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opencc-by-4.0Jul 2020View details →

Data for " SCTR hypermethylation is a diagnostic biomarker in colorectal cancer"

This data set provides data files to accompany the article SCTR hypermethylation is a diagnostic biomarker in colorectal cancer. The data consists of methylation profiles of SCTR gene from The Cancer Genome Atlas (TCGA) CRC methylation data (N = 440), a large-scale test set (N = 938) from the Gene Expression Omnibus (GEO), and our independent validation set (N = 371).

opencc-zeroJul 2020View details →

Discordant Clostridioides difficile diagnostic assay and treatment practice: a cross-sectional study in a tertiary care hospital, Geneva, Switzerland

Objectives: To determine the proportion of patients who received a treatment for Clostridioides difficile infection (CDI) among those presenting a discordant Clostridioides difficile diagnostic assay and to identify patient characteristics associated with the decision to treat CDI. Design: Cross-sectional study. Setting: Monocentric study in a tertiary care hospital, Geneva, Switzerland Participants: Among 4562 adult patients tested for C. difficile between March 2017 and March 2019, 208 patients with discordant tests' results (positive nucleic acid amplification test [NAAT+]/negative enzyme immunoassay [EIA-]) were included. Main outcome measures: Treatment for CDI. Results: CDI treatment was administered in 147 (71%) cases. In multivariate analysis, an abdominal computed tomography scan with signs of colitis (OR 14.7; 95% CI 1.96-110.8) was the only factor associated with CDI treatment. Conclusions: The proportion of NAAT+/EIA- patients who received treatment questions the contribution of the EIA for the detection of toxin A/B after NAAT to limit overtreatment. Additional studies are needed to investigate if other factors are associated with the decision to treat.

opennotspecifiedJun 2020View details →

FIGURE 7 in Comparative morphology of myrmecophilous immature stages of European Microdon species (Diptera: Syrphidae): updated identification key and new diagnostic characters

FIGURE 7. Dorsal reticulation of third instar larvae of M. myrmicae (A, B), M. analis (C, D) and M. devius (E, F); left, general view; right, detail of single reticulation processes. A = 400 µm; B = 50 µm; C, E = 500 µm; D = 100 µm; F = 200 µm.

opencc-by-4.0Nov 2020View details →

Failed Total Hip Arthroplasty: Diagnostic Performance of Conventional MRI Features and Locoregional Lymphadenopathy to Identify Infected Implants

Background: Very little has been published about the diagnostic performance of MRI in total hip arthroplasty (THA) infection. Purpose: To determine the diagnostic performance of conventional MRI features and of new lymph nodal indices to identify infection in patients with failed THA. Study type: Retrospective. Population: In all, 119 patients (66 females; age 66.9 ± 12.4 years) with failed THA. Field strength/sequences: Metal artifact reduction sequence (MARS) protocol including short tau inversion recovery and turbo spin-echo T1 - and T2 -weighted sequences at 1.5T. Assessment: Patients underwent pelvis MRI prior to failed THA revision. MRIs were reviewed to identify periprosthetic bone destruction, soft-tissue mass, effusion, synovitis, lamellated synovitis, extracapsular edema, fibrous periprosthetic membrane, bone edema, and extracapsular collection/sinus tract. The number and maximum diameter of inguinal, obturator and iliac lymph nodes of the affected hip were assessed and normalized to those of the unaffected hip to calculate the ratio of nodal size (RNS), ratio of node number (RNN), difference of nodal size (DNS), and difference of node number (DNN). Statistical tests: The Mann-Whitney U-and chi-square test were used. Diagnostic performance of indices and odds ratios (OR) were calculated. Results: RNS, RNN, DNS, and DNN indices were significantly different (P = 0.000) between infected and noninfected THA, with accuracies ranging from 84.8% (RNS) and 93.1% (RNN). All other MRI features were significantly more prevalent in infected THA (P ≤ 0.002), except bone destruction, periarticular soft-tissue mass, and fibrous membrane (P ≥ 0.031). Sensitivities ranged from 7.9% (soft-tissue mass) to 76.3% (effusion/bone edema), specificity from 45.7% (bone destruction) to 97.5% (synovitis/lamellated synovitis), accuracy from 49.6% (bone destruction) to 81.5% (synovitis), OR from 0.261 (soft-tissue mass) to 35.550 (synovitis). Data conclusion: Conventional MRI features have limited accuracy to differentiate septic and aseptic THA failure. Lymph nodal indices, particularly those related to nodal number, may represent biomarkers of THA infection.

opencc-zeroDec 2020View details →

Diagnostic Accuracy of Adrenal Imaging for Subtype Diagnosis in Primary Aldosteronism: Systematic Review and Meta-Analysis

Objectives: Accurate subtype classification in primary aldosteronism (PA) is critical in assessing the optimal treatment options. This study aimed to evaluate the diagnostic accuracy of adrenal imaging for unilateral PA classification. Methods: Systematic searches of PubMed, EMBASE, and the Cochrane databases were performed from January 1, 2000, to February 1, 2020, for all studies that used computed tomography (CT) or magnetic resonance imaging (MRI) in determining unilateral PA and validated the results against invasive adrenal vein sampling (AVS). Summary diagnostic accuracies were assessed using a bivariate random-effects model. Subgroup analyses, meta-regression and sensitivity analysis were performed to explore the possible sources of heterogeneity. Result: A total of 25 studies, involving a total of 4669 subjects, were identified. The overall analysis revealed a pooled sensitivity of 68% (95% confidence interval [CI]: 61 to 74) and specificity of 57% (95% CI: 50 to 65) for CT/MRI in identifying unilateral PA. Sensitivity was higher in the contrast-enhanced (CT) group versus the traditional CT group [77% (95% CI: 66 to 85) vs. 58% (95% CI: 50 to 66)]. Subgroup analysis stratified by screening test for PA showed that the sensitivity of the aldosterone-to-renin ratio (ARR) group was higher than that of the non-ARR group [78% (95% CI: 69 to 84) vs. 66% (95% CI: 58 to 72)]. The diagnostic accuracy of PA patients aged ≤40 years was reported in 4 studies, and the overall sensitivity was 71%, with 79% specificity. Meta-regression revealed a significant impact of sample size on sensitivity and of age and study quality on specificity. Conclusion: CT/MRI is not a reliable alternative to invasive AVS without excellent sensitivity or specificity for correctly identifying unilateral PA. Even in young patients (≤40 years), 21% of patients would have undergone unnecessary adrenalectomy based on imaging results alone.

opencc-zeroDec 2020View details →

Data from: In search of an optimal DNA diagnosis for taxonomic descriptions with MOLD, a novel tool to identify diagnostic nucleotide characters

While DNA characters are increasingly used for phylogenetic inference, taxa delimitation and identification, their use for formal description of taxa remains scarce and inconsistent. The major impediments until recently was a lack of a suitable algorithm to identify signature DNA characters. The 2019-2020 however were marked by an almost simultaneous release of three softwares, simple to run and designed specifically for taxonomists. There is, nevertheless, a major concern, whether taxonomy will benefit from wide application of these, or any of the previously available tools. The reluctance of using DNA data in taxonomy is partly due to concerns of insufficient reliability of DNA characters, as robustness of DNA based diagnoses, depending on the sampled fraction of the species diversity has not thus far been assessed. We propose a novel program, named MOLD that recovers diagnostic nucleotide combinations (DNCs) for selected taxa with DNA sequences available. We carried our random iterated haplotype subsampling on species in six published DNA data sets of varying complexity, providing a diagnosis to each subsample to evaluate how the robustness of DNA based diagnosis changes depending on the sampled fraction of the taxon's diversity. We demonstrate that the currently used diagnostic DNA characters, or combinations thereof (DNCs) often do not exist for a particular species in a particular data set, or are not sufficiently reliable. We propose a new type of DNA diagnosis, termed herein rDNCs, which is compiled to suit pre-defined criteria of reliability, and is implemented in MOLD. We demonstrate that rDNCs can be successfully identified even in data sets comprising hundreds of species, and allow for notably more reliable diagnoses, than the currently used diagnostic DNA characters. MOLD recovers reliable and reproducible diagnoses in traditionally problematic cases, such as cryptic species or species with pronounced genetic structure, and shows unparalleled efficiency in large DNA data sets, making a valuable complement to the currently existing toolkit.

FIGURE 7 in Insights into the Urogymnid whiprays (Chondrichthyes: Batoidea) in the Persian Gulf and the Gulf of Oman, with an amendment of their diagnostic characteristics and dispersal range

FIGURE 7. Maculabatis gerrardi (MM1619, male, DW= 27.2 cm), off Bushehr in the Persian Gulf. scale=10 cm.

FIGURE 5 in Insights into the Urogymnid whiprays (Chondrichthyes: Batoidea) in the Persian Gulf and the Gulf of Oman, with an amendment of their diagnostic characteristics and dispersal range

FIGURE 5. Maculabatis randalli, MM21 (male, DW=37.7 cm), treated as GN6649 by Naylor et al. (2012). Note a fully banded tail.

FIGURE 6 in Insights into the Urogymnid whiprays (Chondrichthyes: Batoidea) in the Persian Gulf and the Gulf of Oman, with an amendment of their diagnostic characteristics and dispersal range

FIGURE 6. Maculabatis arabica, MM602 (female, DW=43.8 cm), included in the mo;ecular analysis by Fernando et al. (2019) under the accession number MK335258. Note to seed-shaped suprascapular denticle without primary denticles and a plain tail.

FIGURE 4 in Insights into the Urogymnid whiprays (Chondrichthyes: Batoidea) in the Persian Gulf and the Gulf of Oman, with an amendment of their diagnostic characteristics and dispersal range

FIGURE 4. Maculabatis randalli, MM40 (female, DW=57.7 cm), treated as GN6668 by Naylor et al. (2012). Note a row of primary denticles followed by 3–4 suprascapular denticles and a fully banded tail.

FIGURE 3 in Insights into the Urogymnid whiprays (Chondrichthyes: Batoidea) in the Persian Gulf and the Gulf of Oman, with an amendment of their diagnostic characteristics and dispersal range

FIGURE 3. Color pattern of the tail (A) incomplete banded tail of a juvenile Maculabatis arabica (MM1582, female, DW =19.2 cm); (B) complete banded tail of a juvenile of M. randalli (MM1583, male, DW=19.2 cm). The molecular data confirmed the distinct identity of both specimens.

FIGURE 2 in Insights into the Urogymnid whiprays (Chondrichthyes: Batoidea) in the Persian Gulf and the Gulf of Oman, with an amendment of their diagnostic characteristics and dispersal range

FIGURE 2. Squamation of the mid-disc, (A) Maculabatis randalli (MM1567, female, DW=32.8 cm), note a 3 heart-shape suprascapular denticle with a row of the primary denticle band; (B) M. arabica (MM1412, male, DW=36.2 cm), note an enlarged seed-shape suprascapular denticle without a primary denticle band.. Head orientated to the left.

FIGURE 1 in Insights into the Urogymnid whiprays (Chondrichthyes: Batoidea) in the Persian Gulf and the Gulf of Oman, with an amendment of their diagnostic characteristics and dispersal range

FIGURE 1. Bayesian inference topology results from the phylogenetic analysis of 1044-bp of the ND2 gene for urogymnid species from the Persian Gulf, the Gulf of Oman and the relevant taxa from GenBank. Bayesian posterior probabilities (PP) are given at nodes. Taxon names are followed by their collection code and/or GenBank accession numbers. Specimens from the Persian Gulf and the Gulf of Oman for which sequence data were generated in the course of this study are in bold.

FIGURE 6 in Revision of the diagnostic characters of two morphologically similar snook species Centropomus viridis and C. nigrescens (Carangiformes: Centropomidae)

FIGURE 6. Difference between the mean shape of Centropomus nigrescens (solid line) and that of C. viridis (dashed line) based on partial Procrustes distances. Arrows indicate the direction of the change.

FIGURE 5 in Revision of the diagnostic characters of two morphologically similar snook species Centropomus viridis and C. nigrescens (Carangiformes: Centropomidae)

FIGURE 5. Scatter plot showing scores on the first two principal components explaining 56.3% of the total variance. Two taxonomic groups are detected, indicating that shape variables obtained by PCA are significant discriminators. Centropomus nigrescens is represented by black circles and C. viridis by gray circles.

FIGURE 3. Phylogenetic relationships among the Centropomus 16S in Revision of the diagnostic characters of two morphologically similar snook species Centropomus viridis and C. nigrescens (Carangiformes: Centropomidae)

FIGURE 3. Phylogenetic relationships among the Centropomus 16S rRNA gene sequences found in the GenBank (March, 2020), only those sequences which overlap with the sequences from this study were selected. Relationships are based on the neighbor-joining method and the Tamura 3-parameter with a gamma distribution (shape parameter = 1). Node value support higher than 60% are shown.

FIGURE 4 in Revision of the diagnostic characters of two morphologically similar snook species Centropomus viridis and C. nigrescens (Carangiformes: Centropomidae)

FIGURE 4. Some morphological variants of the first dorsal fin of genetically identified Centropomus nigrescens (A-C) and C. viridis (D-F) specimens. A and D represent the typical shape accepted for each species (blunt-shaped fin in C. nigrescens and triangular-shaped fin in C. viridis).

FIGURE 1 in Revision of the diagnostic characters of two morphologically similar snook species Centropomus viridis and C. nigrescens (Carangiformes: Centropomidae)

FIGURE 1. The Tropical Eastern Pacific map shows the geographic distribution of Centropomus nigrescens (black line) and C. viridis (gray line). Sampling localities are shown on the insert. The figure was made based on Robertson & Allen (2015).

FIGURE 2 in Revision of the diagnostic characters of two morphologically similar snook species Centropomus viridis and C. nigrescens (Carangiformes: Centropomidae)

FIGURE 2. Representation of the generalized morphology of Centropomus, indicating ten landmarks (black circles) and one semi-landmark (gray circle) on the position of the anatomical structures compared in this study.