bothP. alpicolaandP. collinasuggested a possible apomictic mode of reproduction.ConclusionsDifferent hybridisation scenarios taking place on geographically small scales resulted in viable progeny presumably stabilised by apomixis. The case study ofP. alpicolasupports that these processes played a significant role in the creation of polymorphism in the genusPotentilla. However, multiple origin of hybrids and backcrossing are considered to produce a variety of evolutionary spontaneous forms existing aside of reproductively stabilised, established lineages.
Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses
Authors: Sundström Elisabeth , Imsland Freyja , Mikko Sofia , Wade Claire , Sigurdsson Snaevar , Pielberg Gerli Rosengren , Golovko Anna , Curik Ino , Seltenhammer Monika H , Sölkner Johann , Lindblad-Toh Kerstin , Andersson Leif 
Published: August 2012

Abstract

Background
Greying with age in horses is an autosomal dominant trait, associated with loss of hair pigmentation, melanoma and vitiligo-like depigmentation. We recently identified a 4.6 kb duplication in STX17 to be associated with the phenotype. The aims of this study were to investigate if the duplication in Grey horses shows copy number variation and to exclude that any other polymorphism is uniquely associated with the Grey mutation.

Results
We found little evidence for copy number expansion of the duplicated sequence in blood DNA from Grey horses. In contrast, clear evidence for copy number expansions was indicated in five out of eight tested melanoma tissues or melanoma cell lines. A tendency of a higher copy number in aggressive tumours was also found. Massively parallel resequencing of the ~350 kb Grey haplotype did not reveal any additional mutations perfectly associated with the phenotype, confirming the duplication as the true causative mutation. We identified three SNP alleles that were present in a subset of Grey haplotypes within the 350 kb region that shows complete linkage disequilibrium with the causative mutation. Thus, these three nucleotide substitutions must have occurred subsequent to the duplication, consistent with our interpretation that the Grey mutation arose more than 2,000 years before present.

Conclusions
These results suggest that the mutation acts as a melanoma-driving regulatory element. The elucidation of the mechanistic features of the duplication will be of considerable interest for the characterization of these horse melanomas as well as for the field of human melanoma research.
The receptor like kinase at Rhg1-a/Rfs2 caused pleiotropic resistance to sudden death syndrome and soybean cyst nematode as a transgene by altering signaling responses
Authors: Srour Ali , Afzal Ahmed J , Blahut-Beatty Laureen , Hemmati Naghmeh , Simmonds Daina H , Li Wenbin , Liu Miao , Town Christopher D , Sharma Hemlata , Arelli Prakash , Lightfoot David A 
Published: August 2012

Abstract

Background
Soybean (Glycine max (L. Merr.)) resistance to any population of Heterodera glycines (I.), or Fusarium virguliforme (Akoi, O’Donnell, Homma & Lattanzi) required a functional allele at Rhg1/Rfs2. H. glycines, the soybean cyst nematode (SCN) was an ancient, endemic, pest of soybean whereas F. virguliforme causal agent of sudden death syndrome (SDS), was a recent, regional, pest. This study examined the role of a receptor like kinase (RLK) GmRLK18-1 (gene model Glyma_18_02680 at 1,071 kbp on chromosome 18 of the genome sequence) within the Rhg1/Rfs2 locus in causing resistance to SCN and SDS.

Results
A BAC (B73p06) encompassing the Rhg1/Rfs2 locus was sequenced from a resistant cultivar and compared to the sequences of two susceptible cultivars from which 800 SNPs were found. Sequence alignments inferred that the resistance allele was an introgressed region of about 59 kbp at the center of which the GmRLK18-1 was the most polymorphic gene and encoded protein. Analyses were made of plants that were either heterozygous at, or transgenic (and so hemizygous at a new location) with, the resistance allele of GmRLK18-1. Those plants infested with either H. glycines or F. virguliforme showed that the allele for resistance was dominant. In the absence of Rhg4 the GmRLK18-1 was sufficient to confer nearly complete resistance to both root and leaf symptoms of SDS caused by F. virguliforme and provided partial resistance to three different populations of nematodes (mature female cysts were reduced by 30–50%). In the presence of Rhg4 the plants with the transgene were nearly classed as fully resistant to SCN (females reduced to 11% of the susceptible control) as well as SDS. A reduction in the rate of early seedling root development was also shown to be caused by the resistance allele of the GmRLK18-1. Field trials of transgenic plants showed an increase in foliar susceptibility to insect herbivory.

Conclusions
The inference that soybean has adapted part of an existing pathogen recognition and defense cascade (H.glycines; SCN and insect herbivory) to a new pathogen (F. virguliforme; SDS) has broad implications for crop improvement. Stable resistance to many pathogens might be achieved by manipulation the genes encoding a small number of pathogen recognition proteins.
A new microspore embryogenesis system under low temperature which mimics zygotic embryogenesis initials, expresses auxin and efficiently regenerates doubled-haploid plants in Brassica napus
Authors: Prem Deepak , Solís María-Teresa , Bárány Ivett , Rodríguez-Sanz Héctor , Risueño María C , Testillano Pilar S 
Published: August 2012

AbstractBackgroundMicrospore embryogenesis represents a unique system of single cell reprogramming in plants wherein a highly specialized cell, the microspore, by specific stress treatment, switches its fate towards an embryogenesis pathway. InBrassica napus,a model species for this phenomenon, incubation of isolated microspores at 32°C is considered to be a pre-requisite for embryogenesis induction.ResultsWe have developed a newin vitrosystem at lower temperature (18°C) to efficiently induce microspore embryogenesis throughout two different developmental pathways: one involving the formation of suspensor-like structures (52.4%) and another producing multicellular embryos without suspensor (13.1%); additionally, a small proportion of non-responsive microspores followed a gametophytic-like development (34.4%) leading to mature pollen. The suspensor-like pathway followed at 18°C involved the establishment of asymmetric identities from the first microspore division and an early polarity leading to different cell fates, suspensor and embryo development, which were formed by cells with different organizations and endogenous auxin distribution, similar to zygotic embryogenesis. In addition, a new strategy for germination of microspore derived embryos was developed for achieving more than 90% conversion of embryos to plantlets, with a predominance of spontaneous doubled haploids plants.ConclusionThe present work reveals a novel mechanism for efficient microspore embryogenesis induction inB. napususing continuous low temperature treatment. Results indicated that low temperature applied for longer periods favours an embryogenesis pathway whose first division originates asymmetric cell identities, early polarity establishment and the formation of suspensor-like structures, mimicking zygotic embryogenesis. This newin vitrosystem provides a convenient tool to analyzein situthe mechanisms underlying different developmental pathways during the microspore reprogramming, breaking or not the cellular symmetry, the establishment of polarity and the developmental embryo patterning, which further produce mature embryos and plants.
Down-regulation of POLYGALACTURONASE1 alters firmness, tensile strength and water loss in apple (Malus x domestica) fruit
Authors: Atkinson Ross G , Sutherland Paul W , Johnston Sarah L , Gunaseelan Kularajathevan , Hallett Ian C , Mitra Deepali , Brummell David A , Schröder Roswitha , Johnston Jason W , Schaffer Robert J 
Published: August 2012

AbstractBackgroundWhile there is now a significant body of research correlating apple (Malusxdomestica) fruit softening with the cell wall hydrolaseENDO-POLYGALACTURONASE1 (PG1), there is currently little knowledge of its physiological effectsin planta. This study examined the effect of down regulation of PG1 expression in ‘Royal Gala’ apples, a cultivar that typically has high levels of PG1, and softens during fruit ripening.ResultsPG1-suppressed ‘Royal Gala’ apples harvested from multiple seasons were firmer than controls after ripening, and intercellular adhesion was higher. Cell wall analyses indicated changes in yield and composition of pectin, and a higher molecular weight distribution of CDTA-soluble pectin. Structural analyses revealed more ruptured cells and free juice in pulled apart sections, suggesting improved integrity of intercellular connections and consequent cell rupture due to failure of the primary cell walls under stress.PG1-suppressed lines also had reduced expansion of cells in the hypodermis of ripe apples, resulting in more densely packed cells in this layer. This change in morphology appears to be linked with reduced transpirational water loss in the fruit.ConclusionsThese findings confirm PG1’s role in apple fruit softening and suggests that this is achieved in part by reducing cellular adhesion. This is consistent with previous studies carried out in strawberry but not with those performed in tomato. In apple PG1 also appears to influence other fruit texture characters such as juiciness and water loss.
Is the APLS formula used to calculate weight-for-age applicable to a Trinidadian population?
Authors: Ali Khalid , Sammy Ian , Nunes Paula 
Published: August 2012

Abstract

Background
In paediatric emergency medicine, estimation of weight in ill children can be performed in a variety of ways. Calculation using the ‘APLS’ formula (weight = [age + 4] × 2) is one very common method. Studies on its validity in developed countries suggest that it tends to under-estimate the weight of children, potentially leading to errors in drug and fluid administration. The formula is not validated in Trinidad and Tobago, where it is routinely used to calculate weight in paediatric resuscitation.

Methods
Over a six-week period in January 2009, all children one to five years old presenting to the Emergency Department were weighed. Their measured weights were compared to their estimated weights as calculated using the APLS formula, the Luscombe and Owens formula and a “best fit” formula derived (then simplified) from linear regression analysis of the measured weights.

Results
The APLS formula underestimated weight in all age groups with a mean difference of −1.4 kg (95% limits of agreement 5.0 to −7.8). The Luscombe and Owens formula was more accurate in predicting weight than the APLS formula, with a mean difference of −0.4 kg (95% limits of agreement 6.9 to −6.1%). Using linear regression analysis, and simplifying the derived equation, the best formula to describe weight and age was (weight = [2.5 x age] + 8). The percentage of children whose actual weight fell within 10% of the calculated weights using any of the three formulae was not significantly different.

Conclusions
The APLS formula slightly underestimates the weights of children in Trinidad, although this is less than in similar studies in developed countries. Both the Luscombe and Owens formula and the formula derived from the results of this study give a better estimate of the measured weight of children in Trinidad. However, the accuracy and precision of all three formulae were not significantly different from each other. It is recommended that the APLS formula should continue to be used to estimate the weight of children in resuscitation situations in Trinidad, as it is well known, easy to calculate and widely taught in this setting.