bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Real-Time Algorithm for the Correction of Brightband Effects in Radar-Derived QPE
Authors: Zhang Jian , Qi Youcun 
Published: May 2010

Abstract
The bright band (BB) is a layer of enhanced reflectivity due to melting of aggregated snow and ice crystals. The locally high reflectivity causes significant overestimation in radar precipitation estimates if an appropriate correction is not applied. The main objective of the current study is to develop a method that automatically corrects for large errors due to BB effects in a real-time national radar quantitative precipitation estimation (QPE) product. An approach that combines the mean apparent vertical profile of reflectivity (VPR) computed from a volume scan of radar reflectivity observations and an idealized linear VPR model was used for computational efficiency. The methodology was tested for eight events from different regions and seasons in the United States. The VPR correction was found to be effective and robust in reducing overestimation errors in radar-derived QPE, and the corrected radar precipitation fields showed physically continuous distributions. The correction worked consistently well for radars in flat land regions because of the relatively uniform spatial distributions of the BB in those areas. For radars in mountainous regions, the performance of the correction is mixed because of limited radar visibility in addition to large spatial variations of the vertical precipitation structure due to underlying topography.
An Experiment on the Nonbreaking Surface-Wave-Induced Vertical Mixing
Authors: Dai Dejun , Qiao Fangli , Sulisz Wojciech , Han Lei , Babanin Alexander 
Published: May 2010

Abstract
Mixing induced by nonbreaking surface waves was investigated in a wave tank by measuring the thermal destratification rate of the water column. One experiment without waves and four experiments with waves of amplitudes ranging from 1.0 to 1.5 cm and wavelength from 30 to 75 cm were conducted. Water temperature variations at depths from 4 to 12 cm below the surface were measured. In the layer from 4 to 7 cm, the originally dense isothermal lines disperse soon after the waves are generated, whereas the vertical gradient from 9 to 12 cm is maintained for a relatively long time. The time span, during which the water temperature becomes well mixed, changes from about 20 h for the case with no waves to tens of minutes for the case with waves, and it decreases with increasing wave amplitude and wavelength. A one-dimensional diffusion numerical model with wave-induced mixing parameterization shows consistent results with the measurement. The study demonstrates that the mixing induced by nonbreaking waves may add an important contribution to the vertical mixing process in the upper ocean and suggests a way to parameterize wave-induced mixing in numerical ocean models.
Clear-Sky Mask for the Advanced Clear-Sky Processor for Oceans
Authors: Petrenko B. , Ignatov A. , Kihai Y. , Heidinger A. 
Published: May 2010

Abstract
The Advanced Clear Sky Processor for Oceans (ACSPO) generates clear-sky products, such as SST, clear-sky radiances, and aerosol, from Advanced Very High Resolution Radiometer (AVHRR)-like measurements. The ACSPO clear-sky mask (ACSM) identifies clear-sky pixels within the ACSPO products. This paper describes the ACSM structure and compares the performances of ACSM and its predecessor, Clouds from AVHRR Extended Algorithm (CLAVRx). ACSM essentially employs online clear-sky radiative transfer simulations enabled within ACSPO with the Community Radiative Transfer Model (CRTM) in conjunction with numerical weather prediction atmospheric [Global Forecast System (GFS)] and SST [Reynolds daily high-resolution blended SST (DSST)] fields. The baseline ACSM tests verify the accuracy of fitting observed brightness temperatures with CRTM, check retrieved SST for consistency with Reynolds SST, and identify ambient cloudiness at the boundaries of cloudy systems. Residual cloud effects are screened out with several tests, adopted from CLAVRx, and with the SST spatial uniformity test designed to minimize misclassification of sharp SST gradients as clouds. Cross-platform and temporal consistencies of retrieved SSTs are maintained by accounting for SST and brightness temperature biases, estimated within ACSPO online and independently from ACSM. The performance of ACSM is characterized in terms of statistics of deviations of retrieved SST from the DSST. ACSM increases the amount of “clear” pixels by 30% to 40% and improves statistics of retrieved SST compared with CLAVRx. ACSM is also shown to be capable of producing satisfactory statistics of SST anomalies if the reference SST field for the exact date of observations is unavailable at the time of processing.
MicroRNA expression in Sézary syndrome: identification, function, and diagnostic potential
Authors: Ballabio Erica , Mitchell Tracey , van Kester Marloes S. , Taylor Stephen , Dunlop Heather M. , Chi Jianxiang , Tosi Isabella , Vermeer Maarten H. , Tramonti Daniela , Saunders Nigel J. , Boultwood Jacqueline , Wainscoat James S. , Pezzella Francesco , Whittaker Sean J. , Tensen Cornelius P. , Hatton Christian S. R. , Lawrie Charles H. 
Published: May 2010

AbstractMicroRNAs are commonly aberrantly expressed in many cancers. Very little is known of their role in T-cell lymphoma, however. We therefore elucidated the complete miRNome of purified T cells from 21 patients diagnosed with Sézary Syndrome (SzS), a rare aggressive primary cutaneous T-cell (CD4+) lymphoma. Unsupervised cluster analysis of microarray data revealed that the microRNA expression profile was distinct from CD4+ T-cell controls and B-cell lymphomas. The majority (104 of 114) of SzS-associated microRNAs (P < .05) were down-regulated and their expression pattern was largely consistent with previously reported genomic copy number abnormalities and were found to be highly enriched (P < .001) for aberrantly expressed target genes. Levels of miR-223 distinguished SzS samples (n = 32) from healthy controls (n = 19) and patients with mycosis fungoides (n = 11) in more than 90% of samples. Furthermore, we demonstrate that the down-regulation of intronically encoded miR-342 plays a role in the pathogenesis of SzS by inhibiting apoptosis, and describe a novel mechanism of regulation for this microRNA via binding of miR-199a* to its host gene. We also provide the first in vivo evidence for down-regulation of the miR-17-92 cluster in malignancy and demonstrate that ectopic miR-17-5p expression increases apoptosis and decreases cell proliferation in SzS cells.
Odefy - From discrete to continuous models
Authors: Krumsiek Jan , Pölsterl Sebastian , Wittmann Dominik M , Theis Fabian J 
Published: May 2010

Abstract

Background
Phenomenological information about regulatory interactions is frequently available and can be readily converted to Boolean models. Fully quantitative models, on the other hand, provide detailed insights into the precise dynamics of the underlying system. In order to connect discrete and continuous modeling approaches, methods for the conversion of Boolean systems into systems of ordinary differential equations have been developed recently. As biological interaction networks have steadily grown in size and complexity, a fully automated framework for the conversion process is desirable.

Results
We present Odefy, a MATLAB- and Octave-compatible toolbox for the automated transformation of Boolean models into systems of ordinary differential equations. Models can be created from sets of Boolean equations or graph representations of Boolean networks. Alternatively, the user can import Boolean models from the CellNetAnalyzer toolbox, GINSim and the PBN toolbox. The Boolean models are transformed to systems of ordinary differential equations by multivariate polynomial interpolation and optional application of sigmoidal Hill functions. Our toolbox contains basic simulation and visualization functionalities for both, the Boolean as well as the continuous models. For further analyses, models can be exported to SQUAD, GNA, MATLAB script files, the SB toolbox, SBML and R script files. Odefy contains a user-friendly graphical user interface for convenient access to the simulation and exporting functionalities. We illustrate the validity of our transformation approach as well as the usage and benefit of the Odefy toolbox for two biological systems: a mutual inhibitory switch known from stem cell differentiation and a regulatory network giving rise to a specific spatial expression pattern at the mid-hindbrain boundary.

Conclusions
Odefy provides an easy-to-use toolbox for the automatic conversion of Boolean models to systems of ordinary differential equations. It can be efficiently connected to a variety of input and output formats for further analysis and investigations. The toolbox is open-source and can be downloaded at http://cmb.helmholtz-muenchen.de/odefy.
A semi-parametric Bayesian model for unsupervised differential co-expression analysis
Authors: Freudenberg Johannes M , Sivaganesan Siva , Wagner Michael , Medvedovic Mario 
Published: May 2010

Abstract

Background
Differential co-expression analysis is an emerging strategy for characterizing disease related dysregulation of gene expression regulatory networks. Given pre-defined sets of biological samples, such analysis aims at identifying genes that are co-expressed in one, but not in the other set of samples.

Results
We developed a novel probabilistic framework for jointly uncovering contexts (i.e. groups of samples) with specific co-expression patterns, and groups of genes with different co-expression patterns across such contexts. In contrast to current clustering and bi-clustering procedures, the implicit similarity measure in this model used for grouping biological samples is based on the clustering structure of genes within each sample and not on traditional measures of gene expression level similarities. Within this framework, biological samples with widely discordant expression patterns can be placed in the same context as long as the co-clustering structure of genes is concordant within these samples. To the best of our knowledge, this is the first method to date for unsupervised differential co-expression analysis in this generality. When applied to the problem of identifying molecular subtypes of breast cancer, our method identified reproducible patterns of differential co-expression across several independent expression datasets. Sample groupings induced by these patterns were highly informative of the disease outcome. Expression patterns of differentially co-expressed genes provided new insights into the complex nature of the ERα regulatory network.

Conclusions
We demonstrated that the use of the co-clustering structure as the similarity measure in the unsupervised analysis of sample gene expression profiles provides valuable information about expression regulatory networks.
Evaluating the transferability of Hapmap SNPs to a Singapore Chinese population
Authors: Andiappan Anand Kumar , Anantharaman Ramani , Nilkanth Pallavi Parate , Wang De Yun , Chew Fook Tim 
Published: May 2010

Abstract

Background
The International Hapmap project serves as a valuable resource for human genome variation data, however its applicability to other populations has yet to be exhaustively investigated. In this paper, we use high density genotyping chips and resequencing strategies to compare the Singapore Chinese population with the Hapmap populations. First we compared 1028 and 114 unrelated Singapore Chinese samples genotyped using the Illumina Human Hapmap 550 k chip and Affymetrix 500 k array respectively against the 270 samples from Hapmap. Secondly, data from 20 candidate genes on 5q31-33 resequenced for an asthma candidate gene based study was also used for the analysis.

Results
A total of 237 SNPs were identified through resequencing of which only 95 SNPs (40%) were in Hapmap; however an additional 56 SNPs (24%) were not genotyped directly but had a proxy SNP in the Hapmap. At the genome-wide level, Singapore Chinese were highly correlated with Hapmap Han Chinese with correlation of 0.954 and 0.947 for the Illumina and Affymetrix platforms respectively with deviant SNPs randomly distributed within and across all chromosomes.

Conclusions
The high correlation between our population and Hapmap Han Chinese reaffirms the applicability of Hapmap based genome-wide chips for GWA studies. There is a clear population signature for the Singapore Chinese samples and they predominantly resemble the southern Han Chinese population; however when new migrants particularly those with northern Han Chinese background were included, population stratification issues may arise. Future studies needs to address population stratification within the sample collection while designing and interpreting GWAS in the Chinese population.
Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood
Authors: Vaz Candida , Ahmad Hafiz M , Sharma Pratibha , Gupta Rashi , Kumar Lalit , Kulshreshtha Ritu , Bhattacharya Alok 
Published: May 2010

Abstract

Background
MicroRNAs are a class of small non-coding RNAs that regulate mRNA expression at the post - transcriptional level and thereby many fundamental biological processes. A number of methods, such as multiplex polymerase chain reaction, microarrays have been developed for profiling levels of known miRNAs. These methods lack the ability to identify novel miRNAs and accurately determine expression at a range of concentrations. Deep or massively parallel sequencing methods are providing suitable platforms for genome wide transcriptome analysis and have the ability to identify novel transcripts.

Results
The results of analysis of small RNA sequences obtained by Solexa technology of normal peripheral blood mononuclear cells, tumor cell lines K562 and HL60 are presented. In general K562 cells displayed overall low level of miRNA population and also low levels of DICER. Some of the highly expressed miRNAs in the leukocytes include several members of the let-7 family, miR-21, 103, 185, 191 and 320a. Comparison of the miRNA profiles of normal versus K562 or HL60 cells revealed a specific set of differentially expressed molecules. Correlation of the miRNA with that of mRNA expression profiles, obtained by microarray, revealed a set of target genes showing inverse correlation with miRNA levels. Relative expression levels of individual miRNAs belonging to a cluster were found to be highly variable. Our computational pipeline also predicted a number of novel miRNAs. Some of the predictions were validated by Real-time RT-PCR and or RNase protection assay. Organization of some of the novel miRNAs in human genome suggests that these may also be part of existing clusters or form new clusters.

Conclusions
We conclude that about 904 miRNAs are expressed in human leukocytes. Out of these 370 are novel miRNAs. We have identified miRNAs that are differentially regulated in normal PBMC with respect to cancer cells, K562 and HL60. Our results suggest that post - transcriptional processes may play a significant role in regulating levels of miRNAs in tumor cells. The study also provides a customized automated computation pipeline for miRNA profiling and identification of novel miRNAs; even those that are missed out by other existing pipelines. The Computational Pipeline is available at the website: http://mirna.jnu.ac.in/deep_sequencing/deep_sequencing.html
Sequence features involved in the mechanism of 3' splice junction wobbling
Authors: Tsai Kuo-Wang , Chan Wen-Ching , Hsu Chun-Nan , Lin Wen-chang 
Published: May 2010

Abstract

Background
Alternative splicing is an important mechanism mediating the diversified functions of genes in multicellular organisms, and such event occurs in around 40-60% of human genes. Recently, a new splice-junction wobbling mechanism was proposed that subtle modifications exist in mRNA maturation by alternatively choosing at 5'- GTNGT and 3'- NAGNAG, which created single amino acid insertion and deletion isoforms.

Results
By browsing the Alternative Splicing Database information, we observed that most 3' alternative splice site choices occur within six nucleotides of the dominant splice site and the incidence significantly decreases further away from the dominant acceptor site. Although a lower frequency of alternative splicing occurs within the intronic region (alternative splicing at the proximal AG) than in the exonic region (alternative splicing at the distal AG), alternative AG sites located within the intronic region show stronger potential as the acceptor. These observations revealed that the choice of 3' splice sites during 3' splicing junction wobbling could depend on the distance between the duplicated AG and the branch point site (BPS). Further mutagenesis experiments demonstrated that the distance of AG-to-AG and BPS-to-AG can greatly influence 3' splice site selection. Knocking down a known alternative splicing regulator, hSlu7, failed to affect wobble splicing choices.

Conclusion
Our results implied that nucleotide distance between proximal and distal AG sites has an important regulatory function. In this study, we showed that occurrence of 3' wobble splicing occurs in a distance-dependent manner and that most of this wobble splicing is probably caused by steric hindrance from a factor bound at the neighboring tandem motif sequence.
Stage effects of negative emotion on spatial and verbal working memory
Authors: Li Xuebing , Chan Raymond CK , Luo Yue-jia 
Published: May 2010

Abstract

Background
The effects of negative emotion on different processing periods in spatial and verbal working memory (WM) and the possible brain mechanism of the interaction between negative emotion and WM were explored using a high-time resolution event-related potential (ERP) technique and time-locked delayed matching-to-sample task (DMST).

Results
Early P3b and late P3b were reduced in the negative emotion condition for both the spatial and verbal tasks at encoding. At retention, the sustained negative slow wave (NSW) showed a significant interaction between emotional state and task type. Spatial trials in the negative emotion condition elicited a more negative deflection than they did in the neutral emotion condition. However, no such effect was observed for the verbal tasks. At retrieval, early P3b and late P3b were markedly more attenuated in the negative emotion condition than in the neutral emotion condition for both the spatial and verbal tasks.

Conclusions
The results indicate that the differential effects of negative emotion on spatial and verbal WM mainly take place during information maintenance processing, which implies that there is a systematic association between specific affects (e.g., negative emotion) and certain cognitive processes (e.g., spatial retention).
Atypical response regulators expressed in the maize endosperm transfer cells link canonical two component systems and seed biology
Authors: Muñiz Luís M , Royo Joaquín , Gómez Elisa , Baudot Gaelle , Paul Wyatt , Hueros Gregorio 
Published: May 2010

Abstract

Background
Two component systems (TCS) are phosphotransfer-based signal transduction pathways first discovered in bacteria, where they perform most of the sensing tasks. They present a highly modular structure, comprising a receptor with histidine kinase activity and a response regulator which regulates gene expression or interacts with other cell components. A more complex framework is usually found in plants and fungi, in which a third component transfers the phosphate group from the receptor to the response regulator. They play a central role in cytokinin mediated functions in plants, affecting processes such as meristem growth, phyllotaxy, seed development, leaf senescence or tissue differentiation. We have previously reported the expression and cellular localization of a type A response regulator, ZmTCRR-1, in the transfer cells of the maize seed, a tissue critical for seed filling and development, and described its regulation by a tissue specific transcription factor. In this work we investigate the expression and localization of other components of the TCS signalling routes in the maize seed and initiate the characterization of their interactions.

Results
The discovery of a new type A response regulator, ZmTCRR-2, specifically expressed in the transfer cells and controlled by a tissue specific transcription factor suggests a previously unknown role for TCS in the biology of transfer cells. We have characterized other canonical TCS molecules, including 6 histidine kinases and 3 phosphotransfer proteins, potentially involved in the atypical transduction pathway defined by ZmTCRR-1 and 2. We have identified potential upstream interactors for both proteins and shown that they both move into the developing endosperm. Furthermore, ZmTCRR-1 expression in an heterologous system (Arabidopsis thaliana) is directed to xylem parenchyma cells, probably involved in transport processes, one of the major roles attributed to the transfer cell layer.

Conclusions
Our data prove the expression of the effector elements of a TCS route operating in the transfer cells under developmental control. Its possible role in integrating external signals with seed developmental processes is discussed.
OCT-4 expression in follicular and luteal phase endometrium: a pilot study
Authors: Bentz Eva-Katrin , Kenning Marina , Schneeberger Christian , Kolbus Andrea , Huber Johannes C , Hefler Lukas A , Tempfer Clemens B 
Published: May 2010

Abstract

Background
The stem cell marker Octamer-4 (OCT-4) is expressed in human endometrium. Menstrual cycle-dependency of OCT-4 expression has not been investigated to date.

Methods
In a prospective, single center cohort study of 98 women undergoing hysteroscopy during the follicular (n = 49) and the luteal (n = 40) phases of the menstrual cycle, we obtained endometrial samples. Specimens were investigated for OCT-4 expression on the mRNA and protein levels using reverse transcriptase polymerase chain reaction (RT-PCR) and immunohistochemistry. Expression of OCT-4 was correlated to menstrual cycle phase.

Results
Of 89 women sampled, 49 were in the follicular phase and 40 were in the luteal phase. OCT-4 mRNA was detected in all samples. Increased OCT-4 mRNA levels in the follicular and luteal phases was found in 35/49 (71%) and 27/40 (68%) of women, respectively (p = 0.9). Increased expression of OCT-4 protein was identified in 56/89 (63%) samples. Increased expression of OCT-4 protein in the follicular and luteal phases was found in 33/49 (67%) and 23/40 (58%) of women, respectively (p = 0.5).

Conclusions
On the mRNA and protein levels, OCT-4 is not differentially expressed during the menstrual cycle. Endometrial OCT-4 is not involved in or modulated by hormone-induced cyclical changes of the endometrium.