Towards semantic software engineering environments

Software tools processing partially common set of data should share an understanding of what these data mean. Since ontologies have been used to express formally a shared understanding of information, we argue that they are a way towards Semantic SEEs. In this paper we discuss an ontology-based approach to tool integration and present ODE, an ontology-based SEE

Deregulated expression of aurora kinases is not a prognostic biomarker in papillary thyroid cancer patients.

Abstract A number of reports indicated that Aurora-A or Aurora-B overexpression represented a negative prognostic factor in several human malignancies. In thyroid cancer tissues a deregulated expression of Aurora kinases has been also demonstrated, butno information regarding its possible prognostic role in differentiated thyroid cancer is available. Here, weevaluated Aurora-A and Aurora-B mRNA expression and its prognostic relevance in a series of 87 papillary thyroid cancers (PTC), with a median follow-up of 63 months. The analysis of Aurora-A and Aurora-B mRNA levels in PTC tissues, compared to normal matched tissues, revealed that their expression was either up-or down-regulatedin the majority of cancer tissues. In particular, Aurora-A and Aurora-B mRNA levels were altered, respectively, in 55 (63.2%) and 79 (90.8%) out of the 87 PTC analyzed. A significant positive correlation between Aurora-A and Aurora-B mRNAswas observed (p=0.001). The expression of both Aurora genes was not affected by the BRAF(V600E) mutation. Univariate, multivariate and Kaplan-Mayer analyses documented the lack of association between Aurora-A or Aurora-B expression and clinicopathological parameterssuch as gender, age, tumor size, histology, TNM stage, lymph node metastasis and BRAF status as well asdisease recurrences or disease-free interval. Only Aurora-B mRNA was significantly higher in T(3-4) tissues, with respect to T(1-2) PTC tissues. The data reported here demonstrate that the expression of Aurora kinases is deregulated in the majority of PTC tissues, likely contributing to PTC progression. However, differently from other human solid cancers, detection of Aurora-A or Aurora-B mRNAs is not a prognostic biomarker inPTC patients

Large genomic aberrations detected by SNP array are independent prognosticators of a shorter time to first treatment in chronic lymphocytic leukemia patients with normal FISH

Background Genomic complexity can predict the clinical course of patients affected by chronic lymphocytic leukemia (CLL) with a normal FISH. However, large studies are still lacking. Here, we analyzed a large series of CLL patients and also carried out the so far largest comparison of FISH versus single-nucleotide polymorphism (SNP) array in this disease. Patients and methods SNP-array data were derived from a previously reported dataset. Results Seventy-seven of 329 CLL patients (23%) presented with a normal FISH. At least one large (>5 Mb) genomic aberration was detected by SNP array in 17 of 77 patients (22%); this finding significantly affected TTT. There was no correlation with the presence of TP53 mutations. In multivariate analysis, including age, Binet stage, IGHV genes mutational status and large genomic lesion, the latter three factors emerged as independent prognosticators. The concordance between FISH and SNP array varied between 84 and 97%, depending on the specific genomic locus investigated. Conclusions SNP array detected additional large genomic aberrations not covered by the standard FISH panel predicting the outcome of CLL patient

Towards automating underwater measurement of fish length: a comparison of semi-automatic and manual stereo–video measurements

Underwater stereo–video systems are widely used for counting and measuring fish in aquaculture, fisheries, and conservation management. Length measurements are generated from stereo–video recordings by a software operator using a mouse to locate the head and tail of a fish in synchronized pairs of images. This data can be used to compare spatial and temporal changes in the mean length and biomass or frequency distributions of populations of fishes. Since the early 1990s stereo–video has also been used for measuring the lengths of fish in aquaculture for quota and farm management. However, the costs of the equipment, software, the time, and salary costs involved in post processing imagery manually and the subsequent delays in the availability of length information inhibit the adoption of this technology. We present a semi-automatic method for capturing stereo–video measurements to estimate the lengths of fish. We compare the time taken to make measurements of the same fish measured manually from stereo–video imagery to that measured semi-automatically. Using imagery recorded during transfers of Southern Bluefin Tuna (SBT) from tow cages to grow out cages, we demonstrate that the semi-automatic algorithm developed can obtain fork length measurements with an error of less than 1% of the true length and with at least a sixfold reduction in operator time in comparison to manual measurements. Of the 22 138 SBT recorded we were able to measure 52.6% (11 647) manually and 11.8% (2614) semi-automatically. For seven of the eight cage transfers recorde,d there were no statistical differences in the mean length, weight, or length frequency between manual and semi-automatic measurements. When the data were pooled across the eight cage transfers, there was no statistical difference in mean length or weight between the stereo–video-based manual and semi-automated measurements. Hence, the presented semi-automatic system can be deployed to significantly reduce the cost involved in adoption of stereo–video technology

SUSY QCD impact on top-pair production associated with a Z0Z^0-boson at a photon-photon collider

The top-pair production in association with a $Z^0$-boson at a photon-photon collider is an important process in probing the coupling between top-quarks and vector boson and discovering the signature of possible new physics. We describe the impact of the complete supersymmetric QCD(SQCD) next-to-leading order(NLO) radiative corrections on this process at a polarized or unpolarized photon collider, and make a comparison between the effects of the SQCD and the standard model(SM) QCD. We investigate the dependence of the lowest-order(LO) and QCD NLO corrected cross sections in both the SM and minimal supersymmetric standard model(MSSM) on colliding energy $\sqrt{s}$ in different polarized photon collision modes. The LO, SM NLO and SQCD NLO corrected distributions of the invariant mass of $t\bar t$-pair and the transverse momenta of final $Z^0$-boson are presented. Our numerical results show that the pure SQCD effects in \ggttz process can be more significant in the $+ +$ polarized photon collision mode than in other collision modes, and the relative SQCD radiative correction in unpolarized photon collision mode varies from 32.09% to $-1.89$ when $\sqrt{s}$ goes up from $500 GeV$ to $1.5 TeV$.Comment: 22 pages and 13 figure

Basal and stimulated calcitonin for the diagnosis of medullary thyroid cancer: updated thresholds and safety assessment

Purpose Reliable cut-offs for basal (bCT) and calcium stimulated calcitonin (casCT) are needed for an early and accurate diagnosis of medullary thyroid cancer (MTC). Patients and methods Fifty-four new patients with nodular goiter were enrolled and analysed together with those previously published by our group for a total of 135 cases. bCT and casCT were measured by a highly sensitive method and the results compared with histological findings. In a subgroup of patients, cardiac rhythm was recorded before and during the calcium test. Results In both females (F) and males (M), there was a significant correlation between tumor size and bCT levels (P < 0.001). The receiver operating characteristic plot analyses showed that, for bCT, the new cut-off points able to separate non-MTC from MTC patients were > 30 (F) and > 34 pg/mL (M), whereas the best casCT thresholds were > 79 (F) and > 466 pg/mL (M). bCT was shown to harbour a high accuracy, though some cases were diagnosed only upon stimulation test. Importantly, combining bCT, below or above the cut-offs, with casCT above the cut-offs, all the MTC cases were correctly identified. A reversible sinus bradycardia was observed in 9% of cases during the test. Conclusions Refined cut-offs for bCT and casCT in patients with nodular goiter are reported. Sensitive bCT was shown to have a high accuracy, but the combination with casCT data was needed to identify all MTC cases. The reliability and safety of calcium test strongly favour the routine use of CT determination in nodular thyroid disease

Basal and stimulated calcitonin for the diagnosis of medullary thyroid cancer: updated thresholds and safety assessment

Purpose: Reliable cut-offs for basal (bCT) and calcium stimulated calcitonin (casCT)are needed for an early and accurate diagnosis of medullary thyroid cancer (MTC). Patients and methods: Fifty-four new patients with nodular goiter were enrolled and analysed together with those previously published by our group for a total of 135 cases. bCT and casCT were measured by a highly sensitive method and the results compared with histological findings. In a subgroup of patients, cardiac rhythm was recorded before and during the calcium test. Results: In both females (F) and males (M), there was a significant correlation between tumor size and bCT levels (P 30 (F) and > 34 pg/mL (M), whereas the best casCT thresholds were > 79 (F) and > 466 pg/mL (M). bCT was shown to harbour a high accuracy, though some cases were diagnosed only upon stimulation test. Importantly, combining bCT, below or above the cut-offs, with casCT above the cut-offs, all the MTC cases were correctly identified. A reversible sinus bradycardia was observed in 9% of cases during the test. Conclusions: Refined cut-offs for bCT and casCT in patients with nodular goiter are reported. Sensitive bCT was shown to have a high accuracy, but the combination with casCT data was needed to identify all MTC cases. The reliability and safety of calcium test strongly favour the routine use of CT determination in nodular thyroid disease

The sieve-element endoplasmic reticulum: A focal point of phytoplasma-host plant interaction?

The rough endoplasmic reticulum (r-ER) is of paramount importance for adaptive responses to biotic stresses due to an increased demand for de novo synthesis of immunity-related proteins and signaling components. In nucleate cells, disturbance of r-ER integrity and functionality leads to the “unfolded protein response” (UPR), which is an important component of innate plant immune signalling. In contrast to an abundance of reports on r-ER responses to biotic challenges, sieve-element endoplasmic reticulum (SE-ER) responses to phytoplasma infection have not been investigated. We found that morphological SE-ER changes, associated with phytoplasma infection, are accompanied by differential expression of genes encoding proteins involved in shaping and anchoring the reticulum. Phytoplasma infection also triggers an increased release of bZIP signals from the (SE-ER)/r-ER and consequent differential expression of UPR-related genes. The modified expression patterns seem to reflect a trade-off between survival of host cells, needed for the phytoplasmic biotrophic lifestyle, and phytoplasmas. Specialized plasmodesmata between sieve element and companion cell may provide a corridor for transfer of phytoplasma effectors inducing UPR-related gene expression in companion cells

A diachronic-comparative analysis for the identification of the most powerful prognostic index for localized diffuse large B-cell lymphoma

BACKGROUND: In the rituximab era, the conventional International Prognostic index (IPI) lost at least in part its predictive power, while the National Comprehensive Cancer Network-IPI (NCCN-IPI) seems to be a new and valid prognosticator. However, it has not yet been evaluated in patients with localized disease and it has not been compared with the modified IPI (mIPI) of the pre-rituximab era. In order to evaluate the different prognosticators and to assess the importance of rituximab and radiotherapy (RT), we carried out the so far largest retrospective analysis of patients with localized diffuse large B-cell lymphoma (DLBCL). PATIENTS AND METHODS: We retrospectively assessed clinical and therapeutical data of 1405 patients treated in from 1987 to 2012 in 10 cancer centers in Italy and 1 in Austria. RESULTS: All patients underwent an anthracycline containing polychemotherapy and 254 additional rituximab. The median follow-up was 5.7 years (range 0.1-23 years). The 5-year overall survival (OS) was 75%, being significantly superior in those who underwent additional rituximab, while RT consolidation did not improve the outcome of those who received immunochemotherapy. Patients with extranodal disease benefited from the addition of rituximab, while RT did not improve OS of the immunochemotherapy subgroup. In the pre-rituximab era, the mIPI showed a better performance than the others. In rituximab-treated patients, the NCCN-IPI had the highest discriminant value and the 5-years OS varied significantly (P < 0.001) between the three risk groups and was 98% in low-risk patients, 82% in those with a low-intermediate risk and 57% among high-intermediate and high-risk cases. CONCLUSIONS: The NCCN-IPI is so far the best prognosticator for patients with localized DLBCL who underwent R-CHOP(-like). The addition of rituximab is indispensable regardless of the risk category and site of involvement, while the addition of RT should be reserved to those cases who are ineligible to rituximab