Are you sure it's an artifact?:Artifact detection and uncertainty quantification in histological images

Modern cancer diagnostics involves extracting tissue specimens from suspicious areas and conducting histotechnical procedures to prepare a digitized glass slide, called Whole Slide Image (WSI), for further examination. These procedures frequently introduce different types of artifacts in the obtained WSI, and histological artifacts might influence Computational Pathology (CPATH) systems further down to a diagnostic pipeline if not excluded or handled. Deep Convolutional Neural Networks (DCNNs) have achieved promising results for the detection of some WSI artifacts, however, they do not incorporate uncertainty in their predictions. This paper proposes an uncertainty-aware Deep Kernel Learning (DKL) model to detect blurry areas and folded tissues, two types of artifacts that can appear in WSIs. The proposed probabilistic model combines a CNN feature extractor and a sparse Gaussian Processes (GPs) classifier, which improves the performance of current state-of-the-art artifact detection DCNNs and provides uncertainty estimates. We achieved 0.996 and 0.938 F1 scores for blur and folded tissue detection on unseen data, respectively. In extensive experiments, we validated the DKL model on unseen data from external independent cohorts with different staining and tissue types, where it outperformed DCNNs. Interestingly, the DKL model is more confident in the correct predictions and less in the wrong ones. The proposed DKL model can be integrated into the preprocessing pipeline of CPATH systems to provide reliable predictions and possibly serve as a quality control tool.</p

Are you sure it's an artifact?:Artifact detection and uncertainty quantification in histological images

Modern cancer diagnostics involves extracting tissue specimens from suspicious areas and conducting histotechnical procedures to prepare a digitized glass slide, called Whole Slide Image (WSI), for further examination. These procedures frequently introduce different types of artifacts in the obtained WSI, and histological artifacts might influence Computational Pathology (CPATH) systems further down to a diagnostic pipeline if not excluded or handled. Deep Convolutional Neural Networks (DCNNs) have achieved promising results for the detection of some WSI artifacts, however, they do not incorporate uncertainty in their predictions. This paper proposes an uncertainty-aware Deep Kernel Learning (DKL) model to detect blurry areas and folded tissues, two types of artifacts that can appear in WSIs. The proposed probabilistic model combines a CNN feature extractor and a sparse Gaussian Processes (GPs) classifier, which improves the performance of current state-of-the-art artifact detection DCNNs and provides uncertainty estimates. We achieved 0.996 and 0.938 F1 scores for blur and folded tissue detection on unseen data, respectively. In extensive experiments, we validated the DKL model on unseen data from external independent cohorts with different staining and tissue types, where it outperformed DCNNs. Interestingly, the DKL model is more confident in the correct predictions and less in the wrong ones. The proposed DKL model can be integrated into the preprocessing pipeline of CPATH systems to provide reliable predictions and possibly serve as a quality control tool.</p

Extending the repertoire of microsatellite markers for genetic linkage mapping and germplasm

To increase the number of polymorphic simple sequence repeat markers (SSRs) in chickpea, a genomic library was constructed, and the SSRs derived from this approach are characterized. A genomic DNA library from the chickpea genotype ICC 4958 was constructed after digesting total DNA of ICC 4958 with MBO/Sau and TaqI at University of Frankfurt, Germany. The study increases the existing SSR repertoire in chickpea, which will help to enhance the coverage of linkage maps especially in intraspecific crosses where marker polymorphism is found to be very less

Cosmological parameter estimation using Very Small Array data out to ℓ= 1500

We estimate cosmological parameters using data obtained by the Very Small Array (VSA) in its extended configuration, in conjunction with a variety of other cosmic microwave background (CMB) data and external priors. Within the flat Λ cold dark matter (ΛCDM) model, we find that the inclusion of high-resolution data from the VSA modifies the limits on the cosmological parameters as compared to those suggested by the Wilkinson Microwave Anisotropy Probe (WMAP) alone, while still remaining compatible with their estimates. We find that Ωbh2= 0.0234+0.0012−0.0014, Ωdmh2= 0.111+0.014−0.016, h= 0.73+0.09−0.05, nS= 0.97+0.06−0.03, 1010AS= 23+7−3 and τ= 0.14+0.14−0.07 for WMAP and VSA when no external prior is included. On extending the model to include a running spectral index of density fluctuations, we find that the inclusion of VSA data leads to a negative running at a level of more than 95 per cent confidence ( nrun=−0.069 ± 0.032 ), something that is not significantly changed by the inclusion of a stringent prior on the Hubble constant. Inclusion of prior information from the 2dF galaxy redshift survey reduces the significance of the result by constraining the value of Ωm. We discuss the veracity of this result in the context of various systematic effects and also a broken spectral index model. We also constrain the fraction of neutrinos and find that fν < 0.087 at 95 per cent confidence, which corresponds to mν < 0.32 eV when all neutrino masses are equal. Finally, we consider the global best fit within a general cosmological model with 12 parameters and find consistency with other analyses available in the literature. The evidence for nrun < 0 is only marginal within this model

Promising antioxidant and antimicrobial food colourants from Lonicera caerulea L. var. Kamtschatica

Lonicera caerulea L. (haskap) berries are widely known for their richness in anthocyanins. In this study, such fruits were assessed for their nutritional and chemical composition, but also as sources of anthocyanins with great colouring properties to be applied in foodstu . Haskap presented high levels of water, four free sugars (mainly fructose and glucose), five organic acids (mainly citric, malic, and quinic), - and -tocopherol, twenty fatty acids (with prevalence of linoleic acid), and eight phenolic compounds, among which six were anthocyanins (mainly cyanidin-3-O-glucoside). The extract presented great antioxidant properties, evaluated through TBARS and OxHLIA assays, as well as antimicrobial capacity against six bacteria and six fungi. Two colourants were obtained by spray-drying haskap juice with maltodextrin and a mixture of maltodextrin and arabic gum. These formulations were stable over 12 weeks of storage at room and refrigerated temperature, without significant variations in colour parameters and in anthocyanins concentration. They were considered safe for consumption once neither microbial contamination nor cytotoxicity in non-tumour cells were detected. The results obtained allow for the consideration of haskap as a promising source of colourants to be applied not only in the food industry, but also in other fields that rely on artificial colourants.The authors are grateful to Foundation for Science and Technology (FCT, Portugal) and FEDER under Programme PT2020 for financial support to CIMO (UID/AGR/00690/2019), and FCT/MCTES (PIDDAC) and FCT for financial support to LSRE-LCM (UID/EQU/50020/2019); national funding by FCT, P.I., through the institutional scientific employment program-contract for M.I. Dias, I.P.F., and L. Barros, and through the individual scientific employment program-contract for S.A. Heleno and J. Barreira; C. Pereira’s contract though the celebration of program-contract foreseen in No. 4, 5 and 6 of article 23º of Decree-Law No. 57/2016, of 29th August, amended by Law No. 57/2017, of 19th July; to FEDER-Interreg España-Portugal programme for financial support through the project 0377_Iberphenol_6_E; the European Regional Development Fund (ERDF) through the Regional Operational Program North 2020, within the scope of Project NORTE-01-0145-FEDER-023289: DeCodE and project Mobilizador Norte-01-0247-FEDER-024479: ValorNatural®.info:eu-repo/semantics/publishedVersio

Anthocyanins from rubus fruticosus l. And morus nigra l. applied as food colorants: a natural alternative

Given the importance of colour in the general acceptance or rejection of a product, the use of colorants is a widespread practice, particularly in the food industry. At the same time, with the increasing consumers’ awareness of the health effects that some artificial colorants can exert, there is a growing tendency to prioritize foodstuffs containing natural additives. In this work, Morus nigra L. and Rubus fruticosus L. fruit juices were characterized in terms of anthocyanins, organic acids, free sugars, and tocopherols, as also regarding their bioactive properties. Given their richness in anthocyanins, this study also aimed to prepare different solid colouring formulations by the spray-drying technique, using as stabilizers maltodextrin and arabic gum. Six free sugars and two organic acids were detected in the fruit juices, as well as the four tocopherol isoforms. Two cyanidin derivatives were found in M. nigra (cyanidin-3-O-glucoside and cyanidin-O-rhamnoside) and other four in R. fruticosus (cyanidin-O-hexoside, cyanidin-3-O-glucoside, cyanidin-O-pentoside, and cyanidin-3-O-dioxaloilglucoside). The developed colouring formulations revealed a good stability over time, in terms of anthocyanin concentration and colour parameters, and revealed to be safe for consumption, either concerning their low microbial load and lack of cytotoxicity. Thus, they represent a promising natural alternative to the massively used artificial colorants.The authors are grateful to the Foundation for Science and Technology (FCT, Portugal) for financial support through national funds FCT/MCTES to CIMO (UIDB/00690/2020); national funding by F.C.T. and P.I., through the institutional scientific employment program-contract for C.P., M.I.D., I.P.F., and L.B. contracts, through the individual scientific employment program-contract for S.A.H., J.C.M.B., and M.C., and A.K.M. PhD grant (2020.06231.BD). To FEDER-Interreg España-Portugal programme for financial support through the project TRANSCoLAB 0612_TRANS_CO_LAB_2_P; to ERDF through the Regional Operational Program North 2020, within the scope of project Mobilizador Norte-01-0247-FEDER-024479: ValorNatural® and Project GreenHealth-Norte-01-0145- FEDER-000042. The authors are grateful to the Ministry of Education, Science and Technological Development of Serbia (Grant No. 451-03-9/2021-14/200007).info:eu-repo/semantics/publishedVersio

Quasinormal modes of Schwarzschild black holes in four and higher dimensions

We make a thorough investigation of the asymptotic quasinormal modes of the four and five-dimensional Schwarzschild black hole for scalar, electromagnetic and gravitational perturbations. Our numerical results give full support to all the analytical predictions by Motl and Neitzke, for the leading term. We also compute the first order corrections analytically, by extending to higher dimensions, previous work of Musiri and Siopsis, and find excellent agreement with the numerical results. For generic spacetime dimension number D the first-order corrections go as $\frac{1}{n^{(D-3)/(D-2)}}$. This means that there is a more rapid convergence to the asymptotic value for the five dimensional case than for the four dimensional case, as we also show numerically.Comment: 12 pages, 5 figures, RevTeX4. v2. Typos corrected, references adde

Effectiveness and safety of obeticholic acid in a Southern European multicenter cohort of patients with primary biliary cholangitis and suboptimal response to ursodeoxycholic acid

Background Obeticholic acid (OCA) was recently approved as the only on-label alternative for patients with primary biliary cholangitis (PBC) with intolerance or suboptimal response to ursodeoxycholic acid (UDCA). However, few data are available outside clinical trials. Aim To assess the effectiveness and safety of OCA in a real-world cohort of patients with non-effective UDCA therapy. Methods Open-label, prospective, real-world, multicentre study, enrolling consecutive patients who did not meet Paris II criteria, from 18 institutions in Spain and Portugal. Effectiveness was assessed by the changes in GLOBE and UK-PBC scores from baseline. POISE and Paris II criteria were evaluated after 12 months of OCA . Liver fibrosis was evaluated by FIB-4 and AST to platelet ratio index (APRI). Results One hundred and twenty patients were eligible, median time since PBC diagnosis 9.3 (4.0-13.8) years, 21.7% had cirrhosis, and 26.7% received had previous or concomitant treatment with fibrates. Seventy-eight patients completed at least 1 year of OCA. The Globe-PBC score decreased to 0.17 (95% CI 0.05 to 0.28; P = 0.005) and the UK-PBC score decreased to 0.81 (95% CI -0.19 to 1.80; P = 0.11). There was a significant decrease in alkaline phosphatase of 81.3 U/L (95% CI 42.5 to 120; P < 0.001), ALT 22.1 U/L (95% CI 10.4 to 33.8; P < 0.001) and bilirubin 0.12 mg/dL (95% CI 0 to 0.24; P = 0.044). FIB-4 and APRI remained stable. According to the POISE criteria, 29.5% (23 out of 78) achieved response. The adverse events rate was 35%; 11.67% discontinued (8.3% due to pruritus). Conclusions This study supports data from phase III trials with significant improvement of PBC-Globe continuous prognostic marker score among OCA-treated patients with good tolerability

Evaluation of allergic and serological tests for diagnosing Brucella melitensis infection in sheep

A total of 291 unvaccinated sheep from Brucella melitensis-infected flocks were examined for delayed-type hypersensitivity (DTH) responses with Brucellergene commercial allergen and with cold saline extract and cytosol from rough B. melitensis 115, and their sera were tested in the rose bengal test (RBT), complement fixation test (CFT), and enzyme-linked immunosorbent assay (ELISA) with lipopolysaccharide. DTH reactions were maximal after 72 h, with no intensity differences among allergens, inoculation sites (eyelid and tail), and doses tested. There were no differences in the results recorded by visual inspection and palpation of inoculation sites, by measuring skin thickness with a caliper, or by microscopic examination of samples taken at necropsy; Six days after DTH testing, anergy was observed in 100% of the animals, and 100% reactivity was recovered only after 24 days. All animals were necropsied, and thorough bacteriological searches were performed. The sensitivities found with the 140 animals from which B. melitensis was isolated were ELISA, 100%; DTH, 97.1%; RBT, 92.1%; and CFT, 88.6%. Those results put into question the value of RBT and CFT as screening and confirmatory tests for sheep brucellosis and at least indicate that their standardization should be modified. For 151 tested sheep from which B. melitensis was not isolated, the percentages of positive animals were ELISA, 100%; DTH, 94.0%; RBT, 57.6%; and CFT, 53.6%. All tests were negative for 100 tested sheep from Brucella-free flocks. The different results of bacteriological and immunological tests suggest the usefulness of developing indirect tests able to distinguish truly infected animals from those that have developed an immunological response

ParadisEO-MOEO: A Software Framework for Evolutionary Multi-Objective Optimization

This chapter presents ParadisEO-MOEO, a white-box object-oriented software framework dedicated to the flexible design of metaheuristics for multi-objective optimization. This paradigm-free software proposes a unified view for major evolutionary multi-objective metaheuristics. It embeds some features and techniques for multi-objective resolution and aims to provide a set of classes allowing to ease and speed up the development of computationally efficient programs. It is based on a clear conceptual distinction between the solution methods and the problems they are intended to solve. This separation confers a maximum design and code reuse. This general-purpose framework provides a broad range of fitness assignment strategies, the most common diversity preservation mechanisms, some elitistrelated features as well as statistical tools. Furthermore, a number of state-of-the-art search methods, including NSGA-II, SPEA2 and IBEA, have been implemented in a user-friendly way, based on the fine-grained ParadisEO-MOEO components