Abstraction, extension and structural auditing with the UMLS semantic network

The Unified Medical Language System (UMLS) is a two-level biomedical terminological knowledge base, consisting of the Metathesaurus (META) and the Semantic Network (SN), which is an upper-level ontology of broad categories called semantic types (STs). The two levels are related via assignments of one or more STs to each concept of the META. Although the SN provides a high-level abstraction for the META, it is not compact enough. Various metaschemas, which are compact higher-level abstraction networks of the SN, have been derived. A methodology is presented to evaluate and compare two given metaschemas, based on their structural properties. A consolidation algorithm is designed to yield a consolidated metaschema maintaining the best and avoiding the worst of the two given metaschemas. The methodology and consolidation algorithm were applied to the pair of heuristic metaschemas, the top-down metaschema and the bottom-up metaschema, which have been derived from two studies involving two groups of UMLS experts. The results show that the consolidated metaschema has better structural properties than either of the two input metaschemas. Better structural properties are expected to lead to better utilization of a metaschema in orientation and visualization of the SN. Repetitive consolidation, which leads to further structural improvements, is also shown. The META and SN were created in the absence of a comprehensive curated genomics terminology. The internal consistency of the SN\u27s categories which are relevant to genomics is evaluated and changes to improve its ability to express genomic knowledge are proposed. The completeness of the SN with respect to genomic concepts is evaluated and conesponding extensions to the SN to fill identified gaps are proposed. Due to the size and complexity of the UMLS, errors are inevitable. A group auditing methodolgy is presented, where the ST assignments for groups of similar concepts are audited. The extent of an ST, which is the group of all concepts assigned this ST, is divided into groups of concepts that have been assigned exactly the same set of STs. An algorithm finds subgroups of suspicious concepts. The auditor is presented with these subgroups, which purportedly exhibit the same semantics, and thus he will notice different concepts with wrong or missing ST assignments. Another methodology partitions these groups into smaller, singly rooted, hierarchically organized sets used to audit the hierarchical relationships. The algorithmic methodologies are compared with a comprehensive manual audit and show a very high error recall with a much higher precision than the manual exhaustive review

The in ovo CAM-assay as a xenograft model for sarcoma

Sarcoma is a very rare disease that is heterogeneous in nature, all hampering the development of new therapies. Sarcoma patients are ideal candidates for personalized medicine after stratification, explaining the current interest in developing a reproducible and low-cost xenotransplant model for this disease. The chick chorioallantoic membrane is a natural immunodeficient host capable of sustaining grafted tissues and cells without species-specific restrictions. In addition, it is easily accessed, manipulated and imaged using optical and fluorescence stereomicroscopy. Histology further allows detailed analysis of heterotypic cellular interactions. This protocol describes in detail the in ovo grafting of the chorioallantoic membrane with fresh sarcoma-derived tumor tissues, their single cell suspensions, and permanent and transient fluorescently labeled established sarcoma cell lines (Saos-2 and SW1353). The chick survival rates are up to 75%. The model is used to study graft-(viability, Ki67 proliferation index, necrosis, infiltration) and host (fibroblast infiltration, vascular ingrowth) behavior. For localized grafting of single cell suspensions, ECM gel provides significant advantages over inert containment materials. The Ki67 proliferation index is related to the distance of the cells from the surface of the CAM and the duration of application on the CAM, the latter determining a time frame for the addition of therapeutic products

Exploring the interdependencies of research funders in the UK

Investment in medical research is vital to the continuing improvement of the UK's health and wealth. It is through research that we expand our understanding of disease and develop new treatments for patients. Medical research charities currently contribute over £1 billion annually to medical research in the UK, of which over £350 million is provided by Cancer Research UK. Many charities, including Cancer Research UK, receive no government funding for their research activity. Cancer Research UK is engaged in a programme of work in order to better understand the medical research funding environment and demonstrate the importance of sustained investment. A key part of that is the Office of Health Economics‟ (OHE) 2011 report “Exploring the interdependency between public and charitable medical research”. This study found that there are substantial benefits, both financial and qualitative, from the existence of a variety of funders and that reductions in the level of government financial support for medical research are likely to have broader negative effects. This contributed to other evidence which found that the activities and funding of the charity, public and private sectors respectively are complementary, i.e. mutually reinforcing, rather than duplicative or merely substituting for one another. “Exploring the interdependencies of research funders in the UK” by the Office of Health Economics (OHE) and SPRU: Science and Technology Policy Research at the University of Sussex, represents a continued effort to build the evidence base around the funding of medical research. This report uncovers the extent to which funders of cancer research are interdependent, nationally and internationally. Key figures show that two thirds of publications acknowledging external support have relied on multiple funders, while just under half benefited from overseas funding, and almost a fifth are also supported by industry. In addition the analysis shows that the general public would not want tax funding of cancer research to be reduced, but would not donate enough to charities to compensate for any such reduction

Local anaesthetic bupivacaine induced ovarian and prostate cancer apoptotic cell death and underlying mechanisms in vitro

Retrospective studies indicate that the use of regional anesthesia can reduce cancer recurrence after surgery which could be due to ranging from immune function preservation to direct molecular mechanisms. This study was to investigate the effects of bupivacaine on ovarian and prostate cancer cell biology and the underlying molecular mechanisms. Cell viability, proliferation and migration of ovarian carcinoma (SKOV-3) and prostate carcinoma (PC-3) were examined following treatment with bupivacaine. Cleaved caspase 3, 8 and 9, and GSK-3β, pGSK-3β(tyr216) and pGSK-3β(ser9) expression were assessed by immunofluorescence. FAS ligand neutralization, caspase and GSK-3 inhibitors and GSK-3β siRNA were applied to further explore underlying mechanisms. Clinically relevant concentrations of bupivacaine reduced cell viability and inhibited cellular proliferation and migration in both cell lines. Caspase 8 and 9 inhibition generated partial cell death reversal in SKOV-3, whilst only caspase 9 was effective in PC-3. Bupivacaine increased the phosphorylation of GSK-3β(Tyr216) in SKOV-3 but without measurable effect in PC3. GSK-3β inhibition and siRNA gene knockdown decreased bupivacaine induced cell death in SKOV-3 but not in PC3. Our data suggests that bupivacaine has direct ‘anti-cancer’ properties through the activation of intrinsic and extrinsic apoptotic pathways in ovarian cancer but only the intrinsic pathway in prostate cancer

Getting rid of caveolins: phenotypes of caveolin-deficient animals

The elucidation of the role of caveolae has been the topic of many investigations which were greatly enhanced after the discovery of caveolin, the protein marker of these flask-shaped plasma membrane invaginations. The generation of mice deficient in the various caveolin genes (cav-1, cav-2 and cav-3) has provided physiological models to unravel the role of caveolins or caveolae at the whole organism level. Remarkably, despite the essential role of caveolins in caveolae biogenesis, all knockout mice are viable and fertile. However, lack of caveolae or caveolins leads to a wide range of phenotypes including muscle, pulmonary or lipid disorders, suggesting their implication in many cellular processes. The aim of this review is to give a broad overview of the phenotypes described for the caveolin-deficient mice and to link them to the numerous functions so far assigned to caveolins/caveolae

Adoptive immunotherapy monitored by micro-MRI in experimental colorectal liver metastasis

In this study we used the colon carcinoma DHDK12 cell line and generated single metastasis after subcapsular injection in BDIX rats as an experimental tumor model. The aim of the work was to set up in vitro experimental conditions to prepare immune effector cells and in vivo conditions for monitoring the effects of such cells injected as adoptive immunotherapy. Dendritic cells can process tumor cell antigens, induce a T-cell response and be used ex vivo to prepare activated lymphocytes. Lymphocytes were harvested from mesenteric lymph nodes and cocultured with bone marrow-derived autologous dendritic cells previously loaded with irradiated tumor cells. In vitro, the coculture: 1) induced the proliferation of lymphocytes, 2) expanded a preferential subpopulation of T CD8 lymphocytes, and 3) was in favor of lymphocyte cytotoxic activity against the DHDK12 tumor cell line. Activated lymphocytes were injected in the tumor-bearing rat portal vein. Parameters could be set to monitor tumor volume by micro MRI. This monitoring before and after treatment and immunohistochemical examinations revealed that: 1) micro MRI is an appropriate tool to survey metastasis growth in rat, 2) injected lymphocytes increase lesional infiltration with T CD8 cells even 15 days after treatment, 3) a dose of 50 millions lymphocytes is not sufficient to act on the course of the tumor

Therapeutic efficacy study of novel 5-FU-loaded PMM 2.1.2-based microspheres on C6 glioma

The aim of this study was to evaluate the potential of poly(methylidene malonate 2.1.2) as a new drug delivery system to the central nervous system. 5-Fluorouracil microspheres were formulated by an emulsion-extraction method, and evaluated on a C6 glioma model. Twenty-seven Sprague-Dawley female rats underwent implantation of various C6 cell concentrations. Magnetic resonance imaging was performed at day 10 to control the setting of the tumor, by using a T2-weighted sequence. At day 12, 18 animals received blank or 5-FU-loaded microspheres, while 9 animals were not implanted and constituted the controls. Thereafter, MRI was performed twice a week to follow the tumor growth. In 12 animals, an alloimmune rejection of the tumor was observed, showing the limitations of the C6 glioma model. When tumor developed, no relationship was observed between the number of C6 cells injected and the tumor volume. 5-FU microsphere efficacy could statistically be demonstrated by significantly improving the median survival of C6 glioma-bearing animals and also by decreasing tumor burden

Knowledge and practice on magnitude, diagnosis, treatment and prevention strategies of Hepatocellular Carcinoma in Ethiopia: A Systematic Review

Introduction: In Ethiopia, hepatocellular carcinoma (HCC) is the most common cancer with 100% fatality rate. HCC cases in low income countries die within few months following diagnosis. There is lack of information on the burden, risk factors, diagnosis modalities, surveillance strategies and treatment approaches to HCC in Ethiopia.Objective: To analyze the existing evidence related to burden, risk factors, diagnosis modalities, surveillance strategies, and treatment and prevention strategies of HCC in Ethiopia.Methods: All studies done on HCC in Ethiopian irrespective of year of publication and study types were included. Literatures were retrieved from electronic database of PubMedand Cochrane library during September/2016 to January 2/2017. Key words and mesh terms such as ‘hepatocellular carcinoma’, ‘hcc’, ‘hepatoma’, ‘malignant hepatoma’, ‘hepatocarcinoma’ were used to search for documents. Besides, we searched for articles, guidelines and reviews from world health organizations, lancet and Google scholar sites. Each of the retrieved studies was assessed by two authors for inclusion based on the eligibility criteria, and for quality using the critical appraisal checklist. Qualitative data were synthesized for analyzing the theories of studies. Medley reference manager was used to manage citations.Results: A total of 1448 literatures were retrieved. Eight studies fulfill the eligibility criteria, however, only three were full-fledged articles. HCC is clinically characterized by exhaustion, loss of appetite, rapid loss of weight, epigastric pain, right upper abdominal quadrant pain with a rapidly growing mass, jaundice, and ascites with or without hepatomegaly and splenomegaly. Data on HCC proportion among liver disease patients lies between 16.1%-19.2%. Cirrhosis followed by hepatotoxic indigenous drugs and viral hepatitis were found to be as major risk factor for HCC. In Ethiopia, there is no surveillance activity and no standard staging systems. Furthermore, there was no policy frame -work for management of HCC.Conclusion: As compared to other countries, Ethiopia is far behind in addressing HCC. There is no national policy framework and guideline for the management of HCC. Moreover, HCC is a neglected cancer that is considered as a death penalty by the community. Health professionals working in health facilities and health offices should share the data they have to the scientific community and policy makers, for further searching solutions and informed decision, respectively. An intensified public health strategy on health education and early case detection is of critical importance. In addition concerted effort should be made to develop HCC prevention and treatment modality.Key words: Hepatocellular Carcinoma, Ethiopi

Is magnetic resonance imaging texture analysis a useful tool for cell therapy in vivo monitoring?

Assessment of anti-tumor treatment efficiency is usually done by measuring tumor size. Treatment may however induce changes in the tumor other than tumor size. Magnetic Resonance Imaging Texture Analysis (MRI-TA) is presently used to follow activated lymphocyte cell therapy. We used a 7T microimager to acquire high-resolution MR images of an experimental liver metastasis from colon carcinoma in rats treated (n = 4) or not (n = 3) with a cell therapy product. MRI-TA was then performed with Linear Discriminant Analysis and showed: i) a significant variation of tumor texture with tumor growth and ii) a significant modification in the texture of tumors treated with activated lymphocytes compared with untreated tumors. T2-weighted images or volume calculation did not evidence any difference. MRI-TA appears as a promising method for early detection and follow-up of response to cell therapy