Draft Genome Sequence of Gordonia lacunae BS2T

We report here the draft genome sequence of the soil bacterium Gordonia lacunae BS2T ( DSM 45085T JCM 14873T NRRL B-24551T), isolated from an estuary in Plettenberg Bay, South Africa. Analysis of the draft genome revealed that more than 40% of the secondary metabolite biosynthetic genes encode new compounds

Image_2_Comparison of O-RADS with the ADNEX model and IOTA SR for risk stratification of adnexal lesions: a systematic review and meta-analysis.tiff

PurposeThis study aims to systematically compare the diagnostic performance of the Ovarian-Adnexal Reporting and Data System with the International Ovarian Tumor Analysis Simple Rules and the Assessment of Different NEoplasias in the adneXa model for risk stratification of ovarian cancer and adnexal masses.MethodsA literature search of online databases for relevant studies up to July 2023 was conducted by two independent reviewers. The summary estimates were pooled with the hierarchical summary receiver-operating characteristic model. The quality of the included studies was assessed with the Quality Assessment of Diagnostic Accuracy Studies–2 and the Quality Assessment of Diagnostic Accuracy Studies-Comparative Tool. Metaregression and subgroup analyses were performed to explore the impact of varying clinical settings.ResultsA total of 13 studies met the inclusion criteria. The pooled sensitivity and specificity for eight head-to-head studies between the Ovarian-Adnexal Reporting and Data System and the Assessment of Different NEoplasias in the adneXa model were 0.96 (95% CI 0.92–0.98) and 0.82 (95% CI 0.71–0.90) vs. 0.94 (95% CI 0.91–0.95) and 0.83 (95% CI 0.77–0.88), respectively, and for seven head-to-head studies between the Ovarian-Adnexal Reporting and Data System and the International Ovarian Tumor Analysis Simple Rules, the pooled sensitivity and specificity were 0.95 (95% CI 0.93–0.97) and 0.75 (95% CI 0.62–0.85) vs. 0.91 (95% CI 0.82–0.96) and 0.86 (95% CI 0.76–0.93), respectively. No significant differences were found between the Ovarian-Adnexal Reporting and Data System and the Assessment of Different NEoplasias in the adneXa model as well as the International Ovarian Tumor Analysis Simple Rules in terms of sensitivity (P = 0.57 and P = 0.21) and specificity (P = 0.87 and P = 0.12). Substantial heterogeneity was observed among the studies for all three guidelines.ConclusionAll three guidelines demonstrated high diagnostic performance, and no significant differences in terms of sensitivity or specificity were observed between the three guidelines.</p

Table_1_Comparison of O-RADS with the ADNEX model and IOTA SR for risk stratification of adnexal lesions: a systematic review and meta-analysis.docx

PurposeThis study aims to systematically compare the diagnostic performance of the Ovarian-Adnexal Reporting and Data System with the International Ovarian Tumor Analysis Simple Rules and the Assessment of Different NEoplasias in the adneXa model for risk stratification of ovarian cancer and adnexal masses.MethodsA literature search of online databases for relevant studies up to July 2023 was conducted by two independent reviewers. The summary estimates were pooled with the hierarchical summary receiver-operating characteristic model. The quality of the included studies was assessed with the Quality Assessment of Diagnostic Accuracy Studies–2 and the Quality Assessment of Diagnostic Accuracy Studies-Comparative Tool. Metaregression and subgroup analyses were performed to explore the impact of varying clinical settings.ResultsA total of 13 studies met the inclusion criteria. The pooled sensitivity and specificity for eight head-to-head studies between the Ovarian-Adnexal Reporting and Data System and the Assessment of Different NEoplasias in the adneXa model were 0.96 (95% CI 0.92–0.98) and 0.82 (95% CI 0.71–0.90) vs. 0.94 (95% CI 0.91–0.95) and 0.83 (95% CI 0.77–0.88), respectively, and for seven head-to-head studies between the Ovarian-Adnexal Reporting and Data System and the International Ovarian Tumor Analysis Simple Rules, the pooled sensitivity and specificity were 0.95 (95% CI 0.93–0.97) and 0.75 (95% CI 0.62–0.85) vs. 0.91 (95% CI 0.82–0.96) and 0.86 (95% CI 0.76–0.93), respectively. No significant differences were found between the Ovarian-Adnexal Reporting and Data System and the Assessment of Different NEoplasias in the adneXa model as well as the International Ovarian Tumor Analysis Simple Rules in terms of sensitivity (P = 0.57 and P = 0.21) and specificity (P = 0.87 and P = 0.12). Substantial heterogeneity was observed among the studies for all three guidelines.ConclusionAll three guidelines demonstrated high diagnostic performance, and no significant differences in terms of sensitivity or specificity were observed between the three guidelines.</p

Image_3_Comparison of O-RADS with the ADNEX model and IOTA SR for risk stratification of adnexal lesions: a systematic review and meta-analysis.tiff

PurposeThis study aims to systematically compare the diagnostic performance of the Ovarian-Adnexal Reporting and Data System with the International Ovarian Tumor Analysis Simple Rules and the Assessment of Different NEoplasias in the adneXa model for risk stratification of ovarian cancer and adnexal masses.MethodsA literature search of online databases for relevant studies up to July 2023 was conducted by two independent reviewers. The summary estimates were pooled with the hierarchical summary receiver-operating characteristic model. The quality of the included studies was assessed with the Quality Assessment of Diagnostic Accuracy Studies–2 and the Quality Assessment of Diagnostic Accuracy Studies-Comparative Tool. Metaregression and subgroup analyses were performed to explore the impact of varying clinical settings.ResultsA total of 13 studies met the inclusion criteria. The pooled sensitivity and specificity for eight head-to-head studies between the Ovarian-Adnexal Reporting and Data System and the Assessment of Different NEoplasias in the adneXa model were 0.96 (95% CI 0.92–0.98) and 0.82 (95% CI 0.71–0.90) vs. 0.94 (95% CI 0.91–0.95) and 0.83 (95% CI 0.77–0.88), respectively, and for seven head-to-head studies between the Ovarian-Adnexal Reporting and Data System and the International Ovarian Tumor Analysis Simple Rules, the pooled sensitivity and specificity were 0.95 (95% CI 0.93–0.97) and 0.75 (95% CI 0.62–0.85) vs. 0.91 (95% CI 0.82–0.96) and 0.86 (95% CI 0.76–0.93), respectively. No significant differences were found between the Ovarian-Adnexal Reporting and Data System and the Assessment of Different NEoplasias in the adneXa model as well as the International Ovarian Tumor Analysis Simple Rules in terms of sensitivity (P = 0.57 and P = 0.21) and specificity (P = 0.87 and P = 0.12). Substantial heterogeneity was observed among the studies for all three guidelines.ConclusionAll three guidelines demonstrated high diagnostic performance, and no significant differences in terms of sensitivity or specificity were observed between the three guidelines.</p

Image_1_Comparison of O-RADS with the ADNEX model and IOTA SR for risk stratification of adnexal lesions: a systematic review and meta-analysis.tiff

PurposeThis study aims to systematically compare the diagnostic performance of the Ovarian-Adnexal Reporting and Data System with the International Ovarian Tumor Analysis Simple Rules and the Assessment of Different NEoplasias in the adneXa model for risk stratification of ovarian cancer and adnexal masses.MethodsA literature search of online databases for relevant studies up to July 2023 was conducted by two independent reviewers. The summary estimates were pooled with the hierarchical summary receiver-operating characteristic model. The quality of the included studies was assessed with the Quality Assessment of Diagnostic Accuracy Studies–2 and the Quality Assessment of Diagnostic Accuracy Studies-Comparative Tool. Metaregression and subgroup analyses were performed to explore the impact of varying clinical settings.ResultsA total of 13 studies met the inclusion criteria. The pooled sensitivity and specificity for eight head-to-head studies between the Ovarian-Adnexal Reporting and Data System and the Assessment of Different NEoplasias in the adneXa model were 0.96 (95% CI 0.92–0.98) and 0.82 (95% CI 0.71–0.90) vs. 0.94 (95% CI 0.91–0.95) and 0.83 (95% CI 0.77–0.88), respectively, and for seven head-to-head studies between the Ovarian-Adnexal Reporting and Data System and the International Ovarian Tumor Analysis Simple Rules, the pooled sensitivity and specificity were 0.95 (95% CI 0.93–0.97) and 0.75 (95% CI 0.62–0.85) vs. 0.91 (95% CI 0.82–0.96) and 0.86 (95% CI 0.76–0.93), respectively. No significant differences were found between the Ovarian-Adnexal Reporting and Data System and the Assessment of Different NEoplasias in the adneXa model as well as the International Ovarian Tumor Analysis Simple Rules in terms of sensitivity (P = 0.57 and P = 0.21) and specificity (P = 0.87 and P = 0.12). Substantial heterogeneity was observed among the studies for all three guidelines.ConclusionAll three guidelines demonstrated high diagnostic performance, and no significant differences in terms of sensitivity or specificity were observed between the three guidelines.</p

A Novel Single-Labeled Fluorescent Oligonucleotide Probe for Silver(I) Ion Detection in Water, Drugs, and Food

Due to the high toxicity of silver­(I) ions, a method for the rapid, sensitive, and selective detection for silver­(I) ions in water, pharmaceutical products, and food is of great importance. Herein, a novel single-labeled fluorescent oligonucleotide (OND) probe based on cytosine–Ag­(I)–cytosine coordination and the inherent fluorescence quenching ability of the G-quadruplex is designed to detect silver­(I) ions. The formation of a hairpin structure in the OND–Ag­(I) complex brings the hexachloro fluorescein (HEX) labeled at the 5′-end of the OND probe close to the G-quadruplex located at the 3′-end of the OND probe, leading to a fluorescence quenching due to photoinduced electron transfer between HEX and the G-quadruplex. Through this method, silver­(I) ions can be detected quantitatively, the linear response range is from 1 to 100 nmol/L with a detection limit of 50 pmol/L, and no obvious interference occurs with other metal ions with a 10-fold concentration. This assay is simple, sensitive, and selective, and it can be used to detect silver­(I) ions in actual water, drug, and food samples

Additional file 1 of Association and biological pathways between lung function and incident depression: a prospective cohort study of 280,032 participants

Additional file 1: Table S1. Mean concentration of biomarkers (n = 231,193). Table S2. Mean concentration of metabolites (n = 62,488). Table S3. Summary of missing data of covariates. Table S4. Baseline characteristics by lung function (n = 280,032). Table S5. Sensitivity analyses for association between incident depression and lung function with further adjustment for covariates. Table S6. Sensitivity analyses for association between incident depression and lung function with different exclusion criteria. Table S7. Sensitivity analyses for association between lung function and risk of incident depression with multiple imputation for missing covariates (n = 297,037). Table S8. Sensitivity analyses for association between lung function and risk of incident depression with further excluding prevalent depression as measured by the PHQ-2 scale at baseline (n = 271,122). Table S9. Selection of biomarkers as potential mediators between lung function and incident depression (n = 231,193). Table S10. Selection of metabolites as potential mediators between lung function and incident depression (n = 62,488). Fig. S1. Subgroup analysis of the association of lung function on depression by potential risk factors

The effects of the net advancement speed of the cell edge on the contact time between the lamellipodium and a filopodia adhesion.

<p><b>A.</b> Scatter plot of the part of the contact time of a filopodia adhesion with the advancing lamellipodium, with respect to the net advancement speed of the cell edge. All data were for REF52-β3-integrin-EGFP cells spreading on FN coated glass. <i>Black:</i> maturing filopodia adhesions. <i>Red:</i> disassembling filopodia adhesions. Due to the fast net advancement speed of the cell edge, the disassembling filopodia adhesions demonstrated a reduced contact time with the advancing lamellipodia, which subsequently had very brief of no pausing at these filopodia adhesions. Open symbols correspond to the filopodia adhesions in B–b. <b>B. a.</b> A fast spreading REF52 fibroblast expressing β3-integrin-EGFP (green) on FN coated glass (5 min–9 min 30 s after plating, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107097#pone.0107097.s013" target="_blank">Video S8</a>). The cell membrane was stained with the fluorophore DiI (red). <b>b.</b> Magnified views of the dashed rectangle regions (I and II) in a. The selected frames from the time-lapse sequences showed the disassembly (I, horizontal arrows) or steady maturation (II, vertical arrows) of the filopodia adhesions as a result of ongoing advancement or prolonged pausing of lamellipodium at the two filopodia adhesions respectively. <b>c.</b> The advancement of cell two edges are represented by the kymographs that were generated along the corresponding kymograph lines (colored arrows in a) from the membrane fluorescence signal at the two filopodia adhesions. The dashed lines indicate the advancing (yellow) and pausing (pink) phases of lamellipodia at the respective filopodia adhesions. The net advancement speeds of the cell edges were measured at the corresponding sections of the kymographs as indicated by the dashed yellow lines (B-c I, 161 nm/s; B–c II, 147 nm/s). Scale bars: 2 µm (B–b), 5 µm (B–a).</p

The actin cytoskeleton organization at filopodia adhesions as seen in ventral cell membrane samples.

<p>Cells were gently blasted open. While this might cause some local disruptions, the main purpose was to distinguish between molecular components that are weak versus strongly bound to the ventral site of the plasma membrane. The colors of stains denote the ventral cell membrane (red) and actin structures (green). Filopodia adhesions were identified (see method) by vinculin immunostaining (cyan, A–b, B–b), interference reflection signals (grey images, B), and β3-integrin-EGFP imaging (grey, C). <b>A and B.</b> Cell edge regions of the exposed ventral cell membranes from HFF cells (20 min (A) or 33 min (B) after plating on FN coated glass). The white square regions (A–a, B–a) were magnified respectively (b, c in A; b–f in B). In merged images, vinculin was alternatively false colored in red (A–c, B–e, B–f) for a better presentation of the colocalization of signals. Pink arrow or arrowheads denote the former filopodia actin bundles and their associated substrate adhesions. The cyan arrowheads indicate circumferential stress fibers with their surface anchorage (A) or tight surface association (B). The white arrow (A–c) indicates the separation between the filopodia adhesion in the cell lamellum and the distal section of the filopodium, which might be fracture that could have occurred during the sample preparation. <b>C.</b> The cell periphery of an exposed ventral cell membrane from a REF52-β3-integrin-EGFP cell (30 min after plating on FN coated glass) showed a β3-integrin cluster at the filopodium (pink arrows), circumferential stress fibers (cyan arrowheads) anchored to the substrate via the β3-integrin clusters formed at the side of this filopodia adhesion, and the sidewise widening of the filopodia β3-integrin cluster (pink arrowheads) following the connected thick circumferential stress fibers in the cell lamellum. Scale bar: 5 µm (A–b & c, B, C), 10 µm (A–a).</p

Growth kinetics of filopodia adhesions after MLCK inhibition (A, B) or on soft polyacrylamide gels (C, D).

<p>The β3-integrin-EGFP (green) expressing REF52 fibroblasts on FN coated glass (A, B) or polyacrylamide gel (C, D) surfaces were time-lapse tracked with confocal microscopy. The cell membrane was stained by the fluorophore DiI (red). <b>A and B.</b> Inhibition of MLCK by ML-7 suppressed the cyclic protrusions and retractions of lamellipodium and the growth of filopodia adhesions. <b>A.</b> Time-lapse montage (b) of the filopodium containing cell edge region (white rectangle, a) showed the loss of the cyclic protrusions and retractions of the lamellipodium in the proximity of the filopodium in ML-7 treated cells (25 min–30 min after plating, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107097#pone.0107097.s009" target="_blank">Video S4</a>). <b>B.</b> Time-lapse montage (b) of the filopodia adhesion cell edge region (white rectangle, a) demonstrated the suppressed size growth of the filopodia β3-integrin adhesion in ML-7 treated cells. c. Comparison of the area (average of the tracked temporal states (0–600 s)) of the filopodia β3-integrin adhesions (7 adhesions, n = 17) in the ML-7 (30 or 40 µM) treated cells with that of the maturing filopodia β3-integrin adhesions (6 adhesions, n = 164) in the cells plated in normal culture media. Error bars correspond to the standard errors. <b>C and D.</b> The growth of filopodia adhesions in REF52-β3-integrin-EGFP cells on soft PAA substrates was associated with the restored cyclic protrusions and retractions of lamellipodia. The PAA substrate (7.4 kPa) was covalently coated with FN. <b>C.</b> Cell without stable surface adhesions (a, 103 min–113 min after plating, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107097#pone.0107097.s010" target="_blank">Video S5</a>) exhibited significant ruffling as shown by the time-lapse montage of the cell edge (b). <b>D.</b> The filopodia adhesion (white rectangle, b) at the edge of a cell (white square in a, 121 min–136 min after plating, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107097#pone.0107097.s011" target="_blank">Video S6</a>) matured in association with the restored cyclic protrusions and retractions of the lamellipodium (c). To better visualize lamellipodium activities, all montages were stretched vertically 2×. Scale bars: 5 µm (A, D–b), 10 µm (B, C, D–a). The width of a single image frame in the montage is indicated by the horizontal grey bar: A–b, 2.5 µm; B–b, 4.5 µm; C–b, 6.2 µm; D–c, 3 µm.</p