bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tropospheric Rossby Wave Breaking and the NAO/NAM
Authors: Strong Courtenay , Magnusdottir Gudrun 
Published: February 2008

Abstract
Objective analysis of several hundred thousand anticyclonic and cyclonic breaking Rossby waves is performed for the Northern Hemisphere (NH) winters of 1958–2006. A winter climatology of both anticyclonic and cyclonic Rossby wave breaking (RWB) frequency and size (zonal extent) is presented for the 350-K isentropic surface over the NH, and the spatial distribution of RWB is shown to agree with theoretical ideas of RWB in shear flow.
Composites of the two types of RWB reveal their characteristic sea level pressure anomalies, upper- and lower-tropospheric velocity fields, and forcing of the upper-tropospheric zonal flow. It is shown how these signatures project onto the centers of action and force the velocity patterns associated with the North Atlantic Oscillation (NAO) and Northern Hemisphere annular mode (NAM). Previous studies have presented evidence that anticyclonic (cyclonic) breaking leads to the positive (negative) polarity of the NAO, and this relationship is confirmed for RWB over the midlatitudes centered near 50°N. However, an opposite and statistically significant relationship, in which cyclonic RWB forces the positive NAO and anticyclonic RWB forces the negative NAO, is shown over regions 20° to the north and south, centered at 70° and 30°N, respectively.
On a winter mean basis, the frequency of RWB over objectively defined regions covering 12% of the area of the NH accounts for 95% of the NAO index and 92% of the NAM index. A 6-hourly analysis of all the winters indicates that RWB over the objectively defined regions affects the NAO/NAM without a time lag. Details of the objective wave-breaking analysis method are provided in the appendix.
Interdecadal Variation of ENSO Predictability in Multiple Models
Authors: Tang Youmin , Deng Ziwang , Zhou Xiaobing , Cheng Yanjie , Chen Dake 
Published: February 2008

AbstractIn this study, El Niño–Southern Oscillation (ENSO) retrospective forecasts were performed for the 120 yr from 1881 to 2000 using three realistic models that assimilate the historic dataset of sea surface temperature (SST). By examining these retrospective forecasts and corresponding observations, as well as the oceanic analyses from which forecasts were initialized, several important issues related to ENSO predictability have been explored, including its interdecadal variability and the dominant factors that control the interdecadal variability.The prediction skill of the three models showed a very consistent interdecadal variation, with high skill in the late nineteenth century and in the middle–late twentieth century, and low skill during the period from 1900 to 1960. The interdecadal variation in ENSO predictability is in good agreement with that in the signal of interannual variability and in the degree of asymmetry of ENSO system. A good relationship was also identified between the degree of asymmetry and the signal of interannual variability, and the former is highly related to the latter. Generally, the high predictability is attained when ENSO signal strength and the degree of asymmetry are enhanced, and vice versa. The atmospheric noise generally degrades overall prediction skill, especially for the skill of mean square error, but is able to favor some individual prediction cases. The possible reasons why these factors control ENSO predictability were also discussed.
Water Masses in the Pacific in CCSM3
Authors: Thompson Lu Anne , Cheng Wei 
Published: February 2008

Abstract
An examination of model water masses in the North Pacific Ocean is performed in the Community Climate System version 3 (CCSM3) and its ocean-only counterpart. While the surface properties of the ocean are well represented in both simulations, biases in thermocline and intermediate-water masses exist that point to errors in both ocean model physics and the atmospheric component of the coupled model. The lack of North Pacific Intermediate Water (NPIW) in both simulations as well as the overexpression of a too-fresh Antarctic Intermediate Water (AAIW) is indicative of ocean model deficiencies. These properties reflect the difficulty of low-resolution ocean models to represent processes that control deep-water formation both in the Southern Ocean and in the Okhotsk Sea. In addition, as is typical of low-resolution ocean models, errors in the position of the Kuroshio, the North Pacific subtropical gyre western boundary current (WBC), impact the formation of the water masses that form the bulk of the thermocline as well as the properties of the NPIW. Biases that arise only in the coupled simulation include too-salty surface water in the subtropical North Pacific and too deep a thermocline, the source of which is the too-strong westerlies at midlatitudes. Biases in the location of the intertropical convergence zone (ITCZ) and the southern Pacific convergence zone (SPCZ) lead to the opposite hemispheric asymmetry in water mass structure when compared to observations. The atmospheric component of the coupled model acts to compound most ocean model biases.
Eddy Formation near the West Coast of Greenland
Authors: Bracco Annalisa , Pedlosky Joseph , Pickart Robert S. 
Published: February 2008

Abstract
This paper extends A. Bracco and J. Pedlosky’s investigation of the eddy-formation mechanism in the eastern Labrador Sea by including a more realistic depiction of the boundary current. The quasigeostrophic model consists of a meridional, coastally trapped current with three vertical layers. The current configuration and topographic domain are chosen to match, as closely as possible, the observations of the boundary current and the varying topographic slope along the West Greenland coast. The role played by the bottom-intensified component of the boundary current on the formation of the Labrador Sea Irminger Rings is explored. Consistent with the earlier study, a short, localized bottom-trapped wave is responsible for most of the perturbation energy growth. However, for the instability to occur in the three-layer model, the deepest component of the boundary current must be sufficiently strong, highlighting the importance of the near-bottom flow. The model is able to reproduce important features of the observed vortices in the eastern Labrador Sea, including the polarity, radius, rate of formation, and vertical structure. At the time of formation, the eddies have a surface signature as well as a strong circulation at depth, possibly allowing for the transport of both surface and near-bottom water from the boundary current into the interior basin. This work also supports the idea that changes in the current structure could be responsible for the observed interannual variability in the number of Irminger Rings formed.
How feasible is the attainment of community ambulation after stroke? A pilot randomized controlled trial to evaluate community-based physiotherapy in subacute stroke
Authors: Lord Susan , McPherson Kathryn M , McNaughton Harry K , Rochester Lynn , Weatherall Mark 
Published: February 2008

Objective: This pilot randomized controlled trial evaluated an assistant-led, community-based intervention to improve community mobility and participation after stroke, and examined the potential for independent community ambulation in people with subacute stroke who present with moderate gait deficit. Design: A multicentre, pilot randomized controlled trial. Setting: Three hospitals and three community settings in New Zealand. Subjects: Thirty post-acute, home-dwelling stroke survivors were randomly allocated to receive intervention in the community (n = 14) or as hospital outpatients (n = 16) twice a week for seven weeks. Interventions: The community intervention involved practice of functional gait activities in community environments relevant to each participant. Hospital-based physiotherapy was based upon a Motor Relearning approach. Main measures: The primary outcome measure was gait speed (m/min). Secondary outcomes included endurance (six-minute walk time), Activities-specific Confidence Balance Scale, and the Subjective Index of Physical and Social Outcomes measured at baseline, post intervention and six months. Results: Large gains in gait speed were obtained for participants in both groups: community group mean (SD) 16 (16.1) m/min; physiotherapy group mean (SD) 15.9 (16.1) m/min, maintained at six months. There were no significant differences between groups for primary and secondary outcomes after treatment (P = 0.86 ANOVA) or at six months (P = 0.83 ANOVA). Only 11 participants reported independent community ambulation. Levels of social integration were low to moderate. Conclusions: A community-based gait recovery programme appears a practicable alternative to routine physiotherapy, however independent community ambulation is a challenging rehabilitation goal.
Multiple-task walking training in people with mild to moderate Parkinson's disease: a pilot study
Authors: Canning Colleen G , Ada Louise , Woodhouse Elke 
Published: February 2008

Objective: To determine whether multiple-task training of walking is feasible and worthwhile in people with mild to moderate Parkinson's disease. Design: Baseline-controlled pilot study with three-week baseline, training and retention phases. Setting: University research laboratory. Subjects: Five people aged 61 ±8 years with mild to moderate Parkinson's disease (Hoehn and Yahr stages II—III). Interventions: Multiple-task training was performed for 30 minutes once a week during the three-week training phase. Main measures: Participants were tested and trained during the `on' phase of medication. Feasibility of training was examined using 10 cm visual analogue scales to measure participant perception of mental fatigue, physical fatigue, difficulty, anxiety and confidence. Walking velocity, stride length and cadence under multiple-task conditions were measured. Results: Participants reported low levels of mental fatigue, physical fatigue, difficulty and anxiety as well as high levels of confidence associated with multiple-task training. No adverse effects of training were reported. Multiple-task walking velocity increased by 0.09 ± 0.06 m/s (95% confidence interval (CI) 0.02 to 0.16) between the baseline and training phase and this increase was maintained in the retention phase. Conclusion: Multiple-task training is feasible in people with mild to moderate Parkinson's disease. The data suggest sustained benefits on multiple-task walking velocity are possible. A randomized controlled trial of multiple-task training efficacy is warranted.
Comparison of the effect of two types of acupuncture on quality of life in secondary progressive multiple sclerosis: a preliminary single-blind randomized controlled trial
Authors: Donnellan Clare P , Shanley Jackie 
Published: February 2008

Objective: To compare the effect of two types of acupuncture on the quality of life of individuals with secondary progressive multiple sclerosis and provide preliminary evidence regarding the safety of this intervention for this population. Design: Preliminary single-blind randomized controlled trial. Setting: Outpatient attendance at rehabilitation unit. Participants: Fourteen participants with secondary progressive multiple sclerosis. Interventions: Chinese medical acupuncture or minimal acupuncture. Participants received 10 treatments over five weeks. Measures: Multiple Sclerosis Impact Scale 29, Fatigue Severity Scale and General Health Questionnaire 12 were measured pre and post intervention. Adverse events and other responses during treatment were recorded prospectively. Results: Participants receiving minimal acupuncture demonstrated statistically significant greater improvement in the Multiple Sclerosis Impact Scale 29 psychological subscale compared with those receiving Chinese medical acupuncture in an intention-to-treat analysis (P=0.04), with mean change in Chinese acupuncture group of 6.0 (SD 13.9) and in minimal acupuncture group of 23.0 (SD 21.0). No other statistically significant difference between the groups was found. No major adverse events were noted. Minor adverse events such as lower limb muscle spasms or pain were noted in some participants in both intervention groups. Conclusion: Minimal acupuncture resulted in greater improvement of Multiple Sclerosis Impact Scale 29 psychological subscale compared with Chinese medical acupuncture. No other differences between the groups were found. In view of the small sample these results are not conclusive. This study provides preliminary evidence to suggest that acupuncture is safe for people with secondary progressive multiple sclerosis. A large-scale trial is required to provide more definitive evidence.
A functional TNFRSF5 gene variant is associated with risk of lymphoma
Authors: Skibola Christine F. , Nieters Alexandra , Bracci Paige M. , Curry John D. , Agana Luz , Skibola Danica R. , Hubbard Alan , Becker Nikolaus , Smith Martyn T. , Holly Elizabeth A. 
Published: February 2008

AbstractCD40 and its ligand, CD154, are major costimulatory molecules whose interactions are important in humoral and cellular immunity. We hypothesized that single nucleotide polymorphisms (SNPs) in TNFRSF5 and TNFSF5 encoding the CD40 and CD154 proteins, respectively, influence lymphoma risk, particularly a functional TNFRSF5 SNP (−1C>T, rs1883832) associated with reduced B-cell CD40 expression. TNFRSF5 and TNFSF5 SNPs were examined in a population-based case-control study of non-Hodgkin lymphoma (376 cases/801 controls with DNA), and compelling findings were followed up in 2 independent populations. Pooled analyses of all 3 case-control studies (total N = 1776 non-Hodgkin lymphoma cases, N = 2482 controls) revealed an increased risk of follicular lymphoma (FL) associated with the TNFRSF5 −1TT genotype (odds ratio = 1.6; 95% confidence interval, 1.1-2.4). In addition, among women, an inverse association was found between the variant A allele for a TNFSF5 6809G>A SNP and FL risk (OR = .61; 95% CI, 0.36-0.98). In genotype-phenotype studies, significantly reduced circulating soluble CD40 was observed in TNFRSF5 −1TT compared with −1CC carriers. Further, dendritic cells from those with −1TT versus −1CC genotypes exhibited lower CD40 cell surface expression. These results suggest that the TNFRSF5 −1C>T polymorphism may increase FL susceptibility through mechanisms that hinder cellular immune responses. Further studies are needed to explore these findings.
Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs
Authors: Chen Yong-Zi , Tang Yu-Rong , Sheng Zhi-Ya , Zhang Ziding 
Published: February 2008

Abstract

Background
As one of the most common protein post-translational modifications, glycosylation is involved in a variety of important biological processes. Computational identification of glycosylation sites in protein sequences becomes increasingly important in the post-genomic era. A new encoding scheme was employed to improve the prediction of mucin-type O-glycosylation sites in mammalian proteins.

Results
A new protein bioinformatics tool, CKSAAP_OGlySite, was developed to predict mucin-type O-glycosylation serine/threonine (S/T) sites in mammalian proteins. Using the composition of k-spaced amino acid pairs (CKSAAP) based encoding scheme, the proposed method was trained and tested in a new and stringent O-glycosylation dataset with the assistance of Support Vector Machine (SVM). When the ratio of O-glycosylation to non-glycosylation sites in training datasets was set as 1:1, 10-fold cross-validation tests showed that the proposed method yielded a high accuracy of 83.1% and 81.4% in predicting O-glycosylated S and T sites, respectively. Based on the same datasets, CKSAAP_OGlySite resulted in a higher accuracy than the conventional binary encoding based method (about +5.0%). When trained and tested in 1:5 datasets, the CKSAAP encoding showed a more significant improvement than the binary encoding. We also merged the training datasets of S and T sites and integrated the prediction of S and T sites into one single predictor (i.e. S+T predictor). Either in 1:1 or 1:5 datasets, the performance of this S+T predictor was always slightly better than those predictors where S and T sites were independently predicted, suggesting that the molecular recognition of O-glycosylated S/T sites seems to be similar and the increase of the S+T predictor's accuracy may be a result of expanded training datasets. Moreover, CKSAAP_OGlySite was also shown to have better performance when benchmarked against two existing predictors.

Conclusion
Because of CKSAAP encoding's ability of reflecting characteristics of the sequences surrounding mucin-type O-glycosylation sites, CKSAAP_ OGlySite has been proved more powerful than the conventional binary encoding based method. This suggests that it can be used as a competitive mucin-type O-glycosylation site predictor to the biological community. CKSAAP_OGlySite is now available at http://bioinformatics.cau.edu.cn/zzd_lab/CKSAAP_OGlySite/.
Association mapping of partitioning loci in barley
Authors: Cockram James , White Jon , Leigh Fiona J , Lea Vincent J , Chiapparino Elena , Laurie David A , Mackay Ian J , Powell Wayne , O'Sullivan Donal M 
Published: February 2008

AbstractBackgroundAssociation mapping, initially developed in human disease genetics, is now being applied to plant species. The model speciesArabidopsisprovided some of the first examples of association mapping in plants, identifying previously cloned flowering time genes, despite high population sub-structure. More recently, association genetics has been applied to barley, where breeding activity has resulted in a high degree of population sub-structure. A major genotypic division within barley is that between winter- and spring-sown varieties, which differ in their requirement for vernalization to promote subsequent flowering. To date, all attempts to validate association genetics in barley by identifying major flowering time loci that control vernalization requirement (VRN-H1andVRN-H2) have failed. Here, we validate the use of association genetics in barley by identifyingVRN-H1andVRN-H2, despite their prominent role in determining population sub-structure.ResultsBy taking barley as a typical inbreeding crop, and seasonal growth habit as a major partitioning phenotype, we develop an association mapping approach which successfully identifiesVRN-H1andVRN-H2, the underlying loci largely responsible for this agronomic division. We find a combination of Structured Association followed by Genomic Control to correct for population structure and inflation of the test statistic, resolved significant associations only withVRN-H1and theVRN-H2candidate genes, as well as two genes closely linked toVRN-H1(HvCSFs1andHvPHYC).ConclusionWe show that, after employing appropriate statistical methods to correct for population sub-structure, the genome-wide partitioning effect of allelic status atVRN-H1andVRN-H2does not result in the high levels of spurious association expected to occur in highly structured samples. Furthermore, we demonstrate that bothVRN-H1and the candidateVRN-H2genes can be identified using association mapping. Discrimination between intragenicVRN-H1markers was achieved, indicating that candidate causative polymorphisms may be discerned and prioritised within a larger set of positive associations. This proof of concept study demonstrates the feasibility of association mapping in barley, even within highly structured populations. A major advantage of this method is that it does not require large numbers of genome-wide markers, and is therefore suitable for fine mapping and candidate gene evaluation, especially in species for which large numbers of genetic markers are either unavailable or too costly.
Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system
Authors: Watson Joseph D , Wang Shenglong , Von Stetina Stephen E , Spencer W Clay , Levy Shawn , Dexheimer Phillip J , Kurn Nurith , Heath Joe Don , Miller David M 
Published: February 2008

Abstract

Background
DNA microarrays provide a powerful method for global analysis of gene expression. The application of this technology to specific cell types and tissues, however, is typically limited by small amounts of available mRNA, thereby necessitating amplification. Here we compare microarray results obtained with two different methods of RNA amplification to profile gene expression in the C. elegans larval nervous system.

Results
We used the mRNA-tagging strategy to isolate transcripts specifically from C. elegans larval neurons. The WT-Ovation Pico System (WT-Pico) was used to amplify 2 ng of pan-neural RNA to produce labeled cDNA for microarray analysis. These WT-Pico-derived data were compared to microarray results obtained with a labeled aRNA target generated by two rounds of In Vitro Transcription (IVT) of 25 ng of pan-neural RNA. WT-Pico results in a higher fraction of present calls than IVT, a finding consistent with the proposal that DNA-DNA hybridization results in lower mismatch signals than the RNA-DNA heteroduplexes produced by IVT amplification. Microarray data sets from these samples were compared to a reference profile of all larval cells to identify transcripts with elevated expression in neurons. These results were validated by the high proportion of known neuron-expressed genes detected in these profiles and by promoter-GFP constructs for previously uncharacterized genes in these data sets. Together, the IVT and WT-Pico methods identified 2,173 unique neuron-enriched transcripts. Only about half of these transcripts (1,044), however, are detected as enriched by both IVT and WT-Pico amplification.

Conclusion
We show that two different methods of RNA amplification, IVT and WT-Pico, produce valid microarray profiles of gene expression in the C. elegans larval nervous system with a low rate of false positives. However, our results also show that each method of RNA amplification detects a unique subset of bona fide neural-enriched transcripts and thus a wider array of authentic neural genes are identified by the combination of these data sets than by the microarray profiles obtained with either method of RNA amplification alone. With its relative ease of implementation and greater sensitivity, WT-Pico is the preferred method of amplification for cases in which sample RNA is limiting.