bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-Time Hazard Approximation of Long-Lasting Convective Storms Using Emergency Data
Authors: Rossi Pekka J. , Hasu Vesa , Halmevaara Kalle , Mäkelä Antti , Koistinen Jarmo , Pohjola Heikki 
Published: December 2012

Abstract
Convective storms cause several types of damage, including economic and ecological losses, every year. This paper focuses on an automatic hazard-level determination of convective storms based on a largely unused information source: real-time emergency report data. In addition to the location of the report, the emergency response centers classify cases into different emergency types and deliver a free-form verbal description of the incident for online use. This study uses archived weather-related emergency reports to determine hazard levels for convective storms detected by the weather radar. To develop an algorithm for estimating the hazard level of convective storms, a weather radar–databased convective storm-tracking algorithm was applied with a method that links reported emergency events to individually tracked convective storms. Based on the relationship between each convective storm track and an emergency report, the algorithm determines the hazard level of the storms automatically. Moreover, the developed algorithm takes into account the population density at the location of the report because, in densely populated areas, the flow of emergency reports is more intense. The proposed algorithm with case studies shows the potential use of real-time emergency call data in operational severe weather nowcasting and warning tools. This study demonstrates that supplementing storms with emergency information is advantageous, especially with long-lasting storms such as supercell storms or mesoscale convective systems.
Sensitivity of Simulated Climate to Two Atmospheric Models: Interpretation of Differences between Dry Models and Moist Models
Authors: Zhang He , Zhang Minghua , Zeng Qing-cun 
Published: December 2012

Abstract
The dynamical core of the Institute of Atmospheric Physics of the Chinese Academy of Sciences Atmospheric General Circulation Model (IAP AGCM) and the Eulerian spectral transform dynamical core of the Community Atmosphere Model, version 3.1 (CAM3.1), developed at the National Center for Atmospheric Research (NCAR) are used to study the sensitivity of simulated climate. The authors report that when the dynamical cores are used with the same CAM3.1 physical parameterizations of comparable resolutions, the model with the IAP dynamical core simulated a colder troposphere than that from the CAM3.1 core, reducing the CAM3.1 warm bias in the tropical and midlatitude troposphere. However, when the two dynamical cores are used in the idealized Held–Suarez tests without moisture physics, the IAP AGCM core simulated a warmer troposphere than that in CAM3.1. The causes of the differences in the full models and in the dry models are then investigated.
The authors show that the IAP dynamical core simulated weaker eddies in both the full physics and the dry models than those in the CAM due to different numerical approximations. In the dry IAP model, the weaker eddies cause smaller heat loss from poleward dynamical transport and thus warmer troposphere in the tropics and midlatitudes. When moist physics is included, however, weaker eddies also lead to weaker transport of water vapor and reduction of high clouds in the IAP model, which then causes a colder troposphere due to reduced greenhouse warming of these clouds. These results show how interactive physical processes can change the effect of a dynamical core on climate simulations between two models.
PU.1 is a potent tumor suppressor in classical Hodgkin lymphoma cells
Authors: Yuki Hiromichi , Ueno Shikiko , Tatetsu Hiro , Niiro Hiroaki , Iino Tadafumi , Endo Shinya , Kawano Yawara , Komohara Yoshihiro , Takeya Motohiro , Hata Hiroyuki , Okada Seiji , Watanabe Toshiki , Akashi Koichi , Mitsuya Hiroaki , Okuno Yutaka 
Published: December 2012

Key PointsPU.1 is a potent tumor suppressor in cHL cells and the induction of PU.1 is a possible therapeutic option for patients with cHL.
q-analogue of a new sequence of linear positive operators
Authors: Gupta Vijay , Kim Taekyun , Lee Sang-Hun 
Published: December 2012

Abstract
This paper deals with Durrmeyer type generalization of q-Baskakov type operators using the concept of q-integral, which introduces a new sequence of positive q-integral operators. We show that this sequence is an approximation process in the polynomial weighted space of continuous functions defined on the interval

[
0
,
∞
)

. An estimate for the rate of convergence and weighted approximation properties are also obtained.

MSC:41A25, 41A36.
Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence
Authors: Chaudhary Ruchi , Burleigh J Gordon , Eulenstein Oliver 
Published: December 2012

Abstract

Background
Gene tree - species tree reconciliation problems infer the patterns and processes of gene evolution within a species tree. Gene tree parsimony approaches seek the evolutionary scenario that implies the fewest gene duplications, duplications and losses, or deep coalescence (incomplete lineage sorting) events needed to reconcile a gene tree and a species tree. While a gene tree parsimony approach can be informative about genome evolution and phylogenetics, error in gene trees can profoundly bias the results.

Results
We introduce efficient algorithms that rapidly search local Subtree Prune and Regraft (SPR) or Tree Bisection and Reconnection (TBR) neighborhoods of a given gene tree to identify a topology that implies the fewest duplications, duplication and losses, or deep coalescence events. These algorithms improve on the current solutions by a factor of n for searching SPR neighborhoods and n
2 for searching TBR neighborhoods, where n is the number of taxa in the given gene tree. They provide a fast error correction protocol for ameliorating the effects of gene tree error by allowing small rearrangements in the topology to improve the reconciliation cost. We also demonstrate a simple protocol to use the gene rearrangement algorithm to improve gene tree parsimony phylogenetic analyses.

Conclusions
The new gene tree rearrangement algorithms provide a fast method to address gene tree error. They do not make assumptions about the underlying processes of genome evolution, and they are amenable to analyses of large-scale genomic data sets. These algorithms are also easily incorporated into gene tree parsimony phylogenetic analyses, potentially producing more credible estimates of reconciliation cost.
Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213
Authors: Reddy Joseph S , Kumar Ranjit , Watt James M , Lawrence Mark L , Burgess Shane C , Nanduri Bindu 
Published: December 2012

Abstract

Background
Computational methods for structural gene annotation have propelled gene discovery but face certain drawbacks with regards to prokaryotic genome annotation. Identification of transcriptional start sites, demarcating overlapping gene boundaries, and identifying regulatory elements such as small RNA are not accurate using these approaches. In this study, we re-visit the structural annotation of Mannheimia haemolytica PHL213, a bovine respiratory disease pathogen. M. haemolytica is one of the causative agents of bovine respiratory disease that results in about $3 billion annual losses to the cattle industry. We used RNA-Seq and analyzed the data using freely-available computational methods and resources. The aim was to identify previously unannotated regions of the genome using RNA-Seq based expression profile to complement the existing annotation of this pathogen.

Results
Using the Illumina Genome Analyzer, we generated 9,055,826 reads (average length ~76 bp) and aligned them to the reference genome using Bowtie. The transcribed regions were analyzed using SAMTOOLS and custom Perl scripts in conjunction with BLAST searches and available gene annotation information. The single nucleotide resolution map enabled the identification of 14 novel protein coding regions as well as 44 potential novel sRNA. The basal transcription profile revealed that 2,506 of the 2,837 annotated regions were expressed in vitro, at 95.25% coverage, representing all broad functional gene categories in the genome. The expression profile also helped identify 518 potential operon structures involving 1,086 co-expressed pairs. We also identified 11 proteins with mutated/alternate start codons.

Conclusions
The application of RNA-Seq based transcriptome profiling to structural gene annotation helped correct existing annotation errors and identify potential novel protein coding regions and sRNA. We used computational tools to predict regulatory elements such as promoters and terminators associated with the novel expressed regions for further characterization of these novel functional elements. Our study complements the existing structural annotation of Mannheimia haemolytica PHL213 based on experimental evidence. Given the role of sRNA in virulence gene regulation and stress response, potential novel sRNA described in this study can form the framework for future studies to determine the role of sRNA, if any, in M. haemolytica pathogenesis.
A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet
Authors: Ma Kelvin , Vitek Olga , Nesvizhskii Alexey I 
Published: December 2012

AbstractPeptideProphet is a post-processing algorithm designed to evaluate the confidence in identifications of MS/MS spectra returned by a database search. In this manuscript we describe the "what and how" of PeptideProphet in a manner aimed at statisticians and life scientists who would like to gain a more in-depth understanding of the underlying statistical modeling. The theory and rationale behind the mixture-modeling approach taken by PeptideProphet is discussed from a statistical model-building perspective followed by a description of how a model can be used to express confidence in the identification of individual peptides or sets of peptides. We also demonstrate how to evaluate the quality of model fit and select an appropriate model from several available alternatives. We illustrate the use of PeptideProphet in association with the Trans-Proteomic Pipeline, a free suite of software used for protein identification.
Modeling and mining term association for improving biomedical information retrieval performance
Authors: Hu Qinmin , Huang Jimmy Xiangji , Hu Xiaohua 
Published: December 2012

Abstract

Background
The growth of the biomedical information requires most information retrieval systems to provide short and specific answers in response to complex user queries. Semantic information in the form of free text that is structured in a way makes it straightforward for humans to read but more difficult for computers to interpret automatically and search efficiently. One of the reasons is that most traditional information retrieval models assume terms are conditionally independent given a document/passage. Therefore, we are motivated to consider term associations within different contexts to help the models understand semantic information and use it for improving biomedical information retrieval performance.

Results
We propose a term association approach to discover term associations among the keywords from a query. The experiments are conducted on the TREC 2004-2007 Genomics data sets and the TREC 2004 HARD data set. The proposed approach is promising and achieves superiority over the baselines and the GSP results. The parameter settings and different indices are investigated that the sentence-based index produces the best results in terms of the document-level, the word-based index for the best results in terms of the passage-level and the paragraph-based index for the best results in terms of the passage2-level. Furthermore, the best term association results always come from the best baseline. The tuning number k in the proposed recursive re-ranking algorithm is discussed and locally optimized to be 10.

Conclusions
First, modelling term association for improving biomedical information retrieval using factor analysis, is one of the major contributions in our work. Second, the experiments confirm that term association considering co-occurrence and dependency among the keywords can produce better results than the baselines treating the keywords independently. Third, the baselines are re-ranked according to the importance and reliance of latent factors behind term associations. These latent factors are decided by the proposed model and their term appearances in the first round retrieved passages.
Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice
Authors: Lan Ying , Su Ning , Shen Yi , Zhang Rongzhi , Wu Fuqing , Cheng Zhijun , Wang Jiulin , Zhang Xin , Guo Xiupin , Lei Cailin , Wang Jie , Jiang Ling , Mao Long , Wan Jianmin 
Published: December 2012

Abstract

Background
MicroRNAs (miRNAs) modulate gene expression in different tissues and at diverse developmental stages, including grain development in japonica rice. To identify novel miRNAs in indica rice and to study their expression patterns during the entire grain filling process, small RNAs from all stages of grain development were sequenced and their expression patterns were studied using customized miRNA chips.

Results
A total of 21 conserved and 91 non-conserved miRNA families were found in developing indica grains. We also discovered 11 potential novel miRNAs based on the presence of their miRNA*s. Expression patterns of these identified miRNAs were analyzed using customized miRNA chips. The results showed that during the filling phase about half of the detected miRNAs were up-regulated, whereas the remainder were down-regulated. Predicted targets of differentially expressed miRNAs may participate in carbohydrate metabolism, hormone signaling and pathways associated with seed maturity, suggesting potentially important roles in rice grain development.

Conclusions
This study is the first genome-wide investigation of miRNAs during the grain-filling phase of an indica variety of rice. The novel miRNAs identified might be involved in new miRNA regulatory pathways for grain development. The complexity of these miRNAs and their targets and interactions require further study to obtain a better understanding of the molecular mechanisms underlying grain development.
The complete swine olfactory subgenome: expansion of the olfactory gene repertoire in the pig genome
Authors: Nguyen Dinh Truong , Lee Kyooyeol , Choi Hojun , Choi Min-kyeung , Le Minh Thong , Song Ning , Kim Jin-Hoi , Seo Han Geuk , Oh Jae-Wook , Lee Kyungtae , Kim Tae-Hun , Park Chankyu 
Published: December 2012

Abstract

Background
Insects and animals can recognize surrounding environments by detecting thousands of chemical odorants. Olfaction is a complicated process that begins in the olfactory epithelium with the specific binding of volatile odorant molecules to dedicated olfactory receptors (ORs). OR proteins are encoded by the largest gene superfamily in the mammalian genome.

Results
We report here the whole genome analysis of the olfactory receptor genes of S. scrofa using conserved OR gene specific motifs and known OR protein sequences from diverse species. We identified 1,301 OR related sequences from the S. scrofa genome assembly, Sscrofa10.2, including 1,113 functional OR genes and 188 pseudogenes. OR genes were located in 46 different regions on 16 pig chromosomes. We classified the ORs into 17 families, three Class I and 14 Class II families, and further grouped them into 349 subfamilies. We also identified inter- and intra-chromosomal duplications of OR genes residing on 11 chromosomes. A significant number of pig OR genes (n = 212) showed less than 60% amino acid sequence similarity to known OR genes of other species.

Conclusion
As the genome assembly Sscrofa10.2 covers 99.9% of the pig genome, our analysis represents an almost complete OR gene repertoire from an individual pig genome. We show that S. scrofa has one of the largest OR repertoires, suggesting an expansion of OR genes in the swine genome. A significant number of unique OR genes in the pig genome may suggest the presence of swine specific olfactory stimulation.
Boolean modeling and fault diagnosis in oxidative stress response
Authors: Sridharan Sriram , Layek Ritwik , Datta Aniruddha , Venkatraj Jijayanagaram 
Published: December 2012

AbstractBackgroundOxidative stress is a consequence of normal and abnormal cellular metabolism and is linked to the development of human diseases. The effective functioning of the pathway responding to oxidative stress protects the cellular DNA against oxidative damage; conversely the failure of the oxidative stress response mechanism can induce aberrant cellular behavior leading to diseases such as neurodegenerative disorders and cancer. Thus, understanding the normal signaling present in oxidative stress response pathways and determining possible signaling alterations leading to disease could provide us with useful pointers for therapeutic purposes. Using knowledge of oxidative stress response pathways from the literature, we developed a Boolean network model whose simulated behavior is consistent with earlier experimental observations from the literature. Concatenating the oxidative stress response pathways with thePI3-Kinase-Aktpathway, the oxidative stress is linked to the phenotype of apoptosis, once again through a Boolean network model. Furthermore, we present an approach for pinpointing possible fault locations by using temporal variations in the oxidative stress input and observing the resulting deviations in the apoptotic signature from the normally predicted pathway. Such an approach could potentially form the basis for designing more effective combination therapies against complex diseases such as cancer.ResultsIn this paper, we have developed a Boolean network model for the oxidative stress response. This model was developed based on pathway information from the current literature pertaining to oxidative stress. Where applicable, the behaviour predicted by the model is in agreement with experimental observations from the published literature. We have also linked the oxidative stress response to the phenomenon of apoptosis via thePI3k/Aktpathway.ConclusionsIt is our hope that some of the additional predictions here, such as those pertaining to the oscillatory behaviour of certain genes in the presence of oxidative stress, will be experimentally validated in the near future. Of course, it should be pointed out that the theoretical procedure presented here for pinpointing fault locations in a biological network with feedback will need to be further simplified before it can be even considered for practical biological validation.
SPRR2A enhances p53 deacetylation through HDAC1 and down regulates p21 promoter activity
Authors: Mizuguchi Yoshiaki , Specht Susan , Lunz John G , Isse Kumiko , Corbitt Natasha , Takizawa Toshihiro , Demetris Anthony J 
Published: December 2012

Abstract

Background
Small proline rich protein (SPRR) 2A is one of 14 SPRR genes that encodes for a skin cross-linking protein, which confers structural integrity to the cornified keratinocyte cell envelope. New evidence, however, shows that SPRR2A is also a critical stress and wound repair modulator: it enables a variety of barrier epithelia to transiently acquire mesenchymal characteristics (EMT) and simultaneously quench reactive oxygen species during wound repair responses. p53 is also widely recognized as the node in cellular stress responses that inhibits EMT and triggers cell-cycle arrest, apoptosis, and cellular senescence. Since some p53-directed processes would seem to impede wound repair of barrier epithelia, we hypothesized that SPRR2A up regulation might counteract these effects and enable/promote wound repair under stressful environmental conditions.

Results
Using a well characterized cholangiocarcinoma cell line we show that levels of SPRR2A expression, similar to that seen during stressful biliary wound repair responses, disrupts acetylation and subsequent p53 transcriptional activity. p53 deacetylation is accomplished via two distinct, but possibly related, mechanisms: 1) a reduction of p300 acetylation, thereby interfering with p300-p53 binding and subsequent p300 acetylation of K382 in p53; and 2) an increase in histone deacetylase 1 (HDAC1) mRNA and protein expression. The p300 CH3 domain is essential for both the autoacetylation of p300 and transference of the acetyl group to p53 and HDAC1 is a component of several non-p300 complexes that enhance p53 deacetylation, ubiquitination, and proteosomal degradation. HDAC1 can also bind the p300-CH3 domain, regulating p300 acetylation and interfering with p300 mediated p53 acetylation. The importance of this pathway is illustrated by showing complete restoration of p53 acetylation and partial restoration of p300 acetylation by treating SPRR2A expressing cells with HDAC1 siRNA.

Conclusion
Up-regulation of SPRR2A, similar to that seen during barrier epithelia wound repair responses reduces p53 acetylation by interfering with p300-p53 interactions and by increasing HDAC1 expression. SPRR2A, therefore, functions as a suppressor of p53-dependent transcriptional activity, which otherwise might impede cellular processes needed for epithelial wound repair responses such as EMT.
Back-to-Back Comparison of Auto-Fluorescence Imaging (AFI) Versus High Resolution White Light Colonoscopy for Adenoma Detection
Authors: Moriichi Kentaro , Fujiya Mikihiro , Sato Ryu , Watari Jiro , Nomura Yoshiki , Nata Toshie , Ueno Nobuhiro , Maeda Shigeaki , Kashima Shin , Itabashi Kentaro , Ishikawa Chisato , Inaba Yuhei , Ito Takahiro , Okamoto Kotaro , Tanabe Hiroki , Mizukami Yusuke , Saitoh Yusuke , Kohgo Yutaka 
Published: December 2012

Abstract

Background
Some patients under close colonoscopic surveillance still develop colorectal cancer, thus suggesting the overlook of colorectal adenoma by endoscopists. AFI detects colorectal adenoma as a clear magenta, therefore the efficacy of AFI is expected to improve the detection ability of colorectal adenoma. The aim of this study is to determine the efficacy of AFI in detecting colorectal adenoma.

Methods
This study enrolled 88 patients who underwent colonoscopy at Asahikawa Medical University and Kushiro Medical Association Hospital. A randomly selected colonoscopist first observed the sigmoid colon and rectum with conventional high resolution endosopy (HRE). Then the colonoscopist changed the mode to AFI and handed to the scope to another colonoscopist who knew no information about the HRE. Then the second colonoscopist observed the sigmoid colon and rectum. Each colonoscopist separately recorded the findings. The detection rate, miss rate and procedural time were assessed in prospective manner.

Results
The detection rate of flat and depressed adenoma, but not elevated adenoma, by AFI is significantly higher than that by HRE. In less-experienced endoscopists, AFI dramatically increased the detection rate (30.3%) and reduced miss rate (0%) of colorectal adenoma in comparison to those of HRE (7.7%, 50.0%), but not for experienced endoscopists. The procedural time of HRE was significantly shorter than that of AFI.

Conclusions
AFI increased the detection rate and reduced the miss rate of flat and depressed adenomas. These advantages of AFI were limited to less-experienced endoscopists because experienced endoscopists exhibited a substantially high detection rate for colorectal adenoma with HRE.