bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability and Predictability of a Three-Dimensional Hurricane in Statistical Equilibrium
Authors: Brown Bonnie R. , Hakim Gregory J. 
Published: December 2012

Abstract
The internal variability and predictability of idealized three-dimensional hurricanes is investigated using 100-day-long, statistically steady simulations in a compressible, nonhydrostatic, cloud-resolving model. The equilibrium solution is free of the confounding effects of initial conditions and environmental variability in order to isolate the “intrinsic” characteristics of the hurricane.
The variance of the axisymmetric tangential velocity is dominated by two patterns: one characterized by a radial shift of the maximum wind, and the other by intensity modulation at the radius of maximum wind. These patterns are associated with convectively coupled bands of anomalous wind speed that propagate inward from large radii with a period of roughly 5 days, the strongest of which is associated with an eyewall replacement cycle. The asymmetric tangential wind is strongest radially inward of the radius of maximum wind. On average, asymmetries decelerate the azimuthal-mean tangential wind at the radius of maximum wind and accelerate it along the inner edge of eyewall.
Predictability of axisymmetric storm structure is measured through the autocorrelation e-folding time and linear inverse modeling. Results from both methods reveal an intrinsic predictability time scale of about 2 days. The predictability and variability of the axisymmetric storm structure are consistent with recently obtained results from idealized axisymmetric hurricane modeling.
Evaluation of the CLM4 Lake Model at a Large and Shallow Freshwater Lake*
Authors: Deng Bin , Liu Shoudong , Xiao Wei , Wang Wei , Jin Jiming , Lee Xuhui 
Published: December 2012

AbstractModels of lake physical processes provide the lower flux boundary conditions for numerical predictions of weather and climate in lake basins. So far, there have been few studies on evaluating lake model performance at the diurnal time scale and against flux observations. The goal of this paper is to evaluate the National Center for Atmospheric Research Community Land Model version 4–Lake, Ice, Snow and Sediment Simulator using the eddy covariance and water temperature data obtained at a subtropical freshwater lake, Lake Taihu, in China. Both observations and model simulations reveal that convective overturning was commonplace at night and timed when water switched from being statically stable to being unstable. By reducing the water thermal diffusivity to 2% of the value calculated with the Henderson–Sellers parameterization, the model was able to reproduce the observed diurnal variations in water surface temperature and in sensible and latent heat fluxes. The small diffusivity suggests that the drag force of the sediment layer in this large (2500 km2) and shallow (2-m depth) lake may be strong, preventing unresolved vertical motions and suppressing wind-induced turbulence. Model results show that a large fraction of the incoming solar radiation energy was stored in the water during the daytime, and the stored energy was diffused upward at night to sustain sensible and latent heat fluxes to the atmosphere. Such a lake–atmosphere energy exchange modulated the local climate at the daily scale in this shallow lake, which is not seen in deep lakes where dominant lake–atmosphere interactions often occur at the seasonal scale.
Some new fractional q-integral Grüss-type inequalities and other inequalities
Authors: Zhu Chaowu , Yang Wengui , Zhao Qingbo 
Published: December 2012

Abstract
In this paper, we employ a fractional q-integral on the specific time scale,

T

t
0

=
{
t
:
t
=

t
0

q
n

,
n
a nonnegative integer
}
∪
{
0
}

, where

t
0

∈
R

and

0
<
q
<
1

, to establish some new fractional q-integral Grüss-type inequalities by using one or two fractional parameters. Furthermore, other fractional q-integral inequalities are also obtained.

MSC:26D10, 26A33.
Insights into the regulation of human CNV-miRNAs from the view of their target genes
Authors: Wu Xudong , Zhang Dinglin , Li Guohui 
Published: December 2012

Abstract

Background
microRNAs (miRNAs) represent a class of small (typically 22 nucleotides in length) non-coding RNAs that can degrade their target mRNAs or block their translation. Recent research showed that copy number alterations of miRNAs and their target genes are highly prevalent in cancers; however, the evolutionary and biological functions of naturally existing copy number variable miRNAs (CNV-miRNAs) among individuals have not been studied extensively throughout the genome.

Results
In this study, we comprehensively analyzed the properties of genes regulated by CNV-miRNAs, and found that CNV-miRNAs tend to target a higher average number of genes and prefer to synergistically regulate the same genes; further, the targets of CNV-miRNAs tend to have higher variability of expression within and between populations. Finally, we found the targets of CNV-miRNAs are more likely to be differentially expressed among tissues and developmental stages, and participate in a wide range of cellular responses.

Conclusions
Our analyses of CNV-miRNAs provide new insights into the impact of copy number variations on miRNA-mediated post-transcriptional networks. The deeper interpretation of patterns of gene expression variation and the functional characterization of CNV-miRNAs will help to broaden the current understanding of the molecular basis of human phenotypic diversity.
GLAD4U: deriving and prioritizing gene lists from PubMed literature
Authors: Jourquin Jérôme , Duncan Dexter , Shi Zhiao , Zhang Bing 
Published: December 2012

Abstract

Background
Answering questions such as "Which genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and creating gene lists. This process is not only time-consuming, but also prone to errors.

Results
We report GLAD4U (Gene List Automatically Derived For You), a new, free web-based gene retrieval and prioritization tool. GLAD4U takes advantage of existing resources of the NCBI to ensure computational efficiency. The quality of gene lists created by GLAD4U for three Gene Ontology (GO) terms and three disease terms was assessed using corresponding "gold standard" lists curated in public databases. For all queries, GLAD4U gene lists showed very high recall but low precision, leading to low F-measure. As a comparison, EBIMed's recall was consistently lower than GLAD4U, but its precision was higher. To present the most relevant genes at the top of a list, we studied two prioritization methods based on publication count and the hypergeometric test, and compared the ranked lists and those generated by EBIMed to the gold standards. Both GLAD4U methods outperformed EBIMed for all queries based on a variety of quality metrics. Moreover, the hypergeometric method allowed for a better performance by thresholding genes with low scores. In addition, manual examination suggests that many false-positives could be explained by the incompleteness of the gold standards. The GLAD4U user interface accepts any valid queries for PubMed, and its output page displays the ranked gene list and information associated with each gene, chronologically-ordered supporting publications, along with a summary of the run and links for file export and functional enrichment and protein interaction network analysis.

Conclusions
GLAD4U has a high overall recall. Although precision is generally low, the prioritization methods successfully rank truly relevant genes at the top of the lists to facilitate efficient browsing. GLAD4U is simple to use, and its interface can be found at: http://bioinfo.vanderbilt.edu/glad4u.
Microarray analysis of gene expression profiles in ripening pineapple fruits
Authors: Koia Jonni H , Moyle Richard L , Botella Jose R 
Published: December 2012

AbstractBackgroundPineapple (Ananas comosus) is a tropical fruit crop of significant commercial importance. Although the physiological changes that occur during pineapple fruit development have been well characterized, little is known about the molecular events that occur during the fruit ripening process. Understanding the molecular basis of pineapple fruit ripening will aid the development of new varieties via molecular breeding or genetic modification. In this study we developed a 9277 element pineapple microarray and used it to profile gene expression changes that occur during pineapple fruit ripening.ResultsMicroarray analyses identified 271 unique cDNAs differentially expressed at least 1.5-fold between the mature green and mature yellow stages of pineapple fruit ripening. Among these 271 sequences, 184 share significant homology with genes encoding proteins of known function, 53 share homology with genes encoding proteins of unknown function and 34 share no significant homology with any database accession. Of the 237 pineapple sequences with homologs, 160 were up-regulated and 77 were down-regulated during pineapple fruit ripening. DAVID Functional Annotation Cluster (FAC) analysis of all 237 sequences with homologs revealed confident enrichment scores for redox activity, organic acid metabolism, metalloenzyme activity, glycolysis, vitamin C biosynthesis, antioxidant activity and cysteine peptidase activity, indicating the functional significance and importance of these processes and pathways during pineapple fruit development. Quantitative real-time PCR analysis validated the microarray expression results for nine out of ten genes tested.ConclusionsThis is the first report of a microarray based gene expression study undertaken in pineapple. Our bioinformatic analyses of the transcript profiles have identified a number of genes, processes and pathways with putative involvement in the pineapple fruit ripening process. This study extends our knowledge of the molecular basis of pineapple fruit ripening and non-climacteric fruit ripening in general.
Can treatment with Cocculine improve the control of chemotherapy-induced emesis in early breast cancer patients? A randomized, multi-centered, double-blind, placebo-controlled Phase III trial
Authors: Pérol David , Provençal Jocelyne , Hardy-Bessard Anne-claire , Coeffic David , Jacquin Jean-Phillipe , Agostini Cécile , Bachelot Thomas , Guastalla Jean-Paul , Pivot Xavier , Martin Jean-Pierre , Bajard Agathe , Ray-Coquard Isabelle 
Published: December 2012

Abstract

Background
Chemotherapy induced nausea and vomiting (CINV) remains a major problem that seriously impairs the quality of life (QoL) in cancer patients receiving chemotherapy regimens. Complementary medicines, including homeopathy, are used by many patients with cancer, usually alongside with conventional treatment. A randomized, placebo-controlled Phase III study was conducted to evaluate the efficacy of a complex homeopathic medicine, Cocculine, in the control of CINV in non-metastatic breast cancer patients treated by standard chemotherapy regimens.

Methods
Chemotherapy-naïve patients with non-metastatic breast cancer scheduled to receive 6 cycles of chemotherapy including at least three initial cycles of FAC 50, FEC 100 or TAC were randomized to receive standard anti-emetic treatment plus either a complex homeopathic remedy (Cocculine, registered in France for treatment of nausea and travel sickness) or the matching placebo (NCT00409071 clinicaltrials.gov). The primary endpoint was nausea score measured after the 1st chemotherapy course using the FLIE questionnaire (Functional Living Index for Emesis) with 5-day recall. Secondary endpoints were: vomiting measured by the FLIE score, nausea and vomiting measured by patient self-evaluation (EVA) and investigator recording (NCI-CTC AE V3.0) and treatment compliance.

Results
From September 2005 to January 2008, 431 patients were randomized: 214 to Cocculine (C) and 217 to placebo (P). Patient characteristics were well-balanced between the 2 arms. Overall, compliance to study treatments was excellent and similar between the 2 arms. A total of 205 patients (50.9%; 103 patients in the placebo and 102 in the homeopathy arms) had nausea FLIE scores > 6 indicative of no impact of nausea on quality of life during the 1st chemotherapy course. There was no difference between the 2 arms when primary endpoint analysis was performed by chemotherapy stratum; or in the subgroup of patients with susceptibility to nausea and vomiting before inclusion. In addition, nausea, vomiting and global emesis FLIE scores were not statistically different at any time between the two study arms. The frequencies of severe (Grade ≥ 2) nausea and vomiting were low in our study (nausea: P: 17.6% vs C: 15.7%, p=0.62; vomiting: P: 10.8% vs C: 12.0%, p=0.72 during the first course).

Conclusion
This double-blinded, placebo-controlled, randomised Phase III study showed that adding a complex homeopathic medicine (Cocculine) to standard anti-emetic prophylaxis does not improve the control of CINV in early breast cancer patients.
An epidemiologic study of factors associated with nasal septum deviation by computed tomography scan: a cross sectional study
Authors: Mohebbi Alireza , Ahmadi Aslan , Etemadi Maryam , Safdarian Manouchehr , Ghourchian Shadi 
Published: December 2012

Abstract

Background
Sinusitis is an inflammation of the paranasal sinuses that can be caused by anatomic variations of the nasal cavity and paranasal sinuses. In this study we aimed to find the relationship between sinusitis and septal deviation (SeD) and concha bullosa.

Methods
Two trained resident of ENT evaluated sinus CT scans of 463 cases presenting with nasal obstruction or chronic sinusitis symptoms from April 2011 to December 2011. CT scans were checked for the presence of conchae bullosa and the degree of septal deviation. The severity of sinusitis was evaluated according to the Lund Mackay criteria. The frequency of patients with different degrees of SeD and different grades of chronic sinusitis were studied.

Results
Of 463 cases, 47% had septal deviation. Concha bullosa was seen in 16.8% of the patients in the left side and 27.6% of them in the right side. There was no significant relationship between the presence of concha bullosa and the severity of sinusitis. Also the P value of analytical tests between the severity of sinusitis, osteomeatal involvement and the degree of septal deviation was not significant. Analysis of the relationship between the presence of SeD (either to right or left) and the severity of sinusitis in different sinuses revealed no significant P value.

Conclusions
By this study, the relationship between concha bullosa in osteomeatal complex and the severity of sinusitis was not cleared. No relationship was found between the severity of sinusitis, osteomeatal involvement and the degree of septal deviation. Also SeD (either to right or left) was not found to be associated with the severity of sinusitis in different sinuses.
MGMT promoter methylation status and MGMT and CD133 immunohistochemical expression as prognostic markers in glioblastoma patients treated with temozolomide plus radiotherapy
Authors: Melguizo Consolación , Prados Jose , González Beatriz , Ortiz Raul , Concha Angel , Alvarez Pablo Juan , Madeddu Roberto , Perazzoli Gloria , Oliver Jaime Antonio , López Rodrigo , Rodríguez-Serrano Fernando , Aránega Antonia 
Published: December 2012

AbstractBackgroundThe CD133 antigen is a marker of radio- and chemo-resistant stem cell populations in glioblastoma (GBM). The O6-methylguanine DNA methyltransferase (MGMT) enzyme is related with temozolomide (TMZ) resistance. Our propose is to analyze the prognostic significance of the CD133 antigen and promoter methylation and protein expression of MGMT in a homogenous group of GBM patients uniformly treated with radiotherapy and TMZ. The possible connection between these GBM markers was also investigated.MethodsSeventy-eight patients with GBM treated with radiotherapy combined with concomitant and adjuvant TMZ were analyzed for MGMT and CD133. MGMT gene promoter methylation was determined by methylation-specific polymerase chain reaction after bisulfite treatment. MGMT and CD133 expression was assessed immunohistochemically using an automatic quantification system. Overall and progression-free survival was calculated according to the Kaplan–Meier method.ResultsThe MGMT gene promoter was found to be methylated in 34 patients (44.7%) and unmethylated in 42 patients (55.3%). A significant correlation was observed between MGMT promoter methylation and patients’ survival. Among the unmethylated tumors, 52.4% showed low expression of MGMT and 47.6% showed high-expression. Among methylated tumors, 58.8% showed low-expression of MGMT and 41.2% showed high-expression. No correlation was found between MGMT promoter methylation and MGMT expression, or MGMT expression and survival. In contrast with recent results, CD133 expression was not a predictive marker in GBM patients. Analyses of possible correlation between CD133 expression and MGMT protein expression or MGMT promoter methylation were negative.ConclusionsOur results support the hypothesis that MGMT promoter methylation status but not MGMT expression may be a predictive biomarker in the treatment of patients with GBM. In addition, CD133 should not be used for prognostic evaluation of these patients. Future studies will be necessary to determine its clinical utility.
Widely linear Markov signals
Authors: Espinosa-Pulido Juan A , Navarro-Moreno Jesús , Fernández-Alcalá Rosa M , Ruiz-Molina Juan C 
Published: December 2012

Abstract
The insufficiency to guarantee the existence of a state-space representation of the classical wide-sense Markov condition for improper complex-valued signals is shown and a generalization is suggested. New characterizations for wide-sense Markov signals which are based either on second-order properties or on state-space representations are studied in a widely linear setting. Moreover, the correlation structure of such signals is revealed and interesting results on modeling in both the forwards and backwards time directions are proved. As an application we give some recursive estimation algorithms obtained from the Kalman filter. The performance of the proposed results is illustrated in a numerical example in the areas of estimation and simulation.
Soluble microbial products (SMPs) release in activated sludge systems: a review
Authors: Azami Hamed , Sarrafzadeh Mohammad Hossein , Mehrnia Mohammad Reza 
Published: December 2012

Abstract
This review discusses the characterization, production and implications of soluble microbial products (SMPs) in biological wastewater treatment. The precise definition of SMPs is open to talk about, but is currently regarded as “the pool of organic compounds that are released into solution from substrate metabolism and biomass decay”'. Some of the SMPs have been identified as humic acids, polysaccharides, proteins, amino acids, antibiotics, extracellular enzymes and structural components of cells and products of energy metabolism. They adversely affect the kinetic activity, flocculating and settling properties of sludge. This review outlines some important findings with regard to biodegradability and treatability of SMPs and also the effect of process parameters on their production. As SMPs are produced during biological treatment process, their trace amounts normally remain in the effluent that defines the highest COD removal efficiency. Their presence in effluent represents a high potential risk of toxic by-product formation during chlorine disinfection. Studies have indicated that among all wastewater post-treatment processes, the adsorption by granular activated carbon combined with biologically induced degradation is the most effective method for removal of SMPs. However, it may be concludes that the knowledge regarding SMPs is still under progress and more work is required to fully understand their contribution to the treatment process.
Inflammatory monocytes and the pathogenesis of viral encephalitis
Authors: Terry Rachael L , Getts Daniel R , Deffrasnes Celine , van Vreden Caryn , Campbell Iain L , King Nicholas JC 
Published: December 2012

Abstract
Monocytes are a heterogeneous population of bone marrow-derived cells that are recruited to sites of infection and inflammation in many models of human diseases, including those of the central nervous system (CNS). Ly6Chi/CCR2hi inflammatory monocytes have been identified as the circulating precursors of brain macrophages, dendritic cells and arguably microglia in experimental autoimmune encephalomyelitis; Alzheimer’s disease; stroke; and more recently in CNS infection caused by Herpes simplex virus, murine hepatitis virus, Theiler’s murine encephalomyelitis virus, Japanese encephalitis virus and West Nile virus. The precise differentiation pathways and functions of inflammatory monocyte-derived populations in the inflamed CNS remains a contentious issue, especially in regard to the existence of monocyte-derived microglia. Furthermore, the contributions of monocyte-derived subsets to viral clearance and immunopathology are not well-defined. Thus, understanding the pathways through which inflammatory monocytes migrate to the brain and their functional capacity within the CNS is critical to inform future therapeutic strategies. This review discusses some of the key aspects of inflammatory monocyte trafficking to the brain and addresses the role of these cells in viral encephalitis.
ABCG2/V-ATPase was associated with the drug resistance and tumor metastasis of esophageal squamous cancer cells
Authors: Huang Lijun , Lu Qiang , Han Yong , Li Zhe , Zhang Zhipei , Li Xiaofei 
Published: December 2012

Abstract

Background
ATP-binding cassette sub-family G member 2 (ABCG2) is a protein that in humans is encoded by the ABCG2 gene. ABCG2 participates in efflux of many chemotherapeutic agents. ABCG2 is often expressed in hematopoietic progenitor or stem cells. Vacuolar-H + −ATPase (V-ATPase) plays a key role in adjusting and maintaining intracellular pH and in regulating the drug tolerance of cells. The TNM Classification of Malignant Tumours (TNM) is a cancer staging system that describes the extent of cancer in a patient’s body. In this study, the expression of ABCG2 and V-ATPase in esophageal squamous cancer cells was detected.

Methods
Immunohistochemistry staining and Immunofluorescence double staining were used to detect the expression of ABCG2 and V-ATPase in in 66 cases of esophageal squamous cancer cells. Associations and differences in expression of ABCG2 with that of V-ATPase were analyzed.

Results
Positive staining patterns for both ABCG2 (66.67%) and V-ATPase (68.18%) were located mainly in the plasma membrane and cytoplasm. Marked differences in expression were also shown (P < 0.001) among 3 groups of pathological grades and TNM stages in these carcinomas. Marked differences were also found for ABCG2 expression between the two groups in the pathological grades and in the TNM staging groups (P < 0.01), but not between the αb and βgroups. V-ATPase expression was statistically significant between the 2 groups in the pathological grades and TNM stages (P < 0.05). This was not evident between α and β groups of pathological grades or between αb and βof the TNM stages. Marked differences in expression of ABCG2 and V-ATPase were found between metastatic and non-metastatic groups in the same carcinomas (P < 0.0001). There was also a clear correlation between the expression of ABCG2 and V-ATPase (P ≤ 0.001) in the various groups of pathological grades and TNM stages.

Conclusions
Both ABCG2 and V-ATPase were over-expressed in esophageal squamous cancer cells. Their expression was associated with pathological grade, TNM stage and tumor metastasis in esophageal squamous cancer cells, suggesting interaction relationship between them. ABCG2 and V-ATPase expression may be strongly associated with drug resistance and tumor metastasis.

Virtual slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/3823783918433897