bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and analysis of MKK and MPK gene families in canola (Brassica napusL.)
Authors: Liang Wanwan , Yang Bo , Yu Bao-Jun , Zhou Zili , Li Cui , Jia Ming , Sun Yun , Zhang Yue , Wu Feifei , Zhang Hanfeng , Wang Boya , Deyholos Michael K , Jiang Yuan-Qing 
Published: June 2013

AbstractBackgroundEukaryotic mitogen-activated protein kinase (MAPK/MPK) signaling cascades transduce and amplify environmental signals via three types of reversibly phosphorylated kinases to activate defense gene expression. Canola (oilseed rape,Brassica napus) is a major crop in temperate regions. Identification and characterization of MAPK and MAPK kinases (MAPKK/MKK) of canola will help to elucidate their role in responses to abiotic and biotic stresses.ResultsWe describe the identification and analysis of sevenMKK(BnaMKK) and 12MPK(BnaMPK) members from canola. Sequence alignments and phylogenetic analyses of the predicted amino acid sequences of BnaMKKs and BnaMPKs classified them into four different groups. We also examined the subcellular localization of four and two members of BnaMKK and BnaMPK gene families, respectively, using green fluorescent protein (GFP) and, found GFP signals in both nuclei and cytoplasm. Furthermore, we identified several interesting interaction pairs through yeast two-hybrid (Y2H) analysis of interactions between BnaMKKs and BnaMPKs, as well as BnaMPK and BnaWRKYs. We defined contiguous signaling modules including BnaMKK9-BnaMPK1/2-BnaWRKY53, BnaMKK2/4/5-BnaMPK3/6-BnaWRKY20/26 and BnaMKK9-BnaMPK5/9/19/20. Of these, several interactions had not been previously described in any species. Selected interactions were validatedin vivoby a bimolecular fluorescence complementation (BiFC) assay. Transcriptional responses of a subset of canola MKK and MPK genes to stimuli including fungal pathogens, hormones and abiotic stress treatments were analyzed through real-time RT-PCR and we identified a few ofBnaMKKsandBnaMPKsresponding to salicylic acid (SA), oxalic acid (OA),Sclerotinia sclerotiorumor other stress conditions. Comparisons of expression patterns of putative orthologs in canola and Arabidopsis showed that transcript expression patterns were generally conserved, with some differences suggestive of sub-functionalization.ConclusionsWe identified sevenMKKand 12MPKgenes from canola and examined their phylogenetic relationships, transcript expression patterns, subcellular localization, and protein-protein interactions. Not all expression patterns and interactions were conserved between canola and Arabidopsis, highlighting the limitations of drawing inferences about crops from model species. The data presented here provide the first systematic description of MKK-MPK-WRKY signaling modules in canola and will further improve our understanding of defense responses in general and provide a basis for future crop improvement.
Changes in the concentrations of biochemical indicators of diet and nutritional status of pregnant women across pregnancy trimesters in Trujillo, Peru, 2004–2005
Authors: Horton D Kevin , Adetona Olorunfemi , Aguilar-Villalobos Manuel , Cassidy Brandon E , Pfeiffer Christine M , Schleicher Rosemary L , Caldwell Kathleen L , Needham Larry L , Rathbun Stephen L , Vena John E , Naeher Luke P 
Published: June 2013

Abstract

Background
In developing countries, deficiencies in essential micronutrients are common, particularly in pregnant women. Although, biochemical indicators of diet and nutrition are useful to assess nutritional status, few studies have examined such indicators throughout pregnancy in women in developing countries.

Methods
The primary objective of this study was to assess the nutritional status of 78 Peruvian women throughout pregnancy for 16 different nutritional indicators including fat-soluble vitamins and carotenoids, iron-status indicators, and selenium. Venous blood samples from which serum was prepared were collected during trimesters one (n = 78), two (n = 65), three (n = 62), and at term via the umbilical cord (n = 52). Questionnaires were completed to determine the demographic characteristics of subjects. Linear mixed effects models were used to study the associations between each maternal indicator and the demographic characteristics.

Results
None of the women were vitamin A and E deficient at any stage of pregnancy and only 1/62 women (1.6%) was selenium deficient during the third trimester. However, 6.4%, 44% and 64% of women had ferritin levels indicative of iron deficiency during the first, second and third trimester, respectively. Statistically significant changes (p ≤ 0.05) throughout pregnancy were noted for 15/16 nutritional indicators for this Peruvian cohort, with little-to-no association with demographic characteristics. Three carotenoids (beta-carotene, beta-cryptoxanthin and trans-lycopene) were significantly associated with education status, while trans-lycopene was associated with age and beta-cryptoxanthin with SES (p < 0.05). Concentrations of retinol, tocopherol, beta-cryptoxanthin, lutein + zeaxanthin and selenium were lower in cord serum compared with maternal serum (p < 0.05). Conversely, levels of iron status indicators (ferritin, transferrin saturation and iron) were higher in cord serum (p < 0.05).

Conclusion
The increasing prevalence of iron deficiency throughout pregnancy in these Peruvian women was expected. It was surprising though not to find deficiencies in other nutrients. The results highlight the importance of continual monitoring of women throughout pregnancy for iron deficiency which could be caused by increasing fetal needs and/or inadequate iron intake as pregnancy progresses.
A panel study of occupational exposure to fine particulate matter and changes in DNA methylation over a single workday and years worked in boilermaker welders
Authors: Kile Molly L , Fang Shona , Baccarelli Andrea A , Tarantini Letizia , Cavallari Jennifer , Christiani David C 
Published: June 2013

Abstract

Background
Exposure to pollutants including metals and particulate air pollution can alter DNA methylation. Yet little is known about intra-individual changes in DNA methylation over time in relationship to environmental exposures. Therefore, we evaluated the effects of acute- and chronic metal-rich PM2.5 exposures on DNA methylation.

Methods
Thirty-eight male boilermaker welders participated in a panel study for a total of 54 person days. Whole blood was collected prior to any welding activities (pre-shift) and immediately after the exposure period (post-shift). The percentage of methylated cytosines (%mC) in LINE-1, Alu, and inducible nitric oxide synthase gene (iNOS) were quantified using pyrosequencing. Personal PM2.5 (particulate matter with an aerodynamic diameter ≤ 2.5 μm) was measured over the work-shift. A questionnaire assessed job history and years worked as a boilermaker. Linear mixed models with repeated measures evaluated associations between DNA methylation, PM2.5 concentration (acute exposure), and years worked as a boilermaker (chronic exposure).

Results
PM2.5 exposure was associated with increased methylation in the promoter region of the iNOS gene (β = 0.25, SE: 0.11, p-value = 0.04). Additionally, the number of years worked as a boilermaker was associated with increased iNOS methylation (β = 0.03, SE: 0.01, p-value = 0.03). No associations were observed for Alu or LINE-1.

Conclusions
Acute and chronic exposure to PM2.5 generated from welding activities was associated with a modest change in DNA methylation of the iNOS gene. Future studies are needed to confirm this association and determine if the observed small increase in iNOS methylation are associated with changes in NO production or any adverse health effect.
Pseudomonas aeruginosa NfsB and nitro-CBI-DEI – a promising enzyme/prodrug combination for gene directed enzyme prodrug therapy
Authors: Green Laura K , Syddall Sophie P , Carlin Kendall M , Bell Glenn D , Guise Christopher P , Mowday Alexandra M , Hay Michael P , Smaill Jeffrey B , Patterson Adam V , Ackerley David F 
Published: June 2013

Abstract

Background
The nitro-chloromethylbenzindoline prodrug nitro-CBI-DEI appears a promising candidate for the anti-cancer strategy gene-directed enzyme prodrug therapy, based on its ability to be converted to a highly cytotoxic cell-permeable derivative by the nitroreductase NfsB from Escherichia coli. However, relative to some other nitroaromatic prodrugs, nitro-CBI-DEI is a poor substrate for E. coli NfsB. To address this limitation we evaluated other nitroreductase candidates from E. coli and Pseudomonas aeruginosa.

Findings
Initial screens of candidate genes in the E. coli reporter strain SOS-R2 identified two additional nitroreductases, E. coli NfsA and P. aeruginosa NfsB, as being more effective activators of nitro-CBI-DEI than E. coli NfsB. In monolayer cytotoxicity assays, human colon carcinoma (HCT-116) cells transfected with P. aeruginosa NfsB were >4.5-fold more sensitive to nitro-CBI-DEI than cells expressing either E. coli enzyme, and 23.5-fold more sensitive than untransfected HCT-116. In three dimensional mixed cell cultures, not only were the P. aeruginosa NfsB expressing cells 540-fold more sensitive to nitro-CBI-DEI than pure cultures of untransfected HCT-116, the activated drug that they generated also displayed an unprecedented local bystander effect.

Conclusion
We posit that the discrepancy in the fold-sensitivity to nitro-CBI-DEI between the two and three dimensional cytotoxicity assays stems from loss of activated drug into the media in the monolayer cultures. This emphasises the importance of evaluating high-bystander GDEPT prodrugs in three dimensional models. The high cytotoxicity and bystander effect exhibited by the NfsB_Pa/nitro-CBI-DEI combination suggest that further preclinical development of this GDEPT pairing is warranted.
A generalized weak contraction principle with applications to coupled coincidence point problems
Authors: Choudhury Binayak S , Metiya Nikhilesh , Postolache Mihai 
Published: June 2013

Abstract
In this paper we establish some coincidence point results for generalized weak contractions with discontinuous control functions. The theorems are proved in metric spaces with a partial order. Our theorems extend several existing results in the current literature. We also discuss several corollaries and give illustrative examples. We apply our result to obtain some coupled coincidence point results which effectively generalize a number of established results.

MSC:54H10, 54H25.
Phenotype, donor age and gender affect function of human bone marrow-derived mesenchymal stromal cells
Authors: Siegel Georg , Kluba Torsten , Hermanutz-Klein Ursula , Bieback Karen , Northoff Hinnak , Schäfer Richard 
Published: June 2013

Abstract

Background
Mesenchymal stromal cells (MSCs) are attractive for cell-based therapies ranging from regenerative medicine and tissue engineering to immunomodulation. However, clinical efficacy is variable and it is unclear how the phenotypes defining bone marrow (BM)-derived MSCs as well as donor characteristics affect their functional properties.

Methods
BM-MSCs were isolated from 53 (25 female, 28 male; age: 13 to 80 years) donors and analyzed by: (1) phenotype using flow cytometry and cell size measurement; (2) in vitro growth kinetics using population doubling time; (3) colony formation capacity and telomerase activity; and (4) function by in vitro differentiation capacity, suppression of T cell proliferation, cytokines and trophic factors secretion, and hormone and growth factor receptor expression. Additionally, expression of Oct4, Nanog, Prdm14 and SOX2 mRNA was compared to pluripotent stem cells.

Results
BM-MSCs from younger donors showed increased expression of MCAM, VCAM-1, ALCAM, PDGFRβ, PDL-1, Thy1 and CD71, and led to lower IL-6 production when co-cultured with activated T cells. Female BM-MSCs showed increased expression of IFN-γR1 and IL-6β, and were more potent in T cell proliferation suppression. High-clonogenic BM-MSCs were smaller, divided more rapidly and were more frequent in BM-MSC preparations from younger female donors. CD10, β1integrin, HCAM, CD71, VCAM-1, IFN-γR1, MCAM, ALCAM, LNGFR and HLA ABC were correlated to BM-MSC preparations with high clonogenic potential and expression of IFN-γR1, MCAM and HLA ABC was associated with rapid growth of BM-MSCs. The mesodermal differentiation capacity of BM-MSCs was unaffected by donor age or gender but was affected by phenotype (CD10, IFN-γR1, GD2). BM-MSCs from female and male donors expressed androgen receptor and FGFR3, and secreted VEGF-A, HGF, LIF, Angiopoietin-1, basic fibroblast growth factor (bFGF) and NGFB. HGF secretion correlated negatively to the expression of CD71, CD140b and Galectin 1. The expression of Oct4, Nanog and Prdm14 mRNA in BM-MSCs was much lower compared to pluripotent stem cells and was not related to donor age or gender. Prdm14 mRNA expression correlated positively to the clonogenic potential of BM-MSCs.

Conclusions
By identifying donor-related effects and assigning phenotypes of BM-MSC preparations to functional properties, we provide useful tools for assay development and production for clinical applications of BM-MSC preparations.
Tuberculous meningitis: presentation, diagnosis and outcome in hiv-infected patients at the douala general hospital, cameroon: a cross sectional study
Authors: Luma Henry Namme , Tchaleu Benjamin Clet Nguenkam , Ngahane Bertrand Hugo Mbatchou , Temfack Elvis , Doualla Marie Solange , Halle Marie Patrice , Joko Henry Achu , Koulla-Shiro Sinata 
Published: June 2013

Abstract

Introduction
Tuberculous meningitis (TBM) the most fatal presentation of tuberculosis (TB) especially in HIV-infected patients is a real diagnostic and therapeutic challenge worldwide. In Cameroon where HIV and TB are amongst the leading public health problems, the magnitude of TBM has not been defined. Therefore, the objective of this cross sectional study was to describe the presentation and in-hospital outcome of TBM among HIV patients in Douala as well as its diagnostic difficulties.

Methods
We did a clinical case note analysis of all HIV-1 infected patients treated for TBM in the Internal medicine unit of the Douala General Hospital, between January 1st 2004 and December 31st 2009. The diagnosis of TBM was made using clinical, laboratory [cerebrospinal fluid (CSF) analysis] and/or brain computerised tomographic (CT) scan features.

Results
During the study period, 8% (54/672) of HIV-infected patients had TBM. Their mean age was 40.3 ± 12.7 years. The main presenting complaint was headache in 74.1% (40/54) of patients. Their median CD4 cell count was 16 cells/mm3 (IQR: 10 – 34). CSF analysis showed median protein levels of 1.7 g/l (IQR: 1.3 – 2.2), median glucose level of 0.4 g/l (IQR: 0.3 – 0.5) and median white cell count (WCC) count of 21 cells/ml (IQR: 12 – 45) of which mononuclear cells were predominant in 74% of CSF. Acid fast bacilli were found in 1.9% (1/54) of CSF samples. On CT scan hydrocephalus was the main finding in 70.6% (24/34) of patients. In hospital case fatality was 79.6% (43/54).

Conclusion
TBM is a common complication in HIV-infected patients in Douala with high case fatality. Its presumptive diagnosis reposes mostly on CSF analysis, so clinicians caring for HIV patients should not hesitate to do lumbar taps in the presence of symptoms of central nervous system disease.
Methylation kinetics and CpG-island methylator phenotyope status in colorectal cancer cell lines
Authors: Wodarz Dominik , Boland C Richard , Goel Ajay , Komarova Natalia L 
Published: June 2013

AbstractBackgroundHypermethylation of CpG islands is thought to contribute to carcinogenesis through the inactivation of tumor suppressor genes. Tumor cells with relatively high levels of CpG island methylation are considered CpG island methylator phenotypes (CIMP). The mechanisms that are responsible for regulating the activity ofde novomethylation are not well understood.ResultsWe quantify and comparede novomethylation kinetics in CIMP and non-CIMP colon cancer cell lines in the context of different loci, following 5-aza-2’deoxycytidine (5-AZA)-mediated de-methylation of cells. In non-CIMP cells, a relatively fast rate of re-methylation is observed that starts with a certain time delay after cessation of 5-AZA treatment. CIMP cells, on the other hand, start re-methylation without a time delay but at a significantly slower rate. A mathematical model can account for these counter-intuitive results by assuming negative feedback regulation ofde novomethylation activity and by further assuming that this regulation is corrupted in CIMP cells. This model further suggests that when methylation levels have grown back to physiological levels,de novomethylation activity ceases in non-CIMP cells, while it continues at a constant low level in CIMP cells.ConclusionsWe propose that the faster rate of re-methylation observed in non-CIMP compared to CIMP cells in our study could be a consequence of feedback-mediated regulation of DNA methyl transferase activity. Testing this hypothesis will involve the search for specific feedback regulatory mechanisms involved in the activation ofde novomethylation.Reviewers’ reportThis article was reviewed by Georg Luebeck, Tomasz Lipniacki, and Anna Marciniak-Czochra
Renal sympathetic denervation versus antiarrhythmic drugs for drug-resistant hypertension and symptomatic atrial fibrillation (RSDforAF) trial: study protocol for a randomized controlled trial
Authors: Qiu Min , Yin Yuehui , Shan Qijun 
Published: June 2013

Abstract

Background
Recently, catheter-based renal sympathetic denervation (RSD) has been verified to be safely used to substantially reduce the levels of blood pressure, left ventricular hypertrophy, sleep apnea severity and norepinephrine spillover, and improve glucose tolerance. All these pathological changes are recognized as independent risk factors for the development and recurrence of atrial fibrillation (AF). A randomized, single-blind, parallel-control, multicenter clinical trial is being conducted to compare RSD with antiarrhythmic drugs (AAD) in patients with drug-resistant hypertension and symptomatic AF (RSDforAF trial).

Methods/design
Patients with drug-resistant hypertension and symptomatic AF will be randomized to RSD and the drug treatment groups. Patients will be followed for 12 months until study closure. Up to 200 patients may be enrolled in six medical centers in China. The primary objective is to study the effects of RSD on AF burden and blood pressure in patients with hypertension and symptomatic AF.

Discussion
RSDforAF trial will test the hypothesis that RSD is superior to AAD in reducing AF burden and blood pressure in patients with drug-resistant hypertension and symptomatic AF.

Trial registration
ClinicalTrials.gov, NCT01713270
Peripheral compound odontoma erupting in the gingiva
Authors: Hanemann João AC , Oliveira Denise T , Garcia Natália Galvão , Santos Mariana RG , Pereira Alessandro AC 
Published: June 2013

Abstract

Background
Peripheral odontoma arising in the extraosseous soft tissues is rare and if not removed early, may enlarge over time and eventually erupt in the oral cavity.

Case presentation
A 15-year-old girl presented with “denticles on the gingiva”. During the intraoral examination, seven small tooth-like structures were found. These were exposed in the anterior left gingiva between the permanent maxillary lateral incisor and canine teeth, and the left first premolar was absent. Radiographic examination revealed irregular tooth-like structures without evidence of bone involvement.

Conclusion
The lesion was surgically removed, and the specimens were analyzed histopathologically. The diagnosis of compound odontoma was established.

Clinical significance
This is the twelfth reported case of peripheral odontoma in the gingiva and the first one that erupted in the oral cavity.
Cultural change and loss of ethnoecological knowledge among the Isthmus Zapotecs of Mexico
Authors: Saynes-Vásquez Alfredo , Caballero Javier , Meave Jorge A , Chiang Fernando 
Published: June 2013

AbstractBackgroundGlobal changes that affect local societies may cause the loss of ecological knowledge. The process of cultural change in Zapotec communities of the Oaxacan Isthmus intensified during the first years of the 20thcentury due to industrial and agro-industrial modernization projects and an increase in the level of formal schooling. Based on the case of the Oaxacan Isthmus, this study assesses the relationship between cultural change and the loss of traditional ecological knowledge (TEK).MethodsThree hundred male heads of family were interviewed from three municipalities in the Isthmus of Tehuantepec, Oaxaca, Mexico selected to span a wide range of cultural change. Each participant was shown herbarium specimens and photographs of a sample of 30 species drawn from a pool of 94 representing local plant diversity. Visual recognition of each species, knowledge of plant form, generic name, specific name, and local uses were scored. The sum of the five scores provided an index of global knowledge which we used as a proxy for TEK. Analysis of variance revealed differences between groups of economic activities. We collected socio-demographic data from the interviewees such as age, level of schooling, and competency in the local language. With these data we ran a principal component analysis and took the first axis as an index of cultural change, and correlated it with the scores obtained each respondent.ResultsWe found statistically significant differences between groups of people with different economic activities, as well as a highly significant negative relationship between the Index of cultural change and ecological knowledge at all levels, with regression coefficients between 81.2% and 88.3%, indicating that cultural change is affecting traditional botanical knowledge.ConclusionsOur results shown that cultural change, as indicated by occupational activity, level of formal schooling, and competence in the indigenous language, is negatively associated with the loss of Zapotec ethnobotanical knowledge. Heads of family engaged in secondary economic activities and services were less culturally competent, especially regarding the knowledge of generic and specific names as well as plant uses.