Visual modeling of OWL-S services

The Semantic Web is slowly gathering interest and becoming a reality. More people are becoming aware of this and are trying to embed Semantic Web technologies into their applications. This involves the use of tools that can handle rapid ontology building and validation in an easy and transparent manner. In the area of Semantic Web Web Services (SWWS) an OWL-S specification defines a set of ontologies through which a semantic description of the service can be created. At times this is not an easy task and could result in an incorrect specification of the description or even lead the fainthearted user to resort to some other type of description language. This paper describes the OWL-S editor tool that provides two methodologies in which such a web services description can be developed without exposing the developer to the underlying OWL-S syntax. These methodologies are based on a mapping from WSDL to OWL-S and on modeling a composite service using standard UML Activity Diagrams.peer-reviewe

Retrospective review of the diagnostic pathway of suspected prostate cancer in Mater Dei Hospital

BACKGROUND: A well-established prostate cancer diagnostic pathway is used in Europe [1] to increase early diagnosis of clinically significant prostate cancers. This retrospective review was aimed to assess the efficiency and accuracy of this pathway within the department of urology at Mater Dei Hospital.METHOD: Data collected included demographic data, digital rectal examination (DRE) findings prior to magnetic resonance imaging (MRI) and prostate specific antigen (PSA) values preceding MRI. PSA doubling time and PSA velocity were calculated. The cohort was divided into three groups according to the MRI result - negative, positive or equivocal for prostate cancer. Prostate gland volume, Prostate Imaging-Reporting and Data System (PI-RADS) score, TNM stage and histology results were documented and compared.RESULTS: 41% of the cohort had a DRE suggestive of cancer. The cohort had a mean PSA value of 4.912 ng/ml, mean PSA density of 0.152 ng/ml, mean PSA velocity of 0.306 ng/ml/year and mean PSA doubling time of 64 months. The mode PIRADS count was 2. Most cancers were staged at T3a . The mean prostate size was 61.46 cubic centi-metres. 93.4% of patients with an MRI of the prostate suggestive of cancer had a prostate biopsy. 79.5% provided samples suggestive of cancer. The most common grade of cancer was Gleason 7 disease.CONCLUSION: Allowing for limitations of a retrospective review and a small cohort, this study has shown that using the European pathway for diagnosis of prostate cancer increases diagnosis of significant prostate cancer.peer-reviewe

Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology

Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease affecting the central nervous system (CNS). Small non-coding RNAs (sncRNAs) and, in particular, microRNAs (miRNAs) have frequently been associated with MS. Here, we performed a comprehensive analysis of all classes of sncRNAs in matching samples of peripheral blood mononuclear cells (PBMCs), plasma, cerebrospinal fluid (CSF) cells, and cell-free CSF from relapsing-remitting (RRMS, n = 12 in relapse and n = 11 in remission) patients, secondary progressive (SPMS, n = 6) MS patients, and noninflammatory and inflammatory neurological disease controls (NINDC, n = 11; INDC, n = 5). We show widespread changes in miRNAs and sncRNA-derived fragments of small nuclear, nucleolar, and transfer RNAs. In CSF cells, 133 out of 133 and 115 out of 117 differentially expressed sncRNAs were increased in RRMS relapse compared to remission and RRMS compared to NINDC, respectively. In contrast, 65 out of 67 differentially expressed PBMC sncRNAs were decreased in RRMS compared to NINDC. The striking contrast between the periphery and CNS suggests that sncRNA-mediated mechanisms, including alternative splicing, RNA degradation, and mRNA translation, regulate the transcriptome of pathogenic cells primarily in the CNS target organ.Peer reviewe

Biomarkers of pituitary adenoma behaviour

The pathological behaviour of pituitary adenomas (PAs) is complex and difficult to predict. In this study, the proliferation marker, Ki-67, pituitary tumour transforming gene (PTTG), vascular endothelial growth factor (VEGF), cyclin D1, c-MYC and pituitary adenylate cyclase-activating peptide (PACAP) protein expression were analyzed using immunohistochemistry in 74 PA samples (48 non-functional PAs, 26 functional PAs) and correlated with tumour characteristics including size, extension and tumour behaviour patterns. Correlation of protein marker expression with clinical characteristics yielded significant results. A correlation between PTTG expression and age at diagnosis, tumour size, tumour regrowth and Ki-67 was observed. Cyclin D1 and c-MYC also showed significant correlations with gender, tumour size, age at diagnosis and other protein markers. Significant differences in protein expression in the chosen markers were also observed between different tumour types, between patients treated pre-operatively with somatostatin analogues and in tumours with different intensity on MR imaging). Significant correlations were also observed between the markers themselves, with a possible direct link between two of the studied markers which substantiate data from other in vitro studies. Differences in protein localization were also analyzed to identify possible differences in biological behaviour arising in relation to nuclear vs cytoplasmic localization of the studied biomarkers. VEGF and PACAP similarly appeared interesting but exhibited few statistically significant correlations on detailed analysis. In conclusion, interesting and novel observations on the differences in expression of tumour markers studied are reported. Specifically, Ki-67 and PTTG appear to be very strongly correlated to tumour regrowth/recurrence and may be considered useful tools in predicting the proliferative potential of the resected tumours. Further data on the differential role of Cyclin D1 and cMYC in pituitary tumorigenesis and possibly tumour prognosis are presented.Principal author (MG, JV) was funded by the University of Malta Research funds (MEDRP02-05) and the Faculty of Medicine and Surgery (MDSIN08-22).RF is funded by the REACH HIGH Scholars Programme – Post-Doctoral Grant. The Research work disclosed in this publication is partially funded by the REACH HIGH Scholars Programme – Post Doctoral Grants. The grant is part-financed by the European Union, Operational Programme II – Cohesion Policy 2014 – 2020 “Investing in human capital to create more opportunities and promote the wellbeing of society” – European Social Fund.peer-reviewe

The JCMT Transient Survey : identifying submillimeter continuum variability over several year timescales using archival JCMT Gould Belt Survey observations

Investigating variability at the earliest stages of low-mass star formation is fundamental in understanding how a protostar assembles mass. While many simulations of protostellar disks predict non-steady accretion onto protostars, deeper investigation requires robust observational constraints on the frequency and amplitude of variability events characterized across the observable SED. In this study, we develop methods to robustly analyze repeated observations of an area of the sky for submillimeter variability in order to determine constraints on the magnitude and frequency of deeply embedded protostars. We compare 850 μm JCMT Transient Survey data with archival JCMT Gould Belt Survey data to investigate variability over 2–4 year timescales. Out of 175 bright, independent emission sources identified in the overlapping fields, we find seven variable candidates, five of which we classify as Strong, and the remaining two we classify as Extended to indicate that the latter are associated with larger-scale structure. For the Strong variable candidates, we find an average fractional peak brightness change per year of |4.0| % yr-1, with a standard deviation of 2.7 % yr-1. In total, 7% of the protostars associated with 850 μm emission in our sample show signs of variability. Four of the five Strong sources are associated with a known protostar. The remaining source is a good follow-up target for an object that is anticipated to contain an enshrouded, deeply embedded protostar. In addition, we estimate the 850 μm periodicity of the submillimeter variable source, EC 53, to be 567 ± 32 days, based on the archival Gould Belt Survey data.PostprintPeer reviewe

Особенности конфликтогенных зон у больных невротическими расстройствами женщин

Представлены данные о различии конфликтогенных зон у женщин и мужчин, страдающих невротическими расстройствами. Показано, что выявленные особенности необходимо учитывать в диагностике и психотерапии невротических расстройств.The authors report the data about the differences in conflectogenic zones among women and men with neurotic disorders. It was shown that the revealed peculiarities should be taken into consideration in diagnosis and psychotherapy of neurotic disorders

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

Distinct DNA Methylation Patterns of Subependymal Giant Cell Astrocytomas in Tuberous Sclerosis Complex

Tuberous sclerosis complex (TSC) is a monogenic disorder caused by mutations in either the TSC1 or TSC2 gene, two key regulators of the mechanistic target of the rapamycin complex pathway. Phenotypically, this leads to growth and formation of hamartomas in several organs, including the brain. Subependymal giant cell astrocytomas (SEGAs) are low-grade brain tumors commonly associated with TSC. Recently, gene expression studies provided evidence that the immune system, the MAPK pathway and extracellular matrix organization play an important role in SEGA development. However, the precise mechanisms behind the gene expression changes in SEGA are still largely unknown, providing a potential role for DNA methylation. We investigated the methylation profile of SEGAs using the Illumina Infinium HumanMethylation450 BeadChip (SEGAs n = 42, periventricular control n = 8). The SEGA methylation profile was enriched for the adaptive immune system, T cell activation, leukocyte mediated immunity, extracellular structure organization and the ERK1 & ERK2 cascade. More interestingly, we identified two subgroups in the SEGA methylation data and show that the differentially expressed genes between the two subgroups are related to the MAPK cascade and adaptive immune response. Overall, this study shows that the immune system, the MAPK pathway and extracellular matrix organization are also affected on DNA methylation level, suggesting that therapeutic intervention on DNA level could be useful for these specific pathways in SEGA. Moreover, we identified two subgroups in SEGA that seem to be driven by changes in the adaptive immune response and MAPK pathway and could potentially hold predictive information on target treatment response