bluuebunny/crossref_metadata_2025_split huggingface dataset:
miRNA164-directed cleavage of ZmNAC1 confers lateral root development in maize (Zea maysL.)
Authors: Li Jing , Guo Guanghui , Guo Weiwei , Guo Ganggang , Tong Dan , Ni Zhongfu , Sun Qixin , Yao Yingyin 
Published: November 2012

Abstract

Background
MicroRNAs are a class of small, non-coding RNAs that regulate gene expression by binding target mRNA, which leads to cleavage or translational inhibition. The NAC proteins, which include NAM, ATAF, and CUC, are a plant-specific transcription factor family with diverse roles in development and stress regulation. It has been reported that miR164 negatively regulates NAC1 expression, which in turn affects lateral root development in Arabidopsis; however, little is known about the involvement of the maize NAC family and miR164 in lateral root development.

Results
We collected 175 maize transcripts with NAC domains. Of these, 7 ZmNACs were putative targets for regulation by miR164. We isolated one gene, called TC258020 (designated ZmNAC1) from 2 maize inbred lines, 87-1 and Zong3. ZmNAC1 had a high expression level in roots and showed higher abundance (1.8 fold) in Zong3 relative to 87-1, which had less lateral roots than Zong3. There was a significant correlation between the expression level of ZmNAC1 and the lateral root density in the recombinant inbred line (RIL) population. Transgenic Arabidopsis that overexpressed ZmNAC1 had increased lateral roots in comparison to the wild type. These findings suggest that ZmNAC1 played a significant role in lateral root development. An allelic expression assay showed that trans-regulatory elements were the dominant mediators of ZmNAC1 differential expression in 87-1 and Zong3, and further analysis revealed that miR164 was a trans-element that guided the cleavage of endogenous ZmNAC1 mRNA. Both mature miR164 and miR164 precursors had higher expression in 87-1 than Zong3, which was the opposite of the expression pattern of ZmNAC1. Additionally, the allelic assay showed that the cis-regulatory element most likely affected Zm-miR164b's expression pattern. A β-glucuronidase (GUS) assay showed that the Zm-miR164b promoter had higher GUS activity in 87-1 than in Zong3. In addition, we detected miR164b expression in the RIL population, and the results indicated that miR164b had a higher expression level in the RILs containing 87-1 promoter than those containing Zong3 promoter.

Conclusion
Our results indicate one possible pathway in maize by which differences in miR164b promoter activity resulted in a different expression pattern for mature miR164 which negatively regulates ZmNAC1 expression in 87-1 and Zong3, thereby contributing to a significantly different lateral root phenotype.
Molecular characterization of LMW-GS genes in Brachypodium distachyon L. reveals highly conserved Glu-3 loci in Triticum and relatedspecies
Authors: Wang Shunli , Wang Ke , Chen Guanxing , Lv Dongwen , Han Xiaofeng , Yu Zitong , Li Xiaohui , Ye Xingguo , Hsam SLK , Ma Wujun , Appels Rudi , Yan Yueming 
Published: November 2012

Abstract

Background

Brachypodium distachyon L. is a newly emerging model plant system for temperate cereal crop species. However, its grain protein compositions are still not clear. In the current study, we carried out a detailed proteomics and molecular genetics study on grain glutenin proteins in B. distachyon.

Results
SDS-PAGE and RP-HPLC analysis of grain proteins showed that Brachypodium has few gliadins and high molecular weight glutenin subunits. In contrast the electrophoretic patterns for the albumin, globulin and low molecular weight glutenin subunit (LMW-GS) fractions of the grain protein were similar to those in wheat. In particular, the LMW-C type subunits in Brachypodium were more abundant than the equivalent proteins in common wheat. Southern blotting analysis confirmed that Brachypodium has 4–5 copies of LMW-GS genes. A total of 18 LMW-GS genes were cloned from Brachypodium by allele specific PCR. LMW-GS and 4 deduced amino acid sequences were further confirmed by using Western-blotting and MALDI-TOF-MS. Phylogenetic analysis indicated that Brachypodium was closer to Ae. markgrafii and Ae. umbellulata than to T. aestivum.

Conclusions

Brachypodium possessed a highly conserved Glu-3 locus that is closely related to Triticum and related species. The presence of LMW-GS in B. distachyon grains indicates that B. distachyon may be used as a model system for studying wheat quality attributes.
Deep-sequencing transcriptome analysis of chilling tolerance mechanisms of a subnival alpine plant, Chorispora bungeana
Authors: Zhao Zhiguang , Tan Lingling , Dang Chunyan , Zhang Hua , Wu Qingbai , An Lizhe 
Published: November 2012

AbstractBackgroundThe plant tolerance mechanisms to low temperature have been studied extensively in the model plant Arabidopsis at the transcriptional level. However, few studies were carried out in plants with strong inherited cold tolerance.Chorispora bungeanais a subnival alpine plant possessing strong cold tolerance mechanisms. To get a deeper insight into its cold tolerance mechanisms, the transcriptome profiles of chilling-treatedC. bungeanaseedlings were analyzed by Illumina deep-sequencing and compared with Arabidopsis.ResultsTwo cDNA libraries constructed from mRNAs of control and chilling-treated seedlings were sequenced by Illumina technology. A total of 54,870 unigenes were obtained byde novoassembly, and 3,484 chilling up-regulated and 4,571 down-regulated unigenes were identified. The expressions of 18 out of top 20 up-regulated unigenes were confirmed by qPCR analysis. Functional network analysis of the up-regulated genes revealed some common biological processes, including cold responses, and molecular functions inC. bungeanaand Arabidopsis responding to chilling. Karrikins were found as new plant growth regulators involved in chilling responses ofC. bungeanaand Arabidopsis. However, genes involved in cold acclimation were enriched in chilling up-regulated genes in Arabidopsis but not inC. bungeana.In addition, although transcription activations were stimulated in bothC. bungeanaand Arabidopsis, noCBFputative ortholog was up-regulated inC. bungeanawhileCBF2andCBF3were chilling up-regulated in Arabidopsis. On the other hand, up-regulated genes related to protein phosphorylation and auto-ubiquitination processes were over-represented inC. bungeanabut not in Arabidopsis.ConclusionsWe conducted the first deep-sequencing transcriptome profiling and chilling stress regulatory network analysis ofC. bungeana, a subnival alpine plant with inherited cold tolerance. Comparative transcriptome analysis suggests that cold acclimation is not a major chilling tolerance mechanism ofC. bungeana. Activation of protein phosphorylation and ubiquitination may confer chilling tolerance toC. bungeanain a more rapid and flexible way than cold acclimation. Such differences may have contributed to the differences in cold tolerance betweenC. bungeanaand Arabidopsis. The results presented in this paper will be informative for gene discovery and the molecular mechanisms related to plant cold tolerance.
Aberrant expression of CD133 in non-small cell lung cancer and its relationship to vasculogenic mimicry
Authors: Wu Shiwu , Yu Lan , Wang Danna , Zhou Lei , Cheng Zenong , Chai Damin , Ma Li , Tao Yisheng 
Published: November 2012

AbstractBackgroundTo investigate on expressions and clinical significances of CD133 protein and vasculogenic mimicry (VM) in primary non-small cell lung cancer (NSCLC).MethodsThe specimens of NSCLC from 305 Chinese patients with follow-up were analyzed for CD133 protein expression and VM by immunohistochemical and histochemical staining.ResultsIn NSCLC, positive rates of 48.9% and 35.7% were obtained for CD133 and VM, respectively. The VM and expression of CD133 were significantly higher in carcinoma than in normal. There were a positive relationship between the VM and expression of CD133 and the tumor grade, lymph node metastasis and clinical stage (all P<0.05). The overall mean survival time of the patients with CD133 and VM positive expression was lower than that of patients with negative expression. Microvessel density (MVD) was positive corresponded with the grade, lymph node metastasis and clinical stage (all P<0.05). The overall mean survival time of the patients with MVD≥22’s group was shorter than that of patients with MVD<22’s group. Pathological-tumor-node-metastasis (pTNM) stage, positive expression of CD133 and VM, postoperative therapy and MVD were independent prognostic factors of NSCLC (P<0.05). Immunohistochemistry revealed an important intratumoral heterogeneity in all four CD133 expression profiles.ConclusionsVM, MVD and expression of CD133 are related to differentiation, lymph node metastasis, clinical stage, and prognosis. It is suggested that CD133, VM and MVD should be considered as a potential marker for the prognosis.
Phase I study of TP300 in patients with advanced solid tumors with pharmacokinetic, pharmacogenetic and pharmacodynamic analyses
Authors: Anthoney D Alan , Naik Jay , MacPherson Iain RJ , Crawford Donna , Hartley John M , Hartley Janet A , Saito Tomohisa , Abe Masaichi , Jones Keith , Miwa Masanori , Twelves Christopher , Evans TRJ 
Published: November 2012

Abstract

Background
A Phase I dose escalation first in man study assessed maximum tolerated dose (MTD), dose-limiting toxicity (DLT) and recommended Phase II dose of TP300, a water soluble prodrug of the Topo-1 inhibitor TP3076, and active metabolite, TP3011.

Methods
Eligible patients with refractory advanced solid tumors, adequate performance status, haematologic, renal, and hepatic function. TP300 was given as a 1-hour i.v. infusion 3-weekly and pharmacokinetic (PK) profiles of TP300, TP3076 and TP3011 were analysed. Polymorphisms in CYP2D6, AOX1 and UGT1A1 were studied and DNA strand-breaks measured in peripheral blood mononuclear cells (PBMCs).

Results
32 patients received TP300 at 1, 2, 4, 6, 8, 10, 12 mg/m2. MTD was 10 mg/m2; DLTs at 12 (2/4 patients) and 10 mg/m2 (3/12) included thrombocytopenia and febrile neutropenia; diarrhoea was uncommon. Six patients (five had received irinotecan), had stable disease for 1.5-5 months. TP3076 showed dose proportionality in AUC and Cmax from 1–10 mg/m2. Genetic polymorphisms had no apparent influence on exposure. DNA strand-breaks were detected after TP300 infusion.

Conclusions
TP300 had predictable hematologic toxicity, and diarrhoea was uncommon. AUC at MTD is substantially greater than for SN38. TP3076 and TP3011 are equi-potent with SN38, suggesting a PK advantage.

Trial registration
EU-CTR2006-001345-33
A cluster randomised trial of a school-based resilience intervention to decrease tobacco, alcohol and illicit drug use in secondary school students: study protocol
Authors: Hodder Rebecca K , Freund Megan , Bowman Jenny , Wolfenden Luke , Campbell Elizabeth , Wye Paula , Hazell Trevor , Gillham Karen , Wiggers John 
Published: November 2012

Abstract

Background
Whilst schools provide a potentially appropriate setting for preventing substance use among young people, systematic review evidence suggests that past interventions in this setting have demonstrated limited effectiveness in preventing tobacco, alcohol and other drug use. Interventions that adopt a mental wellbeing approach to prevent substance use offer considerable promise and resilience theory provides one method to impact on adolescent mental well-being. The aim of the proposed study is to examine the efficacy of a resilience intervention in decreasing the tobacco, alcohol and illicit drug use of adolescents.

Methods
A cluster randomised controlled trial with schools as the unit of randomisation will be undertaken. Thirty two schools in disadvantaged areas will be allocated to either an intervention or a control group. A comprehensive resilience intervention will be implemented, inclusive of explicit program adoption strategies. Baseline surveys will be conducted with students in Grade 7 in both groups and again three years later when the student cohort is in Grade 10. The primary outcome measures will include self-reported tobacco, alcohol, marijuana and other illicit drug use. Comparisons will be made post-test between Grade 10 students in intervention and control schools to determine intervention effectiveness across all measures.

Discussion
To the authors’ knowledge this is the first randomised controlled trial to evaluate the effectiveness of a comprehensive school-based resilience intervention, inclusive of explicit adoption strategies, in decreasing tobacco, alcohol and illicit drug use of adolescents attending disadvantaged secondary schools.

Trial registration
ACTRN12611000606987
User fee exemptions and excessive household spending for normal delivery in Burkina Faso: the need for careful implementation
Authors: Ameur Amal Ben , Ridde Valéry , Bado Aristide R , Ingabire Marie-Gloriose , Queuille Ludovic 
Published: November 2012

Abstract

Background
In 2006, the Parliament of Burkina Faso passed a policy to reduce the direct costs of obstetric services and neonatal care in the country’s health centres, aiming to lower the country’s high national maternal mortality and morbidity rates. Implementation was via a “partial exemption” covering 80% of the costs. In 2008 the German NGO HELP launched a pilot project in two health districts to eliminate the remaining 20% of user fees. Regardless of any exemptions, women giving birth in Burkina Faso’s health centres face additional expenses that often represent an additional barrier to accessing health services. We compared the total cost of giving birth in health centres offering partial exemption versus those with full exemption to assess the impact on additional out-of-pocket fees.

Methods
A case–control study was performed to compare medical expenses. Case subjects were women who gave birth in 12 health centres located in the Dori and Sebba districts, where HELP provided full fee exemption for obstetric services and neonatal care. Controls were from six health centres in the neighbouring Djibo district where a partial fee exemption was in place. A random sample of approximately 50 women per health centre was selected for a total of 870 women.

Results
There was an implementation gap regarding the full exemption for obstetric services and neonatal care. Only 1.1% of the sample from Sebba but 17.5% of the group from Dori had excessive spending on birth related costs, indicating that women who delivered in Sebba were much less exposed to excessive medical expenses than women from Dori. Additional out-of-pocket fees in the full exemption health districts took into account household ability to pay, with poorer women generally paying less.

Conclusions
We found that the elimination of fees for facility-based births benefits especially the poorest households. The existence of excessive spending related to direct costs of giving birth is of concern, making it urgent for the government to remove all direct fees for obstetric and neonatal care. However, the policy of completely abolishing user fees is insufficient; the implementation process must have a thorough monitoring system to reduce implementation gaps.
Novel cancerization marker, TP53, and its role in distinguishing normal tissue adjacent to cancerous tissue from normal tissue adjacent to benign tissue
Authors: Liu Guo-Yan , Liu Kun-Hong , Li Yin , Pan Chao , Su Ji-Qin , Liao Hong-Feng , Yv Ren-Xiang , Li Zhao-Hui , Yuan Li , Zhang Huan-Jing , Tzeng Chi-Meng , Xiong Bing 
Published: November 2012

Abstract

Background
The histopathological and molecular heterogeneity of normal tissue adjacent to cancerous tissue (NTAC) and normal tissue adjacent to benign tissue (NTAB), and the availability of limited specimens make deciphering the mechanisms of carcinogenesis challenging. Our goal was to identify histogenetic biomarkers that could be reliably used to define a transforming fingerprint using RNA in situ hybridization.

Methods
We evaluated 15 tumor-related RNA in situ hybridization biomarkers using tumor microarray and samples of seven tumor-adjacent normal tissues from 314 patients. Biomarkers were determined using comprehensive statistical methods (significance of support vector machine-based artificial intelligence and area under curve scoring of classification distribution).

Results

TP53 was found to be a most reliable index (P <10-7; area under curve >87%) for distinguishing NTAC from NTAB, according to the results of a significance panel (BCL10, BECN1, BRCA2, FITH, PTCH11 and TP53).

Conclusions
The genetic alterations in TP53 between NTAC and NTAB may provide new insight into the field of cancerization and tumor transformation.
Prothrombotic gene variants as risk factors of acute myocardial infarction in young women
Authors: Tomaiuolo Rossella , Bellia Chiara , Caruso Antonietta , Di Fiore Rosanna , Quaranta Sandro , Noto Davide , Cefalù Angelo B , Di Micco Pierpaolo , Zarrilli Federica , Castaldo Giuseppe , Averna Maurizio R , Ciaccio Marcello 
Published: November 2012

Abstract

Background
Acute myocardial infarction (AMI) in young women represent an extreme phenotype associated with a higher mortality compared with similarly aged men. Prothrombotic gene variants could play a role as risk factors for AMI at young age.

Methods
We studied Factor V Leiden, FII G20210A, MTHFR C677T and beta-fibrinogen -455G>A variants by real-time PCR in 955 young AMI (362 females) and in 698 AMI (245 females) patients. The data were compared to those obtained in 909 unrelated subjects (458 females) from the general population of the same geographical area (southern Italy).

Results
In young AMI females, the allelic frequency of either FV Leiden and of FII G20210A was significantly higher versus the general population (O.R.: 3.67 for FV Leiden and O.R.: 3.84 for FII G20210A; p<0.001). Among AMI patients we showed only in males that the allelic frequency of the MTHFR C677T variant was significantly higher as compared to the general population. Such difference was due to a significantly higher frequency in AMI males of the MTHFR C677T variant homozygous genotype (O.R. 3.05).

Discussion and conclusion
Our data confirm that young AMI in females is a peculiar phenotype with specific risk factors as the increased plasma procoagulant activity of FV and FII. On the contrary, the homozygous state for the 677T MTHFR variant may cause increased levels of homocysteine and/or an altered folate status and thus an increased risk for AMI, particularly in males. The knowledge of such risk factors (that may be easily identified by molecular analysis) may help to improve prevention strategies for acute coronary diseases in specific risk-group subjects.
Facile synthesis of hollow Cu2O octahedral and spherical nanocrystals and their morphology-dependent photocatalytic properties
Authors: Feng Lili , Zhang Chunlei , Gao Guo , Cui Daxiang 
Published: November 2012

Abstract
Herein, we report that octahedral and spherical Cu2O samples with hollow structures are synthesized in high yield by reducing Cu(EDA)2
2+ complex with hydrazine. A series of experiments are carried out to investigate the factors which impact on the morphology of the Cu2O samples. It is observed that ethylenediamine (EDA) serves as a molecular template in the formation of hollow structure. Octahedral Cu2O with solid structure is prepared without EDA. When EDA is added, Cu2O sample with hollow structure is formed. Different morphologies of Cu2O such as spherical and octahedral could be obtained by adjusting the concentration of EDA and NaOH. The temporal crystal growth mechanism is proposed. Furthermore, the photocatalytic activities of the as-prepared Cu2O nanoparticles are evaluated by monitoring two dyes (methyl orange and congo red) using UV-visible spectrophotometer. Results show that the order of photocatalytic activity of Cu2O with different morphologies is as follows: hollow octahedral morphology > hollow sphere morphology > solid octahedral morphology. The hollow octahedral Cu2O nanoparticles would be a promising material on applications for photocatalytic degradation of organic pollutants.
Synthesis and characterization of titanium complex with a dithiolate ligand for green LCD color filter dyes
Authors: Shin Hwangyu , Park Youngil , Kim Seungho , An Byeong-Kwan , Park Jongwook 
Published: November 2012

Abstract
Three green compounds for color filter dyes based on bis(cyclopentadienyl) titanium complexes including dithiolate ligand were synthesized. Physical properties by the change of the substitution groups of the synthesized materials were systematically examined. UV-visible absorption spectrum of the synthesized materials showed maximum absorbing wavelengths of 427 to 430 nm and 632 to 635 nm in solution state, and 434 to 438 nm and 637 to 651 nm in film state, indicating green and black colors. It was observed that the extinction coefficient values (log ε) of all the synthesized materials are very high at 4.0 or above. In addition, it was shown that since the T
d values of three synthesized materials show thermal stability higher than 240°C, they possess high potential to be applied as dyes for LCD color filter and black matrix addictive.
High-rate systematic recursive convolutional encoders: minimal trellis and code search
Authors: Benchimol Isaac , Pimentel Cecilio , Souza Richard Demo , Uchôa-Filho Bartolomeu F 
Published: November 2012

Abstract
We consider high-rate systematic recursive convolutional encoders to be adopted as constituent encoders in turbo schemes. Douillard and Berrou showed that, despite its complexity, the construction of high-rate turbo codes by means of high-rate constituent encoders is advantageous over the construction based on puncturing rate-1/2 constituent encoders. To reduce the decoding complexity of high-rate codes, we introduce the construction of the minimal trellis for a systematic recursive convolutional encoding matrix. A code search is conducted and examples are provided which indicate that a more finely grained decoding complexity-error performance trade-off is obtained.
Methodological quality of English-language genetic guidelines on hereditary breast-cancer screening and management: an evaluation using the AGREE instrument
Authors: Simone Benedetto , De Feo Emma , Nicolotti Nicola , Ricciardi Walter , Boccia Stefania 
Published: November 2012

Abstract

Background
We examined the methodological quality of guidelines on syndromes conferring genetic susceptibility to breast cancer.

Methods
PubMed, EMBASE, and Google were searched for guidelines published up to October 2010. All guidelines in English were included. The Appraisal of Guidelines, Research and Evaluation (AGREE) instrument was used to assess the quality of the guidelines, and their reported evidence base was evaluated.

Results
Thirteen guidelines were deemed eligible: seven had been developed by independent associations, and the other six had national/state endorsements. Four guidelines performed satisfactorily, achieving a score of greater than 50% in all six AGREE domains. Mean ± SD standardized scores for the six AGREE domains were: 90 ± 9% for 'scope and purpose', 51 ± 18% for 'stakeholder involvement', 55 ± 27% for 'rigour of development', 80 ± 11% for 'clarity and presentation', 37 ± 32% for 'applicability', and 47 ± 38% for 'editorial independence'. Ten of the thirteen guidelines were found to be based on research evidence.

Conclusions
Given the ethical implications and the high costs of genetic testing for hereditary breast cancer, guidelines on this topic should provide clear and evidence-based recommendations. Our analysis shows that there is scope for improving many aspects of the methodological quality of current guidelines. The AGREE instrument is a useful tool, and could be used profitably by guidelines developers to improve the quality of recommendations.