bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns
Authors: Barvkar Vitthal T , Pardeshi Varsha C , Kale Sandip M , Kadoo Narendra Y , Gupta Vidya S 
Published: May 2012

Abstract

Background
The glycosylation process, catalyzed by ubiquitous glycosyltransferase (GT) family enzymes, is a prevalent modification of plant secondary metabolites that regulates various functions such as hormone homeostasis, detoxification of xenobiotics and biosynthesis and storage of secondary metabolites. Flax (Linum usitatissimum L.) is a commercially grown oilseed crop, important because of its essential fatty acids and health promoting lignans. Identification and characterization of UDP glycosyltransferase (UGT) genes from flax could provide valuable basic information about this important gene family and help to explain the seed specific glycosylated metabolite accumulation and other processes in plants. Plant genome sequencing projects are useful to discover complexity within this gene family and also pave way for the development of functional genomics approaches.

Results
Taking advantage of the newly assembled draft genome sequence of flax, we identified 137 UDP glycosyltransferase (UGT) genes from flax using a conserved signature motif. Phylogenetic analysis of these protein sequences clustered them into 14 major groups (A-N). Expression patterns of these genes were investigated using publicly available expressed sequence tag (EST), microarray data and reverse transcription quantitative real time PCR (RT-qPCR). Seventy-three per cent of these genes (100 out of 137) showed expression evidence in 15 tissues examined and indicated varied expression profiles. The RT-qPCR results of 10 selected genes were also coherent with the digital expression analysis. Interestingly, five duplicated UGT genes were identified, which showed differential expression in various tissues. Of the seven intron loss/gain positions detected, two intron positions were conserved among most of the UGTs, although a clear relationship about the evolution of these genes could not be established. Comparison of the flax UGTs with orthologs from four other sequenced dicot genomes indicated that seven UGTs were flax diverged.

Conclusions
Flax has a large number of UGT genes including few flax diverged ones. Phylogenetic analysis and expression profiles of these genes identified tissue and condition specific repertoire of UGT genes from this crop. This study would facilitate precise selection of candidate genes and their further characterization of substrate specificities and in planta functions.
Comparative analyses reveal potential uses of Brachypodium distachyonas a model for cold stress responses in temperate grasses
Authors: Li Chuan , Rudi Heidi , Stockinger Eric J , Cheng Hongmei , Cao Moju , Fox Samuel E , Mockler Todd C , Westereng Bjørge , Fjellheim Siri , Rognli Odd Arne , Sandve Simen R 
Published: May 2012

Abstract

Background
Little is known about the potential of Brachypodium distachyon as a model for low temperature stress responses in Pooideae. The ice recrystallization inhibition protein (IRIP) genes, fructosyltransferase (FST) genes, and many C-repeat binding factor (CBF) genes are Pooideae specific and important in low temperature responses. Here we used comparative analyses to study conservation and evolution of these gene families in B. distachyon to better understand its potential as a model species for agriculturally important temperate grasses.

Results

Brachypodium distachyon contains cold responsive IRIP genes which have evolved through Brachypodium specific gene family expansions. A large cold responsive CBF3 subfamily was identified in B. distachyon, while CBF4 homologs are absent from the genome. No B. distachyon FST gene homologs encode typical core Pooideae FST-motifs and low temperature induced fructan accumulation was dramatically different in B. distachyon compared to core Pooideae species.

Conclusions
We conclude that B. distachyon can serve as an interesting model for specific molecular mechanisms involved in low temperature responses in core Pooideae species. However, the evolutionary history of key genes involved in low temperature responses has been different in Brachypodium and core Pooideae species. These differences limit the use of B. distachyon as a model for holistic studies relevant for agricultural core Pooideae species.
Identification of pneumonia and influenza deaths using the death certificate pipeline
Authors: Davis Kailah , Staes Catherine , Duncan Jeff , Igo Sean , Facelli Julio C 
Published: May 2012

Abstract

Background
Death records are a rich source of data, which can be used to assist with public surveillance and/or decision support. However, to use this type of data for such purposes it has to be transformed into a coded format to make it computable. Because the cause of death in the certificates is reported as free text, encoding the data is currently the single largest barrier of using death certificates for surveillance. Therefore, the purpose of this study was to demonstrate the feasibility of using a pipeline, composed of a detection rule and a natural language processor, for the real time encoding of death certificates using the identification of pneumonia and influenza cases as an example and demonstrating that its accuracy is comparable to existing methods.

Results
A Death Certificates Pipeline (DCP) was developed to automatically code death certificates and identify pneumonia and influenza cases. The pipeline used MetaMap to code death certificates from the Utah Department of Health for the year 2008. The output of MetaMap was then accessed by detection rules which flagged pneumonia and influenza cases based on the Centers of Disease and Control and Prevention (CDC) case definition. The output from the DCP was compared with the current method used by the CDC and with a keyword search. Recall, precision, positive predictive value and F-measure with respect to the CDC method were calculated for the two other methods considered here. The two different techniques compared here with the CDC method showed the following recall/ precision results: DCP: 0.998/0.98 and keyword searching: 0.96/0.96. The F-measure were 0.99 and 0.96 respectively (DCP and keyword searching). Both the keyword and the DCP can run in interactive form with modest computer resources, but DCP showed superior performance.

Conclusion
The pipeline proposed here for coding death certificates and the detection of cases is feasible and can be extended to other conditions. This method provides an alternative that allows for coding free-text death certificates in real time that may increase its utilization not only in the public health domain but also for biomedical researchers and developers.

Trial Registration
This study did not involved any clinical trials.
Interferon-α enhances antitumor activities of oncolytic adenovirus-mediated IL-24 expression in hepatocellular carcinoma
Authors: Wang Cong-Jun , Xiao Chao-Wen , You Tian-Geng , Zheng Ya-Xin , Gao Wei , Zhou Zhu-Qing , Chen Jun , Xue Xin-Bo , Fan Jia , Zhang Hui 
Published: May 2012

Abstract

Background
Hepatocellular carcinoma (HCC) has a dismal 5-year-survival rate of 10%, so novel strategies are warranted. IL-24 mediates anti-tumor activity reducing STAT3 expression, which suggests that interferon (IFN) alpha may augment tumor cell lysis and reduce angiogenesis. We investigated the antitumor activity of treatment with IFN-α, with the oncolytic adenovirus SG600-IL-24, or the combination of both in HCC in vitro and in vivo.

Results
RT-PCR, ELISA assay and Western-blot confirmed that the exogenous IL-24 gene was highly expressed in HCC cells infected with SG600-IL-24. Treatment with combined IFN-α and SG600-IL-24 suppressed growth and promoted apoptosis of the HepG2, MHCC97L, and HCCLM3 cell lines compared with the normal cell line L02. The combined therapy increased STAT1 and SOCS1 and apoptosis, but decreased the expression of the metastatic and angiogenic proteins MMP-2, XIAP, OPN, and VEGF, which are regulated by STAT3 in HCC cells in vitro. To assess the effects in vivo, the HCC cell line HCCLM3 was transplanted subcutaneously into the right flanks of nude mice. Mice in the IFN-α group, the SG600-IL-24 group, or the combined therapy group had significantly suppressed growth of the HCC xenografted tumors compared to the PBS control group of mice. Among the mice treated with the combination of IFN-α and SG600-IL-24, three of those eight mice had long-term survival and no evidence of a tumor. These mice also had decreased expression of the metastatic and angiogenic proteins MMP-2, XIAP, OPN, and VEGF.

Conclusions
The present study demonstrated for the first time the potential antitumor activity of IFN-α combined with the oncolytic adenovirus SG600-IL-24 in HCC both in vitro and in vivo, and suggests its further development as a potential candidate for HCC cancer gene therapy.
Impact of obesity control on circulating level of endothelial progenitor cells and angiogenesis in response to ischemic stimulation
Authors: Chen Yung-Lung , Chang Chia-Lo , Sun Cheuk-Kwan , Wu Chiung-Jen , Tsai Tzu-Hsien , Chung Sheng-Ying , Chua Sarah , Yeh Kuo-Ho , Leu Steve , Sheu Jiunn-Jye , Lee Fan-Yen , Yen Chia-Hung , Yip Hon-Kan 
Published: May 2012

Abstract

Background and aim
We tested the hypothesis that obesity reduced circulating number of endothelial progenitor cells (EPCs), angiogenic ability, and blood flow in ischemic tissue that could be reversed after obesity control.

Methods
8-week-old C57BL/6J mice (n = 27) were equally divided into group 1 (fed with 22-week control diet), group 2 (22-week high fat diet), and group 3 (14-week high fat diet, followed by 8-week control diet). Critical limb ischemia (CLI) was induced at week 20 in groups 2 and 3. The animals were sacrificed at the end of 22 weeks.

Results
Heart weight, body weight, abdominal fat weight, serum total cholesterol level, and fasting blood sugar were highest in group 2 (all p < 0.001). The numbers of circulating EPCs (C-kit/CD31+, Sca-1/KDR + and CXCR4/CD34+) were lower in groups 1 and 2 than in group 3 at 18 h after CLI induction (p < 0.03). The numbers of differentiated EPCs (C-kit/CD31+, CXCR4/CD34+ and CD133+) from adipose tissue after 14-day cultivation were also lowest in group 2 (p < 0.001). Protein expressions of VCAM-1, oxidative index, Smad3, and TGF-β were higher, whereas the Smad1/5 and BMP-2, mitochondrial cytochrome-C SDF-1α and CXCR4 were lower in group 2 than in groups 1 and 3 (all p < 0.02). Immunofluorescent staining of CD31+ and vWF + cells, the number of small vessel (<15 μm), and blood flow through Laser Doppler scanning of ischemic area were lower in group 2 compared to groups 1 and 3 on day 14 after CLI induction (all p < 0.001).

Conclusion
Obesity suppressed abilities of angiogenesis and recovery from CLI that were reversed by obesity control.
Predictive role of multiple gene alterations in response to cetuximab in metastatic colorectal cancer: A single center study
Authors: Ulivi Paola , Capelli Laura , Valgiusti Martina , Zoli Wainer , Scarpi Emanuela , Chiadini Elisa , Rosetti Paola , Bravaccini Sara , Calistri Daniele , Saragoni Luca , Casadei Gardini Andrea , Ragazzini Angela , Frassineti Giovanni Luca , Amadori Dino , Passardi Alessandro 
Published: May 2012

AbstractBackgroundKRASmutations negatively affect outcome after treatment with cetuximab in metastatic colorectal cancer (mCRC) patients. As only 20% ofKRASwild type (WT) patients respond to cetuximab it is possible that other mutations, constitutively activating the EGFR pathway, are present in the non-respondingKRASWT patients. We retrospectively analyzed objective tumor response rate, (ORR) progression-free (PFS) and overall survival (OS) with respect to the mutational status ofKRAS,BRAF,PIK3CAand PTEN expression in mCRC patients treated with a cetuximab-based regimen.Methods67 mCRC patients were enrolled onto the study. DNA was extracted from paraffin-embedded sections derived from primary or metastatic lesions. Exon 2 ofKRASand exon 15 ofBRAFwere analyzed by direct sequencing,PIK3CAwas evaluated by pyrosequencing and PTEN expression by immunohistochemistry.ResultsBRAFandPIK3CAmutations were independently associated with worse PFS (p = 0.006 andp = 0.028, respectively) and OS (p = 0.008 andp = 0.029, respectively). No differences in clinical outcome were found between patients who were positive or negative for PTEN expression. Conversely, patients negative forKRAS,BRAFandPIK3CAmutations were characterized by significantly better ORR, PFS and OS than patients with at least one of these mutations.ConclusionsBRAFandPIK3CAmutations would seem to be independent predictors of anti-EGFR therapy effectiveness and could be taken into consideration during treatment decision making.
Common fixed point and approximation results for generalized (f, g)-weak contractions
Authors: Akbar Farhana , Khan Abdul Rahim , Sultana Nazra 
Published: May 2012

AbstractThe existence of common fixed points is established for three mappings whereTis generalized (f,g)-weakly contractive mapping on a nonempty subset of a Banach space. As applications, the invariant approximation results are proved. Our results unify and improve several recent results in the literature.Mathematics Subject Classification 2000:Primary, 47H10; 54H25; 47E10.
Histamine modulates microglia function
Authors: Ferreira Raquel , Santos Tiago , Gonçalves Joana , Baltazar Graça , Ferreira Lino , Agasse Fabienne , Bernardino Liliana 
Published: May 2012

Abstract

Background
Histamine is commonly acknowledged as an inflammatory mediator in peripheral tissues, leaving its role in brain immune responses scarcely studied. Therefore, our aim was to uncover the cellular and molecular mechanisms elicited by this molecule and its receptors in microglia-induced inflammation by evaluating cell migration and inflammatory mediator release.

Methods
Firstly, we detected the expression of all known histamine receptor subtypes (H1R, H2R, H3R and H4R), using a murine microglial cell line and primary microglia cell cultures from rat cortex, by real-time PCR analysis, immunocytochemistry and Western blotting. Then, we evaluated the role of histamine in microglial cell motility by performing scratch wound assays. Results were further confirmed using murine cortex explants. Finally, interleukin-1beta (IL-1β) and tumor necrosis factor-alpha (TNF-α) levels were evaluated by ELISA measurements to determine the role of histamine on the release of these inflammatory mediators.

Results
After 12 h of treatment, 100 μM histamine and 10 μg/ml histamine-loaded poly (lactic-co-glycolic acid) microparticles significantly stimulated microglia motility via H4R activation. In addition, migration involves α5β1 integrins, and p38 and Akt signaling pathways. Migration of microglial cells was also enhanced in the presence of lipopolysaccharide (LPS, 100 ng/ml), used as a positive control. Importantly, histamine inhibited LPS-stimulated migration via H4R activation. Histamine or H4R agonist also inhibited LPS-induced IL-1β release in both N9 microglia cell line and hippocampal organotypic slice cultures.

Conclusions
To our knowledge, we are the first to show a dual role of histamine in the modulation of microglial inflammatory responses. Altogether, our data suggest that histamine per se triggers microglia motility, whereas histamine impedes LPS-induced microglia migration and IL-1β release. This last datum assigns a new putative anti-inflammatory role for histamine, acting via H4R to restrain exacerbated microglial responses under inflammatory challenge, which could have strong repercussions in the treatment of CNS disorders accompanied by microglia-derived inflammation.
Molecular characterization of Umbre virus (Bunyaviridae)
Authors: Yadav Pragya D , Mishra Akhilesh C , Mourya Devendra T 
Published: May 2012

Abstract
Umbre (UMB) virus was first isolated from India in 1955 and classified as Orthobunyavirus (Turlock serogroup). Eight isolates of this virus, isolated from Culex mosquitoes were characterized on the basis of partial glycoprotein (G2) gene. Twenty-six percent differences at nucleotide level while 17% differences at amino acid level were noted within different isolates. Phylogentic data shows that this virus represents a distinct group within the genus Orthobunyavirus.
Respiratory syncytial virus (RSV) attachment and nonstructural proteins modify the type I interferon response associated with suppressor of cytokine signaling (SOCS) proteins and IFN-stimulated gene-15 (ISG15)
Authors: Moore Elizabeth C , Barber Jamie , Tripp Ralph A 
Published: May 2012

AbstractRespiratory syncytial virus (RSV) is a major cause of severe lower airway disease in infants and young children, but no safe and effective RSV vaccine is yet available. Factors attributing to this problem are associated with an incomplete understanding of the mechanisms by which RSV modulates the host cell response to infection. In the present study, we investigate suppressor of cytokine signaling (SOCS)-1 and SOCS3 expression associated with the type I IFN and IFN-stimulated gene (ISG)-15 response following infection of mouse lung epithelial (MLE-15) cells with RSV or RSV mutant viruses lacking the G gene, or NS1 and NS2 gene deletions. Studies in MLE-15 cells are important as this cell line represents the distal bronchiolar and alveolar epithelium of mice, the most common animal model used to evaluate the host cell response to RSV infection, and exhibit morphologic characteristics of alveolar type II cells, a primary cell type targeted during RSV infection. These results show an important role for SOCS1 regulation of the antiviral host response to RSV infection, and demonstrate a novel role for RSV G protein manipulation of SOCS3 and modulation of ISG15 and IFNβ mRNA expression.
Developing effective chronic disease interventions in Africa: insights from Ghana and Cameroon
Authors: de-Graft Aikins Ama , Boynton Petra , Atanga Lem L 
Published: May 2012

AbstractBackgroundAfrica faces an urgent but 'neglected epidemic' of chronic disease. In some countries stroke, hypertension, diabetes and cancers cause a greater number of adult medical admissions and deaths compared to communicable diseases such as HIV/AIDS or tuberculosis. Experts propose a three-pronged solution consisting of epidemiological surveillance, primary prevention and secondary prevention. In addition, interventions must be implemented through 'multifaceted multi-institutional' strategies that make efficient use of limited economic and human resources. Epidemiological surveillance has been prioritised over primary and secondary prevention. We discuss the challenge of developing effective primary and secondary prevention to tackle Africa's chronic disease epidemic through in-depth case studies of Ghanaian and Cameroonian responses.MethodsA review of chronic disease research, interventions and policy in Ghana and Cameroon instructed by an applied psychology conceptual framework. Data included published research and grey literature, health policy initiatives and reports, and available information on lay community responses to chronic diseases.ResultsThere are fundamental differences between Ghana and Cameroon in terms of 'multi-institutional and multi-faceted responses' to chronic diseases. Ghana does not have a chronic disease policy but has a national health insurance policy that covers drug treatment of some chronic diseases, a culture of patient advocacy for a broad range of chronic conditions and mass media involvement in chronic disease education. Cameroon has a policy on diabetes and hypertension, has established diabetes clinics across the country and provided training to health workers to improve treatment and education, but lacks community and media engagement. In both countries churches provide public education on major chronic diseases. Neither country has conducted systematic evaluation of the impact of interventions on health outcomes and cost-effectiveness.ConclusionsBoth Ghana and Cameroon require a comprehensive and integrative approach to chronic disease intervention that combines structural, community and individual strategies. We outline research and practice gaps and best practice models within and outside Africa that can instruct the development of future interventions.
Association of umbilical cord blood lead with neonatal behavior at varying levels of exposure
Authors: Patel Archana B , Mamtani Manju R , Thakre Tushar P , Kulkarni Hemant 
Published: May 2012

AbstractBackgroundIn the light of the ongoing debate about lowering the cut-off for acceptable blood lead level to <5 μg/dL from the currently recommended level of <10 μg/dL, we considered whether prenatal exposure to varying levels of lead is associated with similar or disparate effects on neonatal behavior.MethodsUsing Brazelton's Neonatal Behavioral Assessment Scale (NBAS), an epidemiological approach and robust statistical techniques like multivariate linear regression, logistic regression, Poisson regression and structural equations modeling analyses we estimated the simultaneous indirect effects of umbilical cord blood lead (CBL) levels and other neonatal covariates on the NBAS clusters.ResultsWe observed that when analyzed in all study subjects, the CBL levels independently and strongly influenced autonomic stability and abnormal reflexes clusters. However, when the analysis was restricted to neonates with CBL <10 μg/dL, CBL levels strongly influenced the range of state, motor and autonomic stability clusters. Abnormal walking reflex was consistently associated with an increased CBL level irrespective of the cut-off for CBL, however, only at the lower cut-offs were the predominantly behavioral effects of CBL discernible.ConclusionOur results further endorse the need to be cognizant of the detrimental effects of blood lead on neonates even at a low-dose prenatal exposure.