bluuebunny/crossref_metadata_2025_split huggingface dataset:
A systematic analysis of the skeletal muscle miRNA transcriptome of chicken varieties with divergent skeletal muscle growth identifies novel miRNAs and differentially expressed miRNAs
Authors: Li Tingting , Wu Rimao , Zhang Yong , Zhu Dahai 
Published: April 2011

Abstract

Background
Functional studies have demonstrated that microRNAs (miRNAs or miRs) play critical roles in a wide spectrum of biological processes including development and disease pathogenesis. To investigate the functional roles that miRNAs play during chicken skeletal muscle development, the miRNA transcriptomes of skeletal muscles from broiler and layer chickens were profiled using Solexa deep sequencing.

Results
Some miRNAs have multiple isoforms and several miRNAs* are present at higher levels than their corresponding miRNAs. Thirty three novel and 189 known chicken miRNAs were identified using computational approaches. Subsequent miRNA transcriptome comparisons and real-time PCR validation experiments revealed 17 miRNAs that were differentially expressed between broilers and layers, and a number of targets of these miRNAs have been implicated in myogenesis regulation. Using integrative miRNA target-prediction and network-analysis approaches an interaction network of differentially expressed and muscle-related miRNAs and their putative targets was constructed, and miRNAs that could contribute to the divergent muscle growth of broiler and layer chickens by targeting the ACVR2B gene were identified, which can causes dramatic increases in muscle mass.

Conclusions
The present study provides the first transcriptome profiling-based evaluation of miRNA function during skeletal muscle development in chicken. Systematic predictions aided the identification of potential miRNAs and their targets, which could contribute to divergent muscle growth in broiler and layer chickens. Furthermore, these predictions generated information that can be utilized in further research investigating the involvement of interaction networks, containing miRNAs and their targets, in the regulation of muscle development.
Contribution of SecDF to Staphylococcus aureusresistance and expression of virulence factors
Authors: Quiblier Chantal , Zinkernagel Annelies S , Schuepbach Reto A , Berger-Bächi Brigitte , Senn Maria M 
Published: April 2011

Abstract

Background
SecDF is an accessory factor of the conserved Sec protein translocation machinery and belongs to the resistance-nodulation-cell division (RND) family of multidrug exporters. SecDF has been shown in Escherichia coli and Bacillus subtilis to be involved in the export of proteins. RND proteins can mediate resistance against various substances and might be of relevance in antimicrobial therapy. The role of RND proteins in Staphylococcus aureus has not yet been determined.

Results
Markerless deletion mutants were constructed to analyze the impact of the so far uncharacterized RND proteins in S. aureus. While the lack of Sa2056 and Sa2339 caused no phenotype regarding growth and resistance, the secDF mutant resulted in a pleiotropic phenotype. The secDF mutant was cold sensitive, but grew normally in rich medium at 37°C. Resistance to beta-lactams, glycopeptides and the RND substrates acriflavine, ethidium bromide and sodium dodecyl sulfate was reduced. The secDF mutant showed an aberrant cell separation and increased spontaneous and Triton X-100 induced autolysis, although the amounts of penicillin-binding proteins in the membrane were unchanged. The impact of secDF deletion on transcription and expression of specific virulence determinants varied: While coagulase transcription and activity were reduced, the opposite was observed for the autolysin Atl. A reduction of the transcription of the cell wall anchored protein A (spa) was also found. The accumulation of SpA in the membrane and lowered amounts in the cell wall pointed to an impaired translocation.

Conclusions
The combination of different effects of secDF deletion on transcription, regulation and translocation lead to impaired cell division, reduced resistance and altered expression of virulence determinants suggesting SecDF to be of major relevance in S. aureus. Thus SecDF could be a potential target for the control and eradication of S. aureus in the future.
Volume Tracking: A new method for quantitative assessment and visualization of intracardiac blood flow from three-dimensional, time-resolved, three-component magnetic resonance velocity mapping
Authors: Töger Johannes , Carlsson Marcus , Söderlind Gustaf , Arheden Håkan , Heiberg Einar 
Published: April 2011

Abstract

Background
Functional and morphological changes of the heart influence blood flow patterns. Therefore, flow patterns may carry diagnostic and prognostic information. Three-dimensional, time-resolved, three-directional phase contrast cardiovascular magnetic resonance (4D PC-CMR) can image flow patterns with unique detail, and using new flow visualization methods may lead to new insights. The aim of this study is to present and validate a novel visualization method with a quantitative potential for blood flow from 4D PC-CMR, called Volume Tracking, and investigate if Volume Tracking complements particle tracing, the most common visualization method used today.

Methods
Eight healthy volunteers and one patient with a large apical left ventricular aneurysm underwent 4D PC-CMR flow imaging of the whole heart. Volume Tracking and particle tracing visualizations were compared visually side-by-side in a visualization software package. To validate Volume Tracking, the number of particle traces that agreed with the Volume Tracking visualizations was counted and expressed as a percentage of total released particles in mid-diastole and end-diastole respectively. Two independent observers described blood flow patterns in the left ventricle using Volume Tracking visualizations.

Results
Volume Tracking was feasible in all eight healthy volunteers and in the patient. Visually, Volume Tracking and particle tracing are complementary methods, showing different aspects of the flow. When validated against particle tracing, on average 90.5% and 87.8% of the particles agreed with the Volume Tracking surface in mid-diastole and end-diastole respectively. Inflow patterns in the left ventricle varied between the subjects, with excellent agreement between observers. The left ventricular inflow pattern in the patient differed from the healthy subjects.

Conclusion
Volume Tracking is a new visualization method for blood flow measured by 4D PC-CMR. Volume Tracking complements and provides incremental information compared to particle tracing that may lead to a better understanding of blood flow and may improve diagnosis and prognosis of cardiovascular diseases.
Prevalence, predictors and perinatal outcomes of peri-conceptional alcohol exposure - retrospective cohort study in an urban obstetric population in Ireland
Authors: Mullally Aoife , Cleary Brian J , Barry Joe , Fahey Tom P , Murphy Deirdre J 
Published: April 2011

Abstract

Background
Evidence-based advice on alcohol consumption is required for pregnant women and women planning a pregnancy. Our aim was to investigate the prevalence, predictors and perinatal outcomes associated with peri-conceptional alcohol consumption.

Methods
A cohort study of 61,241 women who booked for antenatal care and delivered in a large urban maternity hospital between 2000 and 2007. Self-reported alcohol consumption at the booking visit was categorised as low (0-5 units per week), moderate (6-20 units per week) and high (>20 units per week).

Results
Of the 81% of women who reported alcohol consumption during the peri-conceptional period, 71% reported low intake, 9.9% moderate intake and 0.2% high intake. Factors associated with moderate alcohol consumption included being in employment OR 4.47 (95% CI 4.17 to 4.80), Irish nationality OR 16.5 (95% CI 14.9 to 18.3), private health care OR 5.83 (95% CI 5.38 to 6.31) and smoking OR 1.86 (95% CI 1.73 to 2.01). Factors associated with high consumption included maternal age less than 25 years OR 2.70 (95% CI 1.86 to 3.91) and illicit drug use OR 6.46 (95% CI 3.32 to 12.60). High consumption was associated with very preterm birth (<32 weeks gestation) even after controlling for socio-demographic factors, adjusted OR 3.15 (95% CI 1.26-7.88). Only three cases of Fetal Alcohol Syndrome were recorded (0.05 per 1000 total births), one each in the low, moderate and high consumption groups.

Conclusions
Public Health campaigns need to emphasise the importance of peri-conceptional health and pre-pregnancy planning. Fetal Alcohol Syndrome is likely to be under-reported despite the high prevalence of alcohol consumption in this population.
Developing a method for customized induction of flowering
Authors: Yeoh Chin Chin , Balcerowicz Martin , Laurie Rebecca , Macknight Richard , Putterill Joanna 
Published: April 2011

Abstract

Background
The ability to induce flowering on demand is of significant biotechnological interest. FT protein has been recently identified as an important component of the mobile flowering hormone, florigen, whose function is conserved across the plant kingdom. We therefore focused on manipulation of both endogenous and heterologous FT genes to develop a floral induction system where flowering would be inhibited until it was induced on demand. The concept was tested in the model plant Arabidopsis thaliana (Arabidopsis).

Results
Our starting point was plants with strongly delayed flowering due to silencing of FT with an artificial microRNA directed at FT (amiR-FT) [1]. First, we showed that constitutive expression of a heterologous FT gene (FTa1), from the model legume Medicago truncatula, (Medicago) was able to rescue the amiR-FT late-flowering phenotype. In order to induce flowering in a controlled way, the FTa1 gene was then expressed under the control of an alcohol-inducible promoter in the late flowering amiR-FT plants. Upon exposure to ethanol, FTa1 was rapidly up regulated and this resulted in the synchronous induction of flowering.

Conclusions
We have thus demonstrated a controlled-inducible flowering system using a novel combination of endogenous and heterologous FT genes. The universal florigenic nature of FT suggests that this type of system should be applicable to crops of economic value where flowering control is desirable.
Parasitostatic effect of maslinic acid. I. Growth arrest of Plasmodium falciparum intraerythrocytic stages
Authors: Moneriz Carlos , Marín-García Patricia , García-Granados Andrés , Bautista José M , Diez Amalia , Puyet Antonio 
Published: April 2011

Abstract

Background
Natural products have played an important role as leads for the development of new drugs against malaria. Recent studies have shown that maslinic acid (MA), a natural triterpene obtained from olive pomace, which displays multiple biological and antimicrobial activities, also exerts inhibitory effects on the development of some Apicomplexan, including Eimeria, Toxoplasma and Neospora. To ascertain if MA displays anti-malarial activity, the main objective of this study was to asses the effect of MA on Plasmodium falciparum-infected erythrocytes in vitro.

Methods
Synchronized P. falciparum-infected erythrocyte cultures were incubated under different conditions with MA, and compared to chloroquine and atovaquone treated cultures. The effects on parasite growth were determined by monitoring the parasitaemia and the accumulation of the different infective stages visualized in thin blood smears.

Results
MA inhibits the growth of P. falciparum Dd2 and 3D7 strains in infected erythrocytes in, dose-dependent manner, leading to the accumulation of immature forms at IC50 concentrations, while higher doses produced non-viable parasite cells. MA-treated infected-erythrocyte cultures were compared to those treated with chloroquine or atovaquone, showing significant differences in the pattern of accumulation of parasitic stages. Transient MA treatment at different parasite stages showed that the compound targeted intra-erythrocytic processes from early-ring to schizont stage. These results indicate that MA has a parasitostatic effect, which does not inactivate permanently P. falciparum, as the removal of the compound allowed the infection to continue

Conclusions
MA displays anti-malarial activity at multiple intraerythrocytic stages of the parasite and, depending on the dose and incubation time, behaves as a plasmodial parasitostatic compound. This novel parasitostatic effect appears to be unrelated to previous mechanisms proposed for current anti-malarial drugs, and may be relevant to uncover new prospective plasmodial targets and opens novel possibilities of therapies associated to host immune response.
Icacina senegalensis (Icacinaceae), traditionally used for the treatment of malaria, inhibits in vitro Plasmodium falciparum growth without host cell toxicity
Authors: Sarr Serigne O , Perrotey Sylvie , Fall Ibrahima , Ennahar Saïd , Zhao Minjie , Diop Yérim M , Candolfi Ermanno , Marchioni Eric 
Published: April 2011

Abstract

Background
With the aim of discovering new natural active extracts against malaria parasites, Icacina senegalensis was selected after an ethnopharmacological survey conducted on plants used in traditional malaria treatment in Senegal.

Methods
Different concentrations of the plant extract and fractions were tested on synchronized Plasmodium falciparum cultures at the ring stage using the parasite lactate dehydrogenase assay. Their haemolytic activity and in vitro cytoxicity were evaluated. The chromatographic profiles of active fractions were also established.

Results
The plant extract and fractions revealed anti-plasmodial activity (IC50 < 5 μg/mL) with no toxicity (Selectivity indexes >10). The dichloromethane fraction showed stronger anti-plasmodial activity than the total extract.

Conclusion
Anti-plasmodial activity and toxicity of I. senegalensis are reported for the first time and showed promising results in malaria field research.
Risk assessment of diesel exhaust and lung cancer: combining human and animal studies after adjustment for biases in epidemiological studies
Authors: Pedeli Xanthi , Hoek Gerard , Katsouyanni Klea 
Published: April 2011

Abstract

Background
Risk assessment requires dose-response data for the evaluation of the relationship between exposure to an environmental stressor and the probability of developing an adverse health effect. Information from human studies is usually limited and additional results from animal studies are often needed for the assessment of risks in humans. Combination of risk estimates requires an assessment and correction of the important biases in the two types of studies. In this paper we aim to illustrate a quantitative approach to combining data from human and animal studies after adjusting for bias in human studies. For our purpose we use the example of the association between exposure to diesel exhaust and occurrence of lung cancer.

Methods
Firstly, we identify and adjust for the main sources of systematic error in selected human studies of the association between occupational exposure to diesel exhaust and occurrence of lung cancer. Evidence from selected animal studies is also accounted for by extrapolating to average ambient, occupational exposure concentrations of diesel exhaust. In a second stage, the bias adjusted effect estimates are combined in a common effect measure through meta-analysis.

Results
The random-effects pooled estimate (RR) for exposure to diesel exhaust vs. non-exposure was found 1.37 (95% C.I.: 1.08-1.65) in animal studies and 1.59 (95% C.I.: 1.09-2.10) in human studies, whilst the overall was found equal to 1.49 (95% C.I.: 1.21-1.78) with a greater contribution from human studies. Without bias adjustment in human studies, the pooled effect estimate was 1.59 (95% C.I.: 1.28-1.89).

Conclusions
Adjustment for the main sources of uncertainty produced lower risk estimates showing that ignoring bias leads to risk estimates potentially biased upwards.
Soluble vascular endothelial growth factor receptor-3 suppresses lymphangiogenesis and lymphatic metastasis in bladder cancer
Authors: Yang Hanseul , Kim Chan , Kim Min-Ju , Schwendener Reto A , Alitalo Kari , Heston Warren , Kim Injune , Kim Wun-Jae , Koh Gou Young 
Published: April 2011

Abstract

Background
Most bladder cancer patients experience lymphatic metastasis in the course of disease progression, yet the relationship between lymphangiogenesis and lymphatic metastasis is not well known. The aim of this study is to elucidate underlying mechanisms of how expanded lymphatic vessels and tumor microenvironment interacts each other and to find effective therapeutic options to inhibit lymphatic metastasis.

Results
The orthotopic urinary bladder cancer (OUBC) model was generated by intravesical injection of MBT-2 cell lines. We investigated the angiogenesis, lymphangiogenesis, and CD11b+/CD68+ tumor-associated macrophages (TAM) by using immunofluorescence staining. OUBC displayed a profound lymphangiogenesis and massive infiltration of TAM in primary tumor and lymphatic metastasis in lymph nodes. TAM flocked near lymphatic vessels and express higher levels of VEGF-C/D than CD11b- cells. Because VEGFR-3 was highly expressed in lymphatic vascular endothelial cells, TAM could assist lymphangiogenesis by paracrine manner in bladder tumor. VEGFR-3 expressing adenovirus was administered to block VEGF-C/D signaling pathway and clodronate liposome was used to deplete TAM. The blockade of VEGF-C/D with soluble VEGF receptor-3 markedly inhibited lymphangiogenesis and lymphatic metastasis in OUBC. In addition, the depletion of TAM with clodronate liposome exerted similar effects on OUBC.

Conclusion
VEGF-C/D are the main factors of lymphangiogenesis and lymphatic metastasis in bladder cancer. Moreover, TAM plays an important role in these processes by producing VEGF-C/D. The inhibition of lymphangiogenesis could provide another therapeutic target to inhibit lymphatic metastasis and recurrence in patients with invasive bladder cancer.
Detection of vitellogenin incorporation into zebrafish oocytes by FITC fluorescence
Authors: Matsuda Yohei , Ito Yoshie , Hashimoto Hisashi , Yokoi Hayato , Suzuki Tohru 
Published: April 2011

Abstract

Background
Large volumes of lymph can be collected from the eye-sacs of bubble-eye goldfish. We attempted to induce vitellogenin (Vtg) in the eye-sac lymph of bubble-eye goldfish and develop a method for visualizing Vtg incorporation by zebrafish oocytes using FITC-labeling.

Methods
Estrogen efficiently induced Vtg in the eye-sac lymph of goldfish. After FITC-labeled Vtg was prepared, it was injected into mature female zebrafish.

Results
Incorporation of FITC-labeled Vtg by zebrafish oocytes was detected in in vivo and in vitro experiments. The embryos obtained from zebrafish females injected with FITC-labeled Vtg emitted FITC fluorescence from the yolk sac and developed normally.

Conclusion
This method for achieving Vtg incorporation by zebrafish oocytes could be useful in experiments related to the development and endocrinology of zebrafish oocytes.
A promising routine to fabricate GeSi nanowires via self-assembly on miscut Si (001) substrates
Authors: Zhong Zhenyang , Gong Hua , Ma Yingjie , Fan Yongliang , Jiang Zuimin 
Published: April 2011

AbstractVery small and compactly arranged GeSi nanowires could self-assembled on vicinal Si (001) substrates with ~8° off toward ⟨110⟩ during Ge deposition. The nanowires were all oriented along the miscut direction. The small ration of height over width of the nanowire indicated that the nanowires were bordered partly with {1 0 5} facets. These self-assembled small nanowires were remarkably influenced by the growth conditions and the miscut angle of substrates in comparison with large dome-like islands obtained after sufficient Ge deposition. These results proposed that the formation of the nanowire was energetically driven under growth kinetic assistance. Three-dimensionally self-assembled GeSi nanowires were first realized via multilayer Ge growth separated with Si spacers. These GeSi nanowires were readily embedded in Si matrix and compatible with the sophisticated Si technology, which suggested a feasible strategy to fabricate nanowires for fundamental studies and a wide variety of applications.PACS: 81.07.Gf, 81.16.Dn, 68.65.-k, 68.37.Ps
Myelin ingestion alters macrophage antigen-presenting function in vitro and in vivo
Authors: van Zwam Marloes , Samsom Janneke N , Nieuwenhuis Edward E , Melief Marie-José , Wierenga-Wolf Annet F , Dijke I Esmé , Talens Simone , van Meurs Marjan , Voerman Jane S , Boven Leonie A , Laman Jon D 
Published: April 2011

ABSTRACTDuring MS, phagocytosing myelin-containing macrophages arise and lie in close proximity to T cells. To date, it has not been addressed whether these myelin-laden macrophages have the capacity to present antigens to T cells and whether this contributes to inflammation in disease. We demonstrate that in vitro-generated human and mouse myelin-laden macrophages expressed MHC class I and II and costimulatory molecules and are thus well equipped for antigen presentation. Human myelin-laden macrophages exhibited normal endocytosis of particulate and soluble antigens. In addition, human myelin-laden macrophages elicited active T cell proliferation of naïve as well as memory T cells. Furthermore, mouse myelin-laden macrophages induced primary antigen-specific CD4+ T cell proliferation in vivo but transiently diminished IFN-γ release. Functionally, MOG peptide-loaded myelin-laden mouse macrophages modestly but significantly reduced the severity of MOG peptide-induced EAE. These data show that myelin uptake results in the induction of a population of macrophages that retains antigen-presenting capacity and limits autoimmune-mediated disease.
Introduction of a Quality Management System and Outcome After Hematopoietic Stem-Cell Transplantation
Authors: Gratwohl Alois , Brand Ronald , Niederwieser Dietger , Baldomero Helen , Chabannon Christian , Cornelissen Jan , de Witte Theo , Ljungman Per , McDonald Fiona , McGrath Eoin , Passweg Jakob , Peters Christina , Rocha Vanderson , Slaper-Cortenbach Ineke , Sureda Anna , Tichelli Andre , Apperley Jane 
Published: April 2011

Purpose A comprehensive quality management system called JACIE (Joint Accreditation Committee International Society for Cellular Therapy and the European Group for Blood and Marrow Transplantation), was introduced to improve quality of care in hematopoietic stem-cell transplantation (HSCT). We therefore tested the hypothesis that the introduction of JACIE improved patient survival. Patients and Methods Data on 41,623 allogeneic (39%) and 66,281 autologous (61%) HSCTs for an acquired hematologic disorder performed between 1999 and 2007 by 421 teams in Europe were used to assess the outcomes of patients who received a transplantation at baseline (> 3 years before application or no application), during preparation (3 years before application), during application (time from application to accreditation), and after JACIE accreditation. The analysis was clustered by team and stratified for year of HSCT, donor type, disease, conditioning, and gross national income per capita of the respective country. Patient's risks were adjusted for by their European Group for Blood and Marrow Transplantation score. Results Patient outcome was systematically better when the transplantation center was at a more advanced phase of JACIE accreditation, independent of year of transplantation and other risk factors. Improvement was robust as quantified for relapse-free survival after allogeneic HSCT compared with baseline by a hazard ratio (HR) of 0.96 (95% CI, 0.90 to 1.03; P = .22) for preparation, 0.95 (95% CI, 0.88 to 1.03; P = .20) for application, and 0.86 (95% CI, 0.78 to 0.95; P = .01) for the accreditation (test for trend P = .01). Improvement from baseline was similar after autologous HSCT (HR for accreditation, 0.83; 95% CI, 0.74 to 0.93; P < .01). Conclusion Even with all the limitations of an observational study, these findings support the hypothesis that introduction of a comprehensive clinical quality management system is associated with improved outcome of patients after HSCT.