1,187 research outputs found

    Development of a pilot data management infrastructure for biomedical researchers at University of Manchester – approach, findings, challenges and outlook of the MaDAM Project

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    Management and curation of digital data has been becoming ever more important in a higher education and research environment characterised by large and complex data, demand for more interdisciplinary and collaborative work, extended funder requirements and use of e-infrastructures to facilitate new research methods and paradigms. This paper presents the approach, technical infrastructure, findings, challenges and outlook (including future development within the successor project, MiSS) of the ‘MaDAM: Pilot data management infrastructure for biomedical researchers at University of Manchester’ project funded under the infrastructure strand of the JISC Managing Research Data (JISCMRD) programme. MaDAM developed a pilot research data management solution at the University of Manchester based on biomedical researchers’ requirements, which includes technical and governance components with the flexibility to meet future needs across multiple research groups and disciplines

    Divergent dysregulation of gene expression in murine models of fragile X syndrome and tuberous sclerosis

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    Background: Fragile X syndrome and tuberous sclerosis are genetic syndromes that both have a high rate of comorbidity with autism spectrum disorder (ASD). Several lines of evidence suggest that these two monogenic disorders may converge at a molecular level through the dysfunction of activity-dependent synaptic plasticity. Methods: To explore the characteristics of transcriptomic changes in these monogenic disorders, we profiled genome-wide gene expression levels in cerebellum and blood from murine models of fragile X syndrome and tuberous sclerosis. Results: Differentially expressed genes and enriched pathways were distinct for the two murine models examined, with the exception of immune response-related pathways. In the cerebellum of the Fmr1 knockout (Fmr1-KO) model, the neuroactive ligand receptor interaction pathway and gene sets associated with synaptic plasticity such as long-term potentiation, gap junction, and axon guidance were the most significantly perturbed pathways. The phosphatidylinositol signaling pathway was significantly dysregulated in both cerebellum and blood of Fmr1-KO mice. In Tsc2 heterozygous (+/−) mice, immune system-related pathways, genes encoding ribosomal proteins, and glycolipid metabolism pathways were significantly changed in both tissues. Conclusions: Our data suggest that distinct molecular pathways may be involved in ASD with known but different genetic causes and that blood gene expression profiles of Fmr1-KO and Tsc2+/− mice mirror some, but not all, of the perturbed molecular pathways in the brain

    Using Village Health Teams for Effective Ultrasound Education in Rural Uganda

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    Maternal and child health conditions, many of which can be detected by ultrasound, represent the highest burden of disease in Uganda. Imaging the World (ITW) is a not-for-profit organization which integrates high quality, affordable ultrasound services into rural health facilities. Of all the challenges faced with implementation of ITW programs in Uganda, lack of sensitization to ultrasound represented the greatest barrier. The Village Health Team (VHT) is an existing public health “train the trainer” model sponsored by the Uganda Ministry of Health which provides public health training to community volunteers. Trained VHT members were recruited to help with ultrasound community outreach and education. These VHT members were successful in achieving dramatic community acceptance and increased utilization of ultrasound services in rural communities. This has led to significant contributions in improving population health in low-resource settings

    Prompt atmospheric neutrino fluxes: perturbative QCD models and nuclear effects

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    We evaluate the prompt atmospheric neutrino flux at high energies using three different frameworks for calculating the heavy quark production cross section in QCD: NLO perturbative QCD, kTk_T factorization including low-xx resummation, and the dipole model including parton saturation. We use QCD parameters, the value for the charm quark mass and the range for the factorization and renormalization scales that provide the best description of the total charm cross section measured at fixed target experiments, at RHIC and at LHC. Using these parameters we calculate differential cross sections for charm and bottom production and compare with the latest data on forward charm meson production from LHCb at 77 TeV and at 1313 TeV, finding good agreement with the data. In addition, we investigate the role of nuclear shadowing by including nuclear parton distribution functions (PDF) for the target air nucleus using two different nuclear PDF schemes. Depending on the scheme used, we find the reduction of the flux due to nuclear effects varies from 10%10\% to 50%50 \% at the highest energies. Finally, we compare our results with the IceCube limit on the prompt neutrino flux, which is already providing valuable information about some of the QCD models.Comment: 61 pages, 25 figures, 11 table

    Effect of Inhibition of the Lysophosphatidic Acid Receptor 1 on Metastasis and Metastatic Dormancy in Breast Cancer

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    Background Previous studies identified the human nonmetastatic gene 23 (NME1, hereafter Nm23-H1) as the first metastasis suppressor gene. An inverse relationship between Nm23-H1 and expression of lysophosphatidic acid receptor 1 gene (LPAR1, also known as EDG2 or hereafter LPA1) has also been reported. However, the effects of LPA1 inhibition on primary tumor size, metastasis, and metastatic dormancy have not been investigated. Methods The LPA1 inhibitor Debio-0719 or LPA1 short hairpinned RNA (shRNA) was used. Primary tumor size and metastasis were investigated using the 4T1 spontaneous metastasis mouse model and the MDA-MB-231T experimental metastasis mouse model (n = 13 mice per group). Proliferation and p38 intracellular signaling in tumors and cell lines were determined by immunohistochemistry and western blot to investigate the effects of LPA1 inhibition on metastatic dormancy. An analysis of variance-based two-tailed t test was used to determine a statistically significant difference between treatment groups. Results In the 4T1 spontaneous metastasis mouse model, Debio-0719 inhibited the metastasis of 4T1 cells to the liver (mean = 25.2 liver metastases per histologic section for vehicle-treated mice vs 6.8 for Debio-0719-treated mice, 73.0% reduction, P < .001) and lungs (mean = 6.37 lesions per histologic section for vehicle-treated mice vs 0.73 for Debio-0719-treated mice, 88.5% reduction, P < .001), with no effect on primary tumor size. Similar results were observed using the MDA-MB-231T experimental pulmonary metastasis mouse model. LPA1 shRNA also inhibited metastasis but did not affect primary tumor size. In 4T1 metastases, but not primary tumors, expression of the proliferative markers Ki67 and pErk was reduced by Debio-0719, and phosphorylation of the p38 stress kinase was increased, indicative of metastatic dormancy. Conclusion The data identify Debio-0719 as a drug candidate with metastasis suppressor activity, inducing dormancy at secondary tumor site

    Pevonedistat targets malignant cells in myeloproliferative neoplasms in vitro and in vivo via NFκB pathway inhibition

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    Targeted inhibitors of JAK2 (eg ruxolitinib) often provide symptomatic relief for myeloproliferative neoplasm (MPN) patients, but the malignant clone persists and remains susceptible to disease transformation. These observations suggest that targeting alternative dysregulated signaling pathways may provide therapeutic benefit. Previous studies identified NFκB pathway hyperactivation in myelofibrosis (MF) and secondary acute myeloid leukemia (sAML) that was insensitive to JAK2 inhibition. Here, we provide evidence that NFκB pathway inhibition via pevonedistat targets malignant cells in MPN patient samples as well as in MPN and patient-derived xenograft mouse models that are nonredundant with ruxolitinib. Colony forming assays revealed preferential inhibition of MF colony growth compared with normal colony formation. In mass cytometry studies, pevonedistat blunted canonical TNFα responses in MF and sAML patient CD34+ cells. Pevonedistat also inhibited hyperproduction of inflammatory cytokines more effectively than ruxolitinib. Upon pevonedistat treatment alone or in combination with ruxolitinib, MPN mouse models exhibited reduced disease burden and improved survival. These studies demonstrating efficacy of pevonedistat in MPN cells in vitro as well as in vivo provide a rationale for therapeutic inhibition of NFκB signaling for MF treatment. Based on these findings, a Phase 1 clinical trial combining pevonedistat with ruxolitinib has been initiated

    Compact HI clouds from the GALFA-HI survey

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    The Galactic Arecibo L-band Feed Array HI (GALFA-HI) survey is mapping the entire Arecibo sky at 21-cm, over a velocity range of -700 to +700 km/s (LSR), at a velocity resolution of 0.18 km/s and a spatial resolution of 3.5 arcmin. The unprecedented resolution and sensitivity of the GALFA-HI survey have resulted in the detection of numerous isolated, very compact HI clouds at low Galactic velocities, which are distinctly separated from the HI disk emission. In the limited area of ~4600 deg2^2 surveyed so far, we have detected 96 of such compact clouds. The detected clouds are cold with a median Tk,max_{k,max} (the kinetic temperature in the case in which there is no non-thermal broadening) of 300 K. Moreover, these clouds are quite compact and faint, with median values of 5 arcmin in angular size, 0.75 K in peak brightness temperature, and 5×10185 \times 10^{18} cm2^{-2} in HI column density. Most of the clouds deviate from Galactic rotation at the 20-30 km/s level, and a significant fraction show evidence for a multiphase medium and velocity gradients. No counterparts for these clouds were found in other wavebands. From the modeling of spatial and velocity distributions of the whole compact cloud population, we find that the bulk of the compact clouds are related to the Galactic disk, and their distances are likely to be in the range of 0.1 to a few kpc. We discuss various possible scenarios for the formation and maintenance of this cloud population and its significance for Galactic ISM studies.Comment: Accepted for publication in the Astrophysical Journa
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