bluuebunny/crossref_metadata_2025_split huggingface dataset:
Propagation of Meridional Circulation Anomalies along Western and Eastern Boundaries
Authors: Marshall David P. , Johnson Helen L. 
Published: September 2013

Abstract
Motivated by the adjustment of the meridional overturning circulation to localized forcing, solutions are presented from a reduced-gravity model for the propagation of waves along western and eastern boundaries. For wave periods exceeding a few months, Kelvin waves play no role. Instead, propagation occurs through short and long Rossby waves at the western and eastern boundaries, respectively: these Rossby waves propagate zonally, as predicted by classical theory, and cyclonically along the basin boundaries to satisfy the no-normal flow boundary condition. The along-boundary propagation speed is cLd/δ, where c is the internal gravity/Kelvin wave speed, Ld is the Rossby deformation radius, and δ is the appropriate frictional boundary layer width. This result holds across a wide range of parameter regimes, with either linear friction or lateral viscosity and a no-slip boundary condition. For parameters typical of contemporary ocean climate models, the propagation speed is coincidentally close to the Kelvin wave speed. In the limit of weak dissipation, the western boundary wave dissipates virtually all of its energy as it propagates toward the equator, independent of the dissipation coefficient. In contrast, virtually no energy is dissipated in the eastern boundary wave. The importance of background mean flows is also discussed.
Parallel Implementation of an Ensemble Kalman Filter
Authors: Houtekamer P. L. , He Bin , Mitchell Herschel L. 
Published: September 2013

Abstract
Since mid-February 2013, the ensemble Kalman filter (EnKF) in operation at the Canadian Meteorological Centre (CMC) has been using a 600 × 300 global horizontal grid and 74 vertical levels. This yields 5.4 × 107 model coordinates. The EnKF has 192 members and uses seven time levels, spaced 1 h apart, for the time interpolation in the 6-h assimilation window. It follows that over 7 × 1010 values are required to specify an ensemble of trial field trajectories. This paper focuses on numerical and computational aspects of the EnKF. In response to the increasing computational challenge posed by the ever more ambitious configurations, an ever larger fraction of the EnKF software system has gradually been parallelized over the past decade. In a strong scaling experiment, the way in which the execution time decreases as larger numbers of processes are used is investigated. In fact, using a substantial fraction of one of the CMC's computers, very short execution times are achieved. As it would thus appear that the CMC's computers can handle more demanding configurations, weak scaling experiments are also performed. Here, both the size of the problem and the number of processes are simultaneously increased. The parallel algorithm responds well to an increase in either the number of ensemble members or the number of model coordinates. A substantial increase (by an order of magnitude) in the number of assimilated observations would, however, be more problematic. Thus, to the extent that this depends on computational aspects, it appears that the meteorological quality of the Canadian operational EnKF can be further improved.
An Evaluation of WRF Simulations of Clouds over the Southern Ocean with A-Train Observations
Authors: Huang Yi , Siems Steven T. , Manton Michael J. , Thompson Gregory 
Published: September 2013

Abstract
The representation of the marine boundary layer (BL) clouds remains a formidable challenge for state-of-the-art simulations. A recent study by Bodas-Salcedo et al. using the Met Office Unified Model highlights that the underprediction of the low/midlevel postfrontal clouds contributes to the largest bias of the surface downwelling shortwave radiation over the Southern Ocean (SO). A-Train observations and limited in situ measurements have been used to evaluate the Weather Research and Forecasting Model, version 3.3.1 (WRFV3.3.1), in simulating the postfrontal clouds over Tasmania and the SO. The simulated cloud macro/microphysical properties are compared against the observations. Experiments are also undertaken to test the sensitivity of model resolution, microphysical (MP) schemes, planetary boundary layer (PBL) schemes, and cloud condensation nuclei (CCN) concentration. The simulations demonstrate a considerable level of skill in representing the clouds during the frontal passages and, to a lesser extent, in the postfrontal environment. The simulations, however, have great difficulties in portraying the widespread marine BL clouds that are not immediately associated with fronts. This shortcoming is persistent to the changes of model configuration and physical parameterization. The representation of large-scale conditions and their connections with the BL clouds are discussed. A lack of BL moisture is the most obvious explanation for the shortcoming, which may be a consequence of either strong entrainment or weak surface fluxes. It is speculated that the BL wind shear/turbulence may be an issue over the SO. More comprehensive observations are necessary to fully investigate the deficiency of the simulations.
Ultrasound assessment of the elbow joint in infants and toddlers and its clinical significance
Authors: Shen Xian-tao , Zhou Zhi-guo , Yu Li-song , Wu Xing , Chen Xiao-liang , Xu Yang , Sun Jie 
Published: September 2013

Background Ultrasound can be used for the diagnosis of elbow injuries in infants and toddlers. However, ultrasound is highly operator-dependent and accurate ultrasound examinations require a complete understanding of the complex anatomy of the elbow joint. Purpose To report the normal ultrasound anatomy of the elbow, particularly of the humeroulnar joint, in infants and toddlers. Material and Method Thirty subjects aged <3 years with no history of elbow injuries underwent ultrasound examinations of the elbow joint from six directions: (i) lateral to the humeroradial joint; (ii) anterior to the humeroradial joint; (iii) posterior to the humeroradial joint; (iv) medial to the humeroulnar joint; (v) anterior to the humeroulnar joint; and (vi) posterior to the humeroulnar joint. Results The appearance of the humeroradial joint observed from three directions was similar and resembled a pair of double fists (“double-breast sign”). The appearance of the humeroulnar joint observed from three directions was different, which is related to the irregular morphology of the medial sides of the humerus and ulna. Anteroposteriorly, the coronoid and olecranon epiphyses and coronoid fossa appear anteriorly and the olecranon and trochlear epiphyses and olecranon fossa appear posteriorly, resembling a “check-mark sign”. The medial epicondyle, cubital tunnel and distal humerus appear together (“double-hump sign”). The “anterior hump” is the medial epicondyle and is always higher than the “posterior hump”, which is the bony protrusion on the articular surface of the distal humerus. The ultrasound signal of cortical bone in the metaphysis of the distal humerus is continuous with that of the epiphysis of the medial epicondyle. Conclusion Ultrasound is useful for the diagnosis of elbow injuries in infants and toddlers.
Prenatal developmental toxicity study of n-heneicosane in Wistar rats
Authors: Kumar Pravin , Lomash Vinay , Jatav PC , Kumar A , Pant SC 
Published: September 2013

n-Heneicosane (C21) is one of the vital pheromone for attracting mosquitoes of Aedes spp to lay their eggs in areas of stagnant fresh water, for their subsequent destruction, thus controlling spread of dangerous disease transmission by the vectors. As part of a safety evaluation, we have investigated embryo toxic and teratogenic potential, if any, of C21 following OECD Test Guideline 414. C21 was offered at a dose of 1 g/kg body weight mixed in the standard rat pellet diet to treated rats, whereas the control group received only standard rat pellet diet. There were no mortalities and animals did not show any clinical signs of toxicity. A similar pattern of body weight gain, feed and water intake was observed in treated and control groups. Analysis of maternal toxic response, maternal end points of development of the foetus and developmental end points for litters did not show any gross structural abnormality in dams or foetus of treated group compared to that of the control group. Thus, it was concluded that C21 at a dose of 1 g/kg was neither embryo toxic nor teratogenic in Wister rats. Furthermore, the no observed adverse effect level for teratogenicity for C21 in rats may be considered as 1 g/kg body weight under the present experimental conditions.
Reductions in neuronal peroxisomes in multiple sclerosis grey matter
Authors: Gray Elizabeth , Rice Claire , Hares Kelly , Redondo Juliana , Kemp Kevin , Williams Marcus , Brown Ann , Scolding Neil , Wilkins Alastair 
Published: September 2013

Background: Peroxisomes are organelles in eukaryotic cells with multiple functions including the detoxification of reactive oxygen species, plasmalogen synthesis and β-oxidation of fatty acids. Recent evidence has implicated peroxisomal dysfunction in models of multiple sclerosis (MS) disease progression. Objectives: Our aims were to determine whether there are changes in peroxisomes in MS grey matter (GM) compared to control GM. Methods: We analysed cases of MS and control GM immunocytochemically to assess peroxisomal membrane protein (PMP70) and neuronal proteins. We examined the expression of ABCD3 (the gene that encodes PMP70) in MS and control GM. Analyses of very long chain fatty acid (VLCFA) levels in GM were performed. Results: PMP70 immunolabelling of neuronal somata was significantly lower in MS GM compared to control. Calibration of ABCD3 gene expression with reference to glyceraldehyde 3-phsophate dehydrogenase (GAPDH) revealed overall decreases in expression in MS compared to controls. Mean PMP70 counts in involved MS GM negatively correlated to disease duration. Elevations in C26:0 (hexacosanoic acid) were found in MS GM. Conclusions: Collectively, these observations provide evidence that there is an overall reduction in peroxisomal gene expression and peroxisomal proteins in GM neurons in MS. Changes in peroxisomal function may contribute to neuronal dysfunction and degeneration in MS.
Headache and comorbidity in children and adolescents
Authors: Bellini Benedetta , Arruda Marco , Cescut Alessandra , Saulle Cosetta , Persico Antonello , Carotenuto Marco , Gatta Michela , Nacinovich Renata , Piazza Fausta Paola , Termine Cristiano , Tozzi Elisabetta , Lucchese Franco , Guidetti Vincenzo 
Published: September 2013

AbstractHeadache is one of the most common neurological symptom reported in childhood and adolescence, leading to high levels of school absences and being associated with several comorbid conditions, particularly in neurological, psychiatric and cardiovascular systems. Neurological and psychiatric disorders, that are associated with migraine, are mainly depression, anxiety disorders, epilepsy and sleep disorders, ADHD and Tourette syndrome. It also has been shown an association with atopic disease and cardiovascular disease, especially ischemic stroke and patent foramen ovale (PFO).
Maximum parsimony xor haplotyping by sparse dictionary selection
Authors: Elmas Abdulkadir , Jajamovich Guido H , Wang Xiaodong 
Published: September 2013

Abstract

Background
Xor-genotype is a cost-effective alternative to the genotype sequence of an individual. Recent methods developed for haplotype inference have aimed at finding the solution based on xor-genotype data. Given the xor-genotypes of a group of unrelated individuals, it is possible to infer the haplotype pairs for each individual with the aid of a small number of regular genotypes.

Results
We propose a framework of maximum parsimony inference of haplotypes based on the search of a sparse dictionary, and we present a greedy method that can effectively infer the haplotype pairs given a set of xor-genotypes augmented by a small number of regular genotypes. We test the performance of the proposed approach on synthetic data sets with different number of individuals and SNPs, and compare the performances with the state-of-the-art xor-haplotyping methods PPXH and XOR-HAPLOGEN.

Conclusions
Experimental results show good inference qualities for the proposed method under all circumstances, especially on large data sets. Results on a real database, CFTR, also demonstrate significantly better performance. The proposed algorithm is also capable of finding accurate solutions with missing data and/or typing errors.
Computational prediction of associations between long non-coding RNAs and proteins
Authors: Lu Qiongshi , Ren Sijin , Lu Ming , Zhang Yong , Zhu Dahai , Zhang Xuegong , Li Tingting 
Published: September 2013

AbstractBackgroundThough most of the transcripts are long non-coding RNAs (lncRNAs), little is known about their functions. lncRNAs usually function through interactions with proteins, which implies the importance of identifying the binding proteins of lncRNAs in understanding the molecular mechanisms underlying the functions of lncRNAs. Only a few approaches are available for predicting interactions between lncRNAs and proteins. In this study, we introduce a new method lncPro.ResultsBy encoding RNA and protein sequences into numeric vectors, we used matrix multiplication to score each RNA–protein pair. This score can be used to measure the interactions between an RNA–protein pair. This method effectively discriminates interacting and non-interacting RNA–protein pairs and predicts RNA–protein interactions within a given complex. Applying this method on all human proteins, we found that the long non-coding RNAs we collected tend to interact with nuclear proteins and RNA-binding proteins.ConclusionsCompared with the existing approaches, our method shortens the time for training matrix and obtains optimal results based on the model being used. The ability of predicting the associations between lncRNAs and proteins has also been enhanced. Our method provides an idea on how to integrate different information into the prediction process.
Different patterns of gene structure divergence following gene duplication in Arabidopsis
Authors: Wang Yupeng , Tan Xu , Paterson Andrew H 
Published: September 2013

Abstract

Background
Divergence in gene structure following gene duplication is not well understood. Gene duplication can occur via whole-genome duplication (WGD) and single-gene duplications including tandem, proximal and transposed duplications. Different modes of gene duplication may be associated with different types, levels, and patterns of structural divergence.

Results
In Arabidopsis thaliana, we denote levels of structural divergence between duplicated genes by differences in coding-region lengths and average exon lengths, and the number of insertions/deletions (indels) and maximum indel length in their protein sequence alignment. Among recent duplicates of different modes, transposed duplicates diverge most dramatically in gene structure. In transposed duplications, parental loci tend to have longer coding-regions and exons, and smaller numbers of indels and maximum indel lengths than transposed loci, reflecting biased structural changes in transposed duplications. Structural divergence increases with evolutionary time for WGDs, but not transposed duplications, possibly because of biased gene losses following transposed duplications. Structural divergence has heterogeneous relationships with nucleotide substitution rates, but is consistently positively correlated with gene expression divergence. The NBS-LRR gene family shows higher-than-average levels of structural divergence.

Conclusions
Our study suggests that structural divergence between duplicated genes is greatly affected by the mechanisms of gene duplication and may be not proportional to evolutionary time, and that certain gene families are under selection on rapid evolution of gene structure.
CAWS administration increases the expression of interferon γ and complement factors that lead to severe vasculitis in DBA/2 mice
Authors: Nagi-Miura Noriko , Okuzaki Daisuke , Torigata Kosuke , Sakurai Minami A , Ito Akihiko , Ohno Naohito , Nojima Hiroshi 
Published: September 2013

AbstractBackgroundCandida albicanswater-soluble fraction (CAWS), a mannoprotein-β-glucan complex obtained from the culture supernatant ofC. albicansNBRC1385, causes CAWS-mediated vasculitis (CAWS-vasculitis) in B6 and DBA/2 mice with mild and lethal symptoms, respectively. Why CAWS is lethal only in DBA/2 mice remains unknown.ResultsWe performed DNA microarray analyses using mRNA obtained from peripheral blood mononuclear cells (PBMCs) of B6 and DBA/2 mice and compared their respective transcriptomes. We found that the mRNA levels of interferon-γ (Ifng) and several genes that regulate the complement system, such as C3, C4, Cfb, Cfh, and Fcna, were increased dramatically only in DBA/2 mice at 4 and 8 weeks after CAWS administration. The dramatic increase was confirmed by quantitative real-time polymerase chain reactions (qRT-PCR). Moreover, mRNA levels of immune-related genes, such as Irf1, Irf7, Irf9, Cebpb, Ccl4, Itgam, Icam1, and IL-12rb1, whose expression levels are known to be increased by Ifng, were also increased, but only in DBA/2 mice. By contrast, the mRNA level of Dectin-2, the critical receptor for the α-mannans of CAWS, was increased slightly and similarly in both B6 and DBA/2 mice after CAWS administration.ConclusionsTaken together, our results suggest that CAWS administration induces Dectin-2 mediated CAWS-vasculitis in both B6 and DBA/2 mice and the expression of Ifng, but only in DBA/2 mice, which led to increased expression of C3, C4, Cfb, Cfh, and Fcna and an associated increase in lethality in these mice. This model may contribute to our understanding of the pathogenesis of severe human vasculitis.
Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls
Authors: Mistry Meeta , Gillis Jesse , Pavlidis Paul 
Published: September 2013

Abstract

Background
Gene expression profiling of the postmortem human brain is part of the effort to understand the neuropathological underpinnings of schizophrenia. Existing microarray studies have identified a large number of genes as candidates, but efforts to generate an integrated view of molecular and cellular changes underlying the illness are few. Here, we have applied a novel approach to combining coexpression data across seven postmortem human brain studies of schizophrenia.

Results
We generated separate coexpression networks for the control and schizophrenia prefrontal cortex and found that differences in global network properties were small. We analyzed gene coexpression relationships of previously identified differentially expressed ‘schizophrenia genes’. Evaluation of network properties revealed differences for the up- and down-regulated ‘schizophrenia genes’, with clustering coefficient displaying particularly interesting trends. We identified modules of coexpressed genes in each network and characterized them according to disease association and cell type specificity. Functional enrichment analysis of modules in each network revealed that genes with altered expression in schizophrenia associate with modules representing biological processes such as oxidative phosphorylation, myelination, synaptic transmission and immune function. Although a immune-function enriched module was found in both networks, many of the genes in the modules were different. Specifically, a decrease in clustering of immune activation genes in the schizophrenia network was coupled with the loss of various astrocyte marker genes and the schizophrenia candidate genes.

Conclusion
Our novel network-based approach for evaluating gene coexpression provides results that converge with existing evidence from genetic and genomic studies to support an immunological link to the pathophysiology of schizophrenia.
Prediction of 7-year psychopathology from mother-infant joint attention behaviours: a nested case–control study
Authors: Allely Clare S , Johnson Paul CD , Marwick Helen , Lidstone Emma , Kočovská Eva , Puckering Christine , McConnachie Alex , Golding Jean , Gillberg Christopher , Wilson Philip 
Published: September 2013

AbstractBackgroundTo investigate whether later diagnosis of psychiatric disorder can be predicted from analysis of mother-infant joint attention (JA) behaviours in social-communicative interaction at 12 months.MethodUsing data from a large contemporary birth cohort, we examined 159 videos of a mother-infant interaction for joint attention behaviour when children were aged one year, sampled from within the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Fifty-three of the videos involved infants who were later considered to have a psychiatric disorder at seven years and 106 were same aged controls. Psychopathologies included in the case group were disruptive behaviour disorders, oppositional-conduct disorder, attention-deficit/hyperactivity disorder, pervasive development disorder, anxiety and depressive disorders. Psychiatric diagnoses were obtained using the Development and Wellbeing Assessment when the children were seven years old.ResultsNone of the three JA behaviours (shared look rate, shared attention rate and shared attention intensity) showed a significant association with the primary outcome of case–control status. Only shared look rate predicted any of the exploratory sub-diagnosis outcomes and was found to be positively associated with later oppositional-conduct disorders (OR [95% CI]: 1.5 [1.0, 2.3]; p = 0.041).ConclusionsJA behaviours did not, in general, predict later psychopathology. However, shared look was positively associated with later oppositional-conduct disorders. This suggests that some features of JA may be early markers of later psychopathology. Further investigation will be required to determine whether any JA behaviours can be used to screen for families in need of intervention.
Adherence to osteoporosis regimens among men and analysis of risk factors of poor compliance: a 2-year analytical review
Authors: Chiu Chun-Kai , Kuo Ming-Chun , Yu Shan-Fu , Su Ben Yu-Jih , Cheng Tien-Tsai 
Published: September 2013

Abstract

Background
To investigate adherence and patient-specific factors associated with poor compliance with osteoporosis regimens among men.

Methods
In this retrospective chart review study, we collected data on male patients with osteoporosis treated in accordance with therapeutic recommendations. Adherence was determined by the compliance and persistence of those patients who had been dispensed an osteoporosis regimen after an index prescription. All osteoporosis regimens were considered equivalent for the purpose of investigating adherence.

Results
The prescriptions of 333 males met the inclusion criteria for data collection. The mean age was 68.6 ± 10.4 years. The median medication possession ratio (MPR, %) at years 1 and 2 was 90.1% (interquartile range (IQR) 19–100) and 53.7% (IQR 10.4-100), respectively; 52.3% of male patients at year 1 and 37.5% at year 2 had good compliance (defined as a MPR≧80%). The 1- and 2-year persistence rates were 45.9% and 30.0%, respectively. Patient-specific factors associated with poor compliance (MPR < 80%) during year 1 were first prescriptions given by orthopedists (odds ratio (OR) = 2.67; 95% confidence interval (CI) = 1.58-4.53; adjusted OR = 2.30, 95% CI = 1.26-4.22, p = 0.007). Male patients with rheumatoid arthritis (RA) (OR = 0.22, 95% CI = 0.06-0.78, adjusted OR = 0.19, 95% CI = 0.04-0.81, p = 0.025) and baseline bone mineral density (BMD) measurements (OR = 0.52, 95% CI = 0.32-0.85; adjusted OR = 0.51; 95% CI = 0.28-0.93, p = 0.029) were less likely to have poor compliance.

Conclusions
Adherence to osteoporosis regimens in males was suboptimal in our study. Poor compliance was more likely in prescription of the first anti-osteoporotic regimen by an orthopedist. Men with RA and BMD measurements before therapy had a lower risk of non-adherence. Healthcare professionals need to target patients with specific factors to improve adherence to osteoporotic regimens.