bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interannual Climate Variability over the Tropical Pacific Ocean Induced by the Indian Ocean Dipole through the Indonesian Throughflow
Authors: Yuan Dongliang , Zhou Hui , Zhao Xia 
Published: November 2012

Abstract
The authors’ previous dynamical study has suggested a link between the Indian and Pacific Ocean interannual climate variations through the transport variations of the Indonesian Throughflow. In this study, the consistency of this oceanic channel link with observations is investigated using correlation analyses of observed ocean temperature, sea surface height, and surface wind data. The analyses show significant lag correlations between the sea surface temperature anomalies (SSTA) in the southeastern tropical Indian Ocean in fall and those in the eastern Pacific cold tongue in the following summer through fall seasons, suggesting potential predictability of ENSO events beyond the period of 1 yr. The dynamics of this teleconnection seem not through the atmospheric bridge, because the wind anomalies in the far western equatorial Pacific in fall have insignificant correlations with the cold tongue anomalies at time lags beyond one season. Correlation analyses between the sea surface height anomalies (SSHA) in the southeastern tropical Indian Ocean and those over the Indo-Pacific basin suggest eastward propagation of the upwelling anomalies from the Indian Ocean into the equatorial Pacific Ocean through the Indonesian Seas. Correlations in the subsurface temperature in the equatorial vertical section of the Pacific Ocean confirm the propagation. In spite of the limitation of the short time series of observations available, the study seems to suggest that the ocean channel connection between the two basins is important for the evolution and predictability of ENSO.
The Hadley Circulation in Reanalyses: Climatology, Variability, and Change
Authors: Nguyen H. , Evans A. , Lucas C. , Smith I. , Timbal B. 
Published: November 2012

Abstract
Analysis of the annual cycle of intensity, extent, and width of the Hadley circulation across a 31-yr period (1979–2009) from all existent reanalyses reveals a good agreement among the datasets. All datasets show that intensity is at a maximum in the winter hemisphere and at a minimum in the summer hemisphere. Maximum and minimum values of meridional extent are reached in the respective autumn and spring hemispheres. While considering the horizontal momentum balance, where a weakening of the Hadley cell (HC) is expected in association with a widening, it is shown here that there is no direct relationship between intensity and extent on a monthly time scale.
All reanalyses show an expansion in both hemispheres, most pronounced and statistically significant during summer and autumn at an average rate of expansion of 0.55° decade−1 in each hemisphere. In contrast, intensity trends are inconsistent among the datasets, although there is a tendency toward intensification, particularly in winter and spring.
Correlations between the HC and tropical and extratropical large-scale modes of variability suggest interactions where the extent of the HC is influenced by El Niño–Southern Oscillation (ENSO) and the annular modes. The cells tend to shrink (expand) during the warm (cold) phase of ENSO and during the low (high) phase of the annular modes. Intensity appears to be influenced only by ENSO and only during spring for the southern cell and during winter for the northern cell.
Response of the HadGEM2 Earth System Model to Future Greenhouse Gas Emissions Pathways to the Year 2300*
Authors: Caesar John , Palin Erika , Liddicoat Spencer , Lowe Jason , Burke Eleanor , Pardaens Anne , Sanderson Michael , Kahana Ron 
Published: November 2012

Abstract
A new ensemble of simulations from the Earth System configuration of the Hadley Centre Global Environmental Model, version 2 (HadGEM2-ES), is used to evaluate the response to historical and projected future greenhouse gas forcings that follow Representative Concentration Pathways (RCPs). In addition to the projected changes during the twenty-first century, extended simulations to the year 2300 allow an investigation into inertia in the climate system post-2100 that may occur even if atmospheric CO2 concentrations have stabilized. Projections of temperature, precipitation, sea level, permafrost, heat waves, and compatible carbon emissions are analyzed. The low emissions scenario RCP2.6 is the only scenario considered here that is approximately consistent with a 2°C global warming limit, though there are regions where local changes in temperature are projected to considerably exceed 2°C, particularly over northern high-latitude areas. An aggressive mitigation approach, represented here by RCP2.6, could contribute to avoiding the larger-magnitude future climate changes projected under higher emissions scenarios. Despite these benefits, changes should still be expected under an aggressive mitigation pathway and may require adaptation.
Fall risk six weeks from onset of stroke and the ability of the Prediction of Falls in Rehabilitation Settings Tool and motor function to predict falls
Authors: Nyström Anna , Hellström Karin 
Published: November 2012

Objective: To investigate whether the Prediction of Falls in Rehabilitation Settings Tool (Predict FIRST) and motor function could be used to identify people at risk of falling during the first six weeks after stroke, and to compare the risk of falling according to Predict FIRST with real falls frequency. Design: A longitudinal, prospective study. Patients: Sixty-eight people newly diagnosed with stroke admitted to an acute stroke unit. Methods: The participants underwent an assessment of motor ability (Modified Motor Assessment Scale according to Uppsala University Hospital version 99 (M-MAS UAS-99)) and falls risk (Predict FIRST) on the first to fourth day at the acute stroke unit. Falls occurring in the acute stroke unit were recorded and falls occurring after discharge were reported by telephone follow-up. The prediction of falls was analysed with binary logistic regression. Results: Fourteen of the patients (21%) fell at least once during the first six weeks after stroke. The strongest significant predictor for falls was a high score on Predict FIRST (odds ratio 5.21, confidence interval (CI) 1.10–24.78) followed by M-MAS UAS-99 parts C–E (odds ratio 0.65, CI 0.44–0.95). Predict FIRST underestimated the risk of falling as the median fall risk was 9% according to Predict FIRST. Conclusion: Although Predict FIRST has the ability to predict falls in people with recent onset of stroke, there is some underestimation of fall risk.
A preliminary approach to simulating cyclic variability in a port fuel injection spark ignition engine
Authors: Suyabodha Apiwat , Pennycott Andrew , Brace Chris J 
Published: November 2012

Differences in the combustion process from one cycle to the next, termed cyclic variations, are an important feature of spark ignition engines. These variations cause fluctuations in the work output of the engine and can therefore degrade engine and vehicle performance. In addition, the uneven running caused by cyclic variability of combustion constrains the engine operating range and thus has a direct effect on fuel consumption. Existing one-dimensional engine models typically represent cyclic variability using some form of stochastic behaviour defined by a pre-set normal distribution. This approach does not offer an insight into the mechanisms underlying variability, and makes it difficult to include variability when calibrating the engine using simulation. Three-dimensional modelling approaches can offer an insight but are too complex to be used extensively within a calibration exercise. In this paper, a simple, preliminary approach using empirical functions easily generated using standard engine instrumentation is used to augment a one-dimensional engine model via co-simulation approach to include a representation of the effects of the air–fuel ratio and residual gas fraction on combustion efficiency, early rate of combustion and duration of combustion. These parameters allow the engine model to simulate the effects of deterministic aspects of cyclic variability on heat release, in-cylinder pressure and indicated mean effective pressure. The model is validated by comparing its prediction of cyclic variability under both rich and lean operation to experimental data. The resulting predictions match experimental results qualitatively and quantitatively. The model can be used to inform subsequent optimization processes, representing the variability-induced constraints on the operating envelope. This will assist in the generation of fuel efficient calibrations and also allow cycle-to-cycle variation effects to be included much earlier in the design process. The model will also aid the development of online control approaches aiming to reduce cycle-to-cycle engine variability.
Multi-dimensional time-frequency control of micro-milling instability
Authors: Liu Meng-Kun , Halfmann Eric B , Suh C Steve 
Published: November 2012

Micro-milling is inherently unstable and chattering with aberrational tool vibrations. While the time response is bounded, however, micro-milling can become unstably broadband and chaotic in the frequency domain, inadvertently rendering poor tolerance and frequent tool damage. A novel simultaneous time-frequency control theory is applied to negate the various nonlinear dynamic instabilities including tool chatter and tool resonance displayed by a multi-dimensional, time-delayed micro-milling model. The time and frequency responses of the force and vibration of the model agree well with the experimental results published by Jun et al. A multi-variable control scheme is realized by implementing two independent controllers in parallel to follow a target signal representing the desired micro-milling state of stability. The control of unstable cutting at high spindle speeds ranging from 63,000 to 180,000 rpm and different axial depth-of-cuts are investigated using phase portrait, Poincaré section, and instantaneous frequency (IF). The time-frequency control scheme effectively restores dynamic instabilities, including repelling manifold and chaotic response, back to an attracting limit cycle or periodic motion of reduced vibration amplitude and frequency response. The force magnitude of the dynamically unstable cutting process is also reduced to the range of stable cutting.
Oculus: faster sequence alignment by streaming read compression
Authors: Veeneman Brendan A , Iyer Matthew K , Chinnaiyan Arul M 
Published: November 2012

Abstract

Background
Despite significant advancement in alignment algorithms, the exponential growth of nucleotide sequencing throughput threatens to outpace bioinformatic analysis. Computation may become the bottleneck of genome analysis if growing alignment costs are not mitigated by further improvement in algorithms. Much gain has been gleaned from indexing and compressing alignment databases, but many widely used alignment tools process input reads sequentially and are oblivious to any underlying redundancy in the reads themselves.

Results
Here we present Oculus, a software package that attaches to standard aligners and exploits read redundancy by performing streaming compression, alignment, and decompression of input sequences. This nearly lossless process (> 99.9%) led to alignment speedups of up to 270% across a variety of data sets, while requiring a modest amount of memory. We expect that streaming read compressors such as Oculus could become a standard addition to existing RNA-Seq and ChIP-Seq alignment pipelines, and potentially other applications in the future as throughput increases.

Conclusions
Oculus efficiently condenses redundant input reads and wraps existing aligners to provide nearly identical SAM output in a fraction of the aligner runtime. It includes a number of useful features, such as tunable performance and fidelity options, compatibility with FASTA or FASTQ files, and adherence to the SAM format. The platform-independent C++ source code is freely available online, at http://code.google.com/p/oculus-bio.
Transcriptomic and phylogenetic analysis of Culex pipiens quinquefasciatus for three detoxification gene families
Authors: Yan Liangzhen , Yang Pengcheng , Jiang Feng , Cui Na , Ma Enbo , Qiao Chuanling , Cui Feng 
Published: November 2012

AbstractBackgroundThe genomes of three major mosquito vectors of human diseases,Anopheles gambiae,Aedes aegypti, andCulex pipiens quinquefasciatus, have been previously sequenced.C. p. quinquefasciatushas the largest number of predicted protein-coding genes, which partially results from the expansion of three detoxification gene families: cytochrome P450 monooxygenases (P450), glutathione S-transferases (GST), and carboxyl/cholinesterases (CCE). However, unlikeAn. gambiaeandAe. aegypti, which have large amounts of gene expression data,C. p. quinquefasciatushas limited transcriptomic resources. Knowledge of complete gene expression information is very important for the exploration of the functions of genes involved in specific biological processes. In the present study, the three detoxification gene families ofC. p. quinquefasciatuswere analyzed for phylogenetic classification and compared with those of three other dipteran insects. Gene expression during various developmental stages and the differential expression responsible for parathion resistance were profiled using the digital gene expression (DGE) technique.ResultsA total of 302 detoxification genes were found inC. p. quinquefasciatus, including 71 CCE, 196 P450, and 35 cytosolic GST genes. Compared with three other dipteran species, gene expansion inCulexmainly occurred in the CCE and P450 families, where the genes of α-esterases, juvenile hormone esterases, and CYP325 of the CYP4 subfamily showed the most pronounced expansion on the genome. For the five DGE libraries, 3.5-3.8 million raw tags were generated and mapped to 13314 reference genes. Among 302 detoxification genes, 225 (75%) were detected for expression in at least one DGE library. One fourth of the CCE and P450 genes were detected uniquely in one stage, indicating potential developmentally regulated expression. A total of 1511 genes showed different expression levels between a parathion-resistant and a susceptible strain. Fifteen detoxification genes, including 2 CCEs, 6 GSTs, and 7 P450s, were expressed at higher levels in the resistant strain.ConclusionsThe results of the present study provide new insights into the functions and evolution of three detoxification gene families in mosquitoes and comprehensive transcriptomic resources forC. p. quinquefasciatus, which will facilitate the elucidation of molecular mechanisms underlying the different biological characteristics of the three major mosquito vectors.
Functional characterization of a tomato COBRA-likegene functioning in fruit development and ripening
Authors: Cao Ying , Tang Xiaofeng , Giovannoni Jim , Xiao Fangming , Liu Yongsheng 
Published: November 2012

Abstract

Background
Extensive studies have demonstrated that the COBRA gene is critical for biosynthesis of cell wall constituents comprising structural tissues of roots, stalks, leaves and other vegetative organs, however, its role in fruit development and ripening remains largely unknown.

Results
We identified a tomato gene (SlCOBRA-like) homologous to Arabidopsis COBRA, and determined its role in fleshy fruit biology. The SlCOBRA-like gene is highly expressed in vegetative organs and in early fruit development, but its expression in fruit declines dramatically during ripening stages, implying a primary role in early fruit development. Fruit-specific suppression of SlCOBRA-like resulted in impaired cell wall integrity and up-regulation of genes encoding proteins involved in cell wall degradation during early fruit development. In contrast, fruit-specific overexpression of SlCOBRA-like resulted in increased wall thickness of fruit epidermal cells, more collenchymatous cells beneath the epidermis, elevated levels of cellulose and reduced pectin solubilization in the pericarp cells of red ripe fruits. Moreover, transgenic tomato fruits overexpressing SlCOBRA-like exhibited desirable early development phenotypes including enhanced firmness and a prolonged shelf life.

Conclusions
Our results suggest that SlCOBRA-like plays an important role in fruit cell wall architecture and provides a potential genetic tool for extending the shelf life of tomato and potentially additional fruits.
Predictors of first-line antiretroviral therapy discontinuation due to drug-related adverse events in HIV-infected patients: a retrospective cohort study
Authors: Prosperi Mattia CF , Fabbiani Massimiliano , Fanti Iuri , Zaccarelli Mauro , Colafigli Manuela , Mondi Annalisa , D’Avino Alessandro , Borghetti Alberto , Cauda Roberto , Di Giambenedetto Simona 
Published: November 2012

AbstractBackgroundDrug-related toxicity has been one of the main causes of antiretroviral treatment discontinuation. However, its determinants are not fully understood. Aim of this study was to investigate predictors of first-line antiretroviral therapy discontinuation due to adverse events and their evolution in recent years.MethodsPatients starting first-line antiretroviral therapy were retrospectively selected. Primary end-point was the time to discontinuation of therapy due to adverse events, estimating incidence, fitting Kaplan-Meier and multivariable Cox regression models upon clinical/demographic/chemical baseline patients’ markers.Results1,096 patients were included: 302 discontinuations for adverse events were observed over 1,861 person years of follow-up between 1988 and 2010, corresponding to an incidence (95% CI) of 0.16 (0.14-0.18). By Kaplan-Meier estimation, the probabilities (95% CI) of being free from an adverse event at 90 days, 180 days, one year, two years, and five years were 0.88 (0.86-0.90), 0.85 (0.83-0.87), 0.79 (0.76-0.81), 0.70 (0.67-0.74), 0.55 (0.50-0.61), respectively. The most represented adverse events were gastrointestinal symptoms (28.5%), hematological (13.2%) or metabolic (lipid and glucose metabolism, lipodystrophy) (11.3%) toxicities and hypersensitivity reactions (9.3%). Factors associated with an increased hazard of adverse events were: older age, CDC stage C, female gender, homo/bisexual risk group (vs. heterosexual), HBsAg-positivity. Among drugs, zidovudine, stavudine, zalcitabine, didanosine, full-dose ritonavir, indinavir but also efavirenz (actually recommended for first-line regimens) were associated to an increased hazard of toxicity. Moreover, patients infected by HIV genotype F1 showed a trend for a higher risk of adverse events.ConclusionsAfter starting antiretroviral therapy, the probability of remaining free from adverse events seems to decrease over time. Among drugs associated with increased toxicity, only one is currently recommended for first-line regimens but with improved drug formulation. Older age, CDC stage, MSM risk factor and gender are also associated with an increased hazard of toxicity and should be considered when designing a first-line regimen.
Using Audience Response Technology to provide formative feedback on pharmacology performance for non-medical prescribing students - a preliminary evaluation
Authors: Mostyn Alison , Meade Oonagh , Lymn Joanne S 
Published: November 2012

Abstract

Background
The use of anonymous audience response technology (ART) to actively engage students in classroom learning has been evaluated positively across multiple settings. To date, however, there has been no empirical evaluation of the use of individualised ART handsets and formative feedback of ART scores. The present study investigates student perceptions of such a system and the relationship between formative feedback results and exam performance.

Methods
Four successive cohorts of Non-Medical Prescribing students (n=107) had access to the individualised ART system and three of these groups (n=72) completed a questionnaire about their perceptions of using ART. Semi-structured interviews were carried out with a purposive sample of seven students who achieved a range of scores on the formative feedback. Using data from all four cohorts of students, the relationship between mean ART scores and summative pharmacology exam score was examined using a non-parametric correlation.

Results
Questionnaire and interview data suggested that the use of ART enhanced the classroom environment, motivated students and promoted learning. Questionnaire data demonstrated that students found the formative feedback helpful for identifying their learning needs (95.6%), guiding their independent study (86.8%), and as a revision tool (88.3%). Interviewees particularly valued the objectivity of the individualised feedback which helped them to self-manage their learning. Interviewees’ initial anxiety about revealing their level of pharmacology knowledge to the lecturer and to themselves reduced over time as students focused on the learning benefits associated with the feedback.
A significant positive correlation was found between students’ formative feedback scores and their summative pharmacology exam scores (Spearman’s rho = 0.71, N=107, p<.01).

Conclusions
Despite initial anxiety about the use of individualised ART units, students rated the helpfulness of the individualised handsets and personalised formative feedback highly. The significant correlation between ART response scores and student exam scores suggests that formative feedback can provide students with a useful reference point in terms of their level of exam-readiness.
Optimal vaccination schedule search using genetic algorithm over MPI technology
Authors: Calonaci Cristiano , Chiacchio Ferdinando , Pappalardo Francesco 
Published: November 2012

Abstract

Background
Immunological strategies that achieve the prevention of tumor growth are based on the presumption that the immune system, if triggered before tumor onset, could be able to defend from specific cancers. In supporting this assertion, in the last decade active immunization approaches prevented some virus-related cancers in humans. An immunopreventive cell vaccine for the non-virus-related human breast cancer has been recently developed. This vaccine, called Triplex, targets the HER-2-neu oncogene in HER-2/neu transgenic mice and has shown to almost completely prevent HER-2/neu-driven mammary carcinogenesis when administered with an intensive and life-long schedule.

Methods
To better understand the preventive efficacy of the Triplex vaccine in reduced schedules we employed a computational approach. The computer model developed allowed us to test in silico specific vaccination schedules in the quest for optimality. Specifically here we present a parallel genetic algorithm able to suggest optimal vaccination schedule.

Results & Conclusions
The enormous complexity of combinatorial space to be explored makes this approach the only possible one. The suggested schedule was then tested in vivo, giving good results. Finally, biologically relevant outcomes of optimization are presented.
A novel facile synthesis and characterization of molybdenum nanowires
Authors: Kovic Andrej , Znidarsic Andrej , Jesih Adolf , Mrzel Ales , Gaberscek Miran , Hassanien Abdou 
Published: November 2012

Abstract
We describe a straightforward technique to synthesize pure Mo nanowires (NWs) from Mo6S
y
I
z
(8,2 < y + z ≤ 10) NWs as precursor templates. The structural transformations occur when Mo6S
y
I
z
NWs are annealed in Ar/H2 mixture leading to the formation of pure Mo NWs with similar structures as initial morphologies. Detailed microscopic characterizations show that large diameters (>15 nm) Mo NWs are highly porous, while small diameters (<7 nm) are made of solid nanocrystalline grains. We find NW of diameter 4 nm can carry up to 30 μA current without suffering structural degradation. Moreover, NWs can be elastically deformed over several cycles without signs of plastic deformation.