bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic Estimates of Initial-Value Decadal Predictability for Six AOGCMs
Authors: Branstator Grant , Teng Haiyan , Meehl Gerald A. , Kimoto Masahide , Knight Jeff R. , Latif Mojib , Rosati A. 
Published: September 2011

Abstract
Initial-value predictability measures the degree to which the initial state can influence predictions. In this paper, the initial-value predictability of six atmosphere–ocean general circulation models in the North Pacific and North Atlantic is quantified and contrasted by analyzing long control integrations with time invariant external conditions. Through the application of analog and multivariate linear regression methodologies, average predictability properties are estimated for forecasts initiated from every state on the control trajectories. For basinwide measures of predictability, the influence of the initial state tends to last for roughly a decade in both basins, but this limit varies widely among the models, especially in the North Atlantic. Within each basin, predictability varies regionally by as much as a factor of 10 for a given model, and the locations of highest predictability are different for each model. Model-to-model variations in predictability are also seen in the behavior of prominent intrinsic basin modes. Predictability is primarily determined by the mean of forecast distributions rather than the spread about the mean. Horizontal propagation plays a large role in the evolution of these signals and is therefore a key factor in differentiating the predictability of the various models.
Postprocessing of Ensemble Precipitation Predictions with Extended Logistic Regression Based on Hindcasts
Authors: Roulin Emmanuel , Vannitsem Stéphane 
Published: September 2011

Abstract
Extended logistic regression is used to calibrate areal precipitation forecasts over two small catchments in Belgium computed with the European Centre for Medium-Range Weather Forecasts (ECMWF) Ensemble Prediction System (EPS) between 2006 and 2010. The parameters of the postprocessing are estimated from the hindcast database, characterized by a much lower number of members (5) than the EPS (51). Therefore, the parameters have to be corrected for predictor uncertainties. They have been fitted on the 51-member EPS ensembles, on 5-member subensembles drawn from the same EPS, and on the 5-member hindcasts. For small ensembles, a simple “regression calibration” method by which the uncertain predictors are corrected has been applied. The different parameter sets have been compared, and the corresponding extended logistic regressions have been applied to the 51-member EPS. The forecast probabilities have then been validated using rain gauge data and compared with the raw EPS. In addition, the calibrated distributions are also used to modify the ensembles of precipitation traces.
The postprocessing with the extended logistic regression is shown to improve the continuous ranked probability skill score relative to the raw ensemble, and the regression calibration to remove a large portion of the bias in parameter estimation with small ensembles. With a training phase limited to a 5-week moving window, the benefit lasts for the first 2 forecast days in winter and the first 5 or 6 days in summer. In general, substantial improvements of the mean error and of the continuous ranked probability score have been shown.
A Comprehensive Assessment of CFS Seasonal Forecasts over the Tropics*
Authors: Sooraj K. P. , Annamalai H. , Kumar Arun , Wang Hui 
Published: September 2011

Abstract
The 15-member ensemble hindcasts performed with the National Centers for Environmental Prediction Climate Forecast System (CFS) for the period 1981–2005, as well as real-time forecasts for the period 2006–09, are assessed for seasonal prediction skills over the tropics, from deterministic (anomaly correlation), categorical (Heidke skill score), and probabilistic (rank probability skill score) perspectives. Further, persistence, signal-to-noise ratio, and root-mean-square error analyses are also performed. The CFS demonstrates high skill in forecasting El Niño–Southern Oscillation (ENSO) related sea surface temperature (SST) anomalies during developing and mature phases, including that of different types of El Niño. During ENSO, the space–time evolution of anomalous SST, 850-hPa wind, and rainfall along the equatorial Pacific, as well as the mechanisms involved in the teleconnection to the tropical Indian Ocean, are also well represented. During ENSO phase transition and in the summer, the skill of forecasting Pacific SST anomalies is modest. An examination of CFS ability in forecasting seasonal rainfall anomalies over the U.S. Affiliated Pacific Islands (USAPI) indicates that forecasting the persistence of dryness from El Niño winter into the following spring/summer is skillful at leads &gt; 3 months. During strong El Niño years the persistence is predicted by all members with a 6-month lead time. Also, the model is skillful in predicting regional rainfall responses during different types of El Niño. Since both deterministic and probabilistic skill scores converge, the suggestion is that the forecast is useful. The model’s skill in the real-time forecasts for the period 2006–09 is also discussed. The results suggest the feasibility that a dynamical-system-based seasonal prediction of precipitation over the USAPI can be considered.
‘Do as I say, but not as I do’: Are next generation nurses role models for health?
Authors: Blake Holly , Malik Sumaira , Mo Phoenix K. H. , Pisano Charlotte 
Published: September 2011

Aim: Promoting healthy lifestyles plays a key role in professional nursing yet nurses do not always practice what they preach. Efforts are currently being made to improve the health of NHS staff, yet little is known about the health and lifestyle behaviours of pre-registration nurses in the UK although these individuals are our next generation of NHS employees. The aim of this study was to investigate the health behaviours and wellbeing of pre-registration nurses based at an acute NHS teaching hospital in England. Methods: In this cross-sectional questionnaire survey, 325 pre-registration nurses (50% response rate) completed a health and lifestyle questionnaire, measuring levels of physical activity, smoking and alcohol behaviour, dietary practices and general health. Results: Age ranged from 19-53 years, and 96% of the sample was female. More than half of the sample did not meet public health recommendations for physical activity. Just under one-fifth were current smokers and over three-quarters did not consume five servings of fruit/vegetables per day. Two-thirds reported exceeding the recommended maximum daily alcohol intake and around one third were classified as either overweight or obese. Those who were physically inactive were less likely to report good general health, good dietary practices and more sleep, and were more likely to report cigarette smoking and alcohol consumption than their active counterparts. Conclusions: This study indicates that the health profile of pre-registration nurses is relatively poor, and that those who are sedentary engage in other negative lifestyle behaviours also. Despite significant education relating to health promotion and health behaviours of patients being targeted at pre-registered nurses, it seems that this knowledge is not always transferred to their own behaviour. There is a need for timely intervention to establish healthy lifestyle behaviours amongst nurses early in their career.
Social shaping of food intervention initiatives at worksites: Canteen takeaway schemes at two Danish hospitals
Authors: Poulsen Signe , Jørgensen Michael Søgaard 
Published: September 2011

Aims: The aim of this article is to analyse the social shaping of worksite food interventions at two Danish worksites. The overall aims are to contribute first, to the theoretical frameworks for the planning and analysis of food and health interventions at worksites and second, to a foodscape approach to worksite food interventions. Methods: The article is based on a case study of the design of a canteen takeaway (CTA) scheme for employees at two Danish hospitals. This was carried out as part of a project to investigate the shaping and impact of schemes that offer employees meals to buy, to take home or to eat at the worksite during irregular working hours. Data collection was carried out through semi-structured interviews with stakeholders within the two change processes. Two focus group interviews were also carried out at one hospital and results from a user survey carried out by other researchers at the other hospital were included. Theoretically, the study was based on the social constitution approach to change processes at worksites and a co-evolution approach to problem–solution complexes as part of change processes. Results: Both interventions were initiated because of the need to improve the food supply for the evening shift and the work–life balance. The shaping of the schemes at the two hospitals became rather different change processes due to the local organizational processes shaped by previously developed norms and values. At one hospital the change process challenged norms and values about food culture and challenged ideas in the canteen kitchen about working hours. At the other hospital, the change was more of a learning process that aimed at finding the best way to offer a CTA scheme. Conclusions: Worksite health promotion practitioners should be aware that the intervention itself is an object of negotiation between different stakeholders at a worksite based on existing norms and values. The social contextual model and the setting approach to worksite health interventions lack reflections about how such norms and values might influence the shaping of the intervention. It is recommended that future planning and analyses of worksite health promotion interventions apply a combination of the social constitution approach to worksites and an integrated food supply and demand perspective based on analyses of the co-evolution of problem–solution complexes.
Overexpression of Foxn1 attenuates age-associated thymic involution and prevents the expansion of peripheral CD4 memory T cells
Authors: Zook Erin C. , Krishack Paulette A. , Zhang Shubin , Zeleznik-Le Nancy J. , Firulli Anthony B. , Witte Pamela L. , Le Phong T. 
Published: September 2011

Abstract
The forkhead box n1 (Foxn1) transcription factor is essential for thymic organogenesis during embryonic development; however, a functional role of Foxn1 in the postnatal thymus is less well understood. We developed Foxn1 transgenic mice (Foxn1Tg), in which overexpression of Foxn1 is driven by the human keratin-14 promoter. Expression of the Foxn1 transgene increased the endogenous Foxn1 levels. In aged mice, overexpression of Foxn1 in the thymus attenuated the decline in thymocyte numbers, prevented the decline in frequency of early thymic progenitors, and generated a higher number of signal joint TCR excised circle. Histologic studies revealed that structural alterations associated with thymic involution were diminished in aged Foxn1 Tg. Total numbers of EpCAM+ MHC II+ and MHC IIhi thymic epithelial cells were higher in young and old Foxn1Tg and more EpCAM+ MHC IIhi TEC expressed Ki-67 in aged Foxn1Tg compared with WT. Furthermore, Foxn1Tg displayed a significant reduction in the expansion of splenic CD4+ memory compartments and attenuated the decline in CD4+ and CD8+ naive compartments. Our data indicate that manipulation of Foxn1 expression in the thymus ameliorates thymopoiesis in aged mice and offer a strategy to combat the age-associated decline in naive T-cell production and CD4 naive/memory ratios in the elderly.
Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum
Authors: Etebari Kayvan , Palfreyman Robin W , Schlipalius David , Nielsen Lars K , Glatz Richard V , Asgari Sassan 
Published: September 2011

Abstract

Background
Parasitoid insects manipulate their hosts' physiology by injecting various factors into their host upon parasitization. Transcriptomic approaches provide a powerful approach to study insect host-parasitoid interactions at the molecular level. In order to investigate the effects of parasitization by an ichneumonid wasp (Diadegma semiclausum) on the host (Plutella xylostella), the larval transcriptome profile was analyzed using a short-read deep sequencing method (Illumina). Symbiotic polydnaviruses (PDVs) associated with ichneumonid parasitoids, known as ichnoviruses, play significant roles in host immune suppression and developmental regulation. In the current study, D. semiclausum ichnovirus (Ds IV) genes expressed in P. xylostella were identified and their sequences compared with other reported PDVs. Five of these genes encode proteins of unknown identity, that have not previously been reported.

Results

De novo assembly of cDNA sequence data generated 172,660 contigs between 100 and 10000 bp in length; with 35% of > 200 bp in length. Parasitization had significant impacts on expression levels of 928 identified insect host transcripts. Gene ontology data illustrated that the majority of the differentially expressed genes are involved in binding, catalytic activity, and metabolic and cellular processes. In addition, the results show that transcription levels of antimicrobial peptides, such as gloverin, cecropin E and lysozyme, were up-regulated after parasitism. Expression of ichnovirus genes were detected in parasitized larvae with 19 unique sequences identified from five PDV gene families including vankyrin, viral innexin, repeat elements, a cysteine-rich motif, and polar residue rich protein. Vankyrin 1 and repeat element 1 genes showed the highest transcription levels among the Ds IV genes.

Conclusion
This study provides detailed information on differential expression of P. xylostella larval genes following parasitization, Ds IV genes expressed in the host and also improves our current understanding of this host-parasitoid interaction.
Cancer vaccines at an inflexion point: what next?
Authors: Bot Adrian , Obrocea Mihail , Marincola Francesco M 
Published: September 2011

Abstract
With the approval of the first therapeutic cancer vaccines for veterinarian and human use, the field reached a significant milestone after a considerable interval of tumultuous research and development marked by numerous ups and downs. As the mechanism of action and clinical benefit afforded by this class of agents are starkly different from that of conventional or small targeted therapies for cancer, there are still numerous hurdles that need to be overcome to fully unleash their potential. These challenges and efforts are illustrated in a book just published on this subject, a non-exhaustive yet representative synopsis of the latest advances in cancer vaccine technologies in various stages of development. Major lessons resulting from clinical testing of cancer vaccines and other immune interventions, are being integrated in novel, cutting edge platform technologies that blur the distinction between passive and active immunotherapies as well as carry the promise of fundamentally changing and improving the management of patients with cancer.
Ultra-long metal nanowire arrays on solid substrate with strong bonding
Authors: Xu Ju , Chen Lan , Mathewson Alan , Razeeb Kafil M 
Published: September 2011

Abstract
Ultra-long metal nanowire arrays with large circular area up to 25 mm in diameter were obtained by direct electrodeposition on metalized Si and glass substrates via a template-based method. Nanowires with uniform length up to 30 μm were obtained. Combining this deposition process with lithography technology, micrometre-sized patterned metal nanowire array pads were successfully fabricated on a glass substrate. Good adhesion between the patterned nanowire array pads and the substrate was confirmed using scanning acoustic microscopy characterization. A pull-off tensile test showed strong bonding between the nanowires and the substrate. Conducting atomic force microscopy (C-AFM) measurements showed that approximately 95% of the nanowires were electrically connected with the substrate, demonstrating its viability to use as high-density interconnect.
SNIT: SNP identification for strain typing
Authors: Satya Ravi Vijaya , Zavaljevski Nela , Reifman Jaques 
Published: September 2011

Abstract
With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strain-level identification of any newly sequenced genome. Here, we present the SNP identification for strain typing (SNIT) pipeline, a fast and accurate software system that compares a newly sequenced bacterial genome with other genomes of the same species to identify single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels). Based on this information, the pipeline analyzes the polymorphic loci present in all input genomes to identify the genome that has the fewest differences with the newly sequenced genome. Similarly, for each of the other genomes, SNIT identifies the input genome with the fewest differences. Results from five bacterial species show that the SNIT pipeline identifies the correct closest neighbor with 75% to 100% accuracy. The SNIT pipeline is available for download at http://www.bhsai.org/snit.html
MiR-206-mediated dynamic mechanism of the mammalian circadian clock
Authors: Zhou Wei , Li Yan , Wang Xia , Wu Lianqi , Wang Yonghua 
Published: September 2011

Abstract

Background
As a group of highly conserved small non-coding RNAs with a length of 21~23 nucleotides, microRNAs (miRNAs) regulate the gene expression post-transcriptionally by base pairing with the partial or full complementary sequences in target mRNAs, thus resulting in the repression of mRNA translation and the acceleration of mRNA degradation. Recent work has revealed that miRNAs are essential for the development and functioning of the skeletal muscles where they are. In particular, miR-206 has not only been identified as the only miRNA expressed in skeletal muscles, but also exhibited crucial roles in regulation of the muscle development. Although miRNAs are known to regulate various biological processes ranging from development to cancer, much less is known about their role in the dynamic regulation of the mammalian circadian clock.

Results
A detailed dynamic model of miR-206-mediated mammalian circadian clock system was developed presently by using Hill-type terms, Michaelis-Menten type and mass action kinetics. Based on a system-theoretic approach, the model accurately predicts both the periodicity and the entrainment of the circadian clock. It also explores the dynamics properties of the oscillations mediated by miR-206 by means of sensitivity analysis and alterations of parameters. Our results show that miR-206 is an important regulator of the circadian clock in skeletal muscle, and thus by study of miR-206 the main features of its mediation on the clock may be captured. Simulations of these processes display that the amplitude and frequency of the oscillation can be significantly altered through the miR-206-mediated control.

Conclusions
MiR-206 has a profound effect on the dynamic mechanism of the mammalian circadian clock, both by control of the amplitude and control or alteration of the frequency to affect the level of the gene expression and to interfere with the temporal sequence of the gene production or delivery. This undoubtedly uncovers a new mechanism for regulation of the circadian clock at a post-transcriptional level and provides important insights into the normal development as well as the pathological conditions of skeletal muscles, such as the aging, chronic disease and cancer.
Comparison of image quality and radiation dose between combined automatic tube current modulation and fixed tube current technique in CT of abdomen and pelvis
Authors: Lee Sanghee , Yoon Sang-Wook , Yoo Seung-Min , Ji Young Geon , Kim Kyoung Ah , Kim Sang Heum , Lee Jong Tae 
Published: September 2011

Background Tube current is an important determinant of radiation dose and image quality in X-ray-based examination. The combined automatic tube current modulation technique (ATCM) enables automatic adjustment of the tube current in various planes ( x-y and z) based on the size and attenuation of the body area scanned. Purpose To compare image quality and radiation dose of the ATCM with those of a fixed tube current technique (FTC) in CT of the abdomen and pelvis performed with a 16-slice multidetector row CT. Material and Methods We reviewed 100 patients in whom initial and follow-up CT of the abdomen and pelvis were performed with FTC and ATCM. All acquisition parameters were identical in both techniques except for tube current. We recorded objective image noise in liver parenchyma, subjective image noise and diagnostic acceptability by using a five-point scale, radiation dose, and body mass index (BMI, kg/m2). Data were analyzed with parametric and non-parametric statistical tests. Results There was no significant difference in image noise and diagnostic acceptability between two techniques. All subjects had acceptable subjective image noise in both techniques. The significant reduction in radiation dose (45.25% reduction) was noted with combined ATCM ( P < 0.001). There was a significant linear statistical correlation between BMI and dose reduction (r = –0.78, P < 0.05). Conclusion The ATCM for CT of the abdomen and pelvis substantially reduced radiation dose while maintaining diagnostic image quality. Patients with lower BMI showed more reduction in radiation dose.
The intra- and inter-rater reliability of manual muscle testing and a hand-held dynamometer for measuring wrist strength in symptomatic and asymptomatic subjects
Authors: Toemen Angela , Dalton Sarah , Sandford Fiona 
Published: September 2011

Objective The objective of this study was to assess the intra- and inter-rater reliability of manual muscle testing (MMT) and hand-held dynamometer (HHD) in the measurement of isometric wrist strength in asymptomatic and symptomatic (distal radius fractures [DRF] and non-specific wrist pain [NSWP]) populations. Method Thirty-nine adults participated in an intra session, repeat measure, crossover study design. MMT and HHD isometric wrist strength was tested in six standardized test positions by two raters. Results Poor-to-excellent intra- and inter-rater reliability with MMT was found in all patient populations (ICC = 0.04–1.00). Excellent intra-rater reliability with HHD in the DRF (ICC = 0.86–0.95) and NSWP (ICC = 0.92–0.97) populations and excellent inter-rater reliability in the asymptomatic (ICC = 0.77–0.93) and DRF (ICC = 0.82–0.95) populations. Fair to excellent intra-rater reliability with HHD was seen in the asymptomatic population (ICC = 0.71–0.94) and fair to excellent inter-rater reliability in the NSWP population (ICC = 0.59–0.90). Conclusion MMT is shown to have variable reliability when assessing isometric wrist strength and is insensitive to small strength changes. HHD has been shown to be an objective and reliable measure of isometric wrist strength in specific positions in asymptomatic, DRF and NSWP populations. Further studies are required to ensure adequate dynamometry stabilization and obtain an optimal testing procedure for these populations.