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52 results for “ROC”
Supplemental data for "Intramolecular feedback regulation of the LRRK2 Roc G domain by a LRRK2 kinase dependent mechanism" (Gilsbach et al., eLife 2024, doi:10.7554/eLife.91083)
<p><strong>Supportive data for the eLife version of record.</strong></p> <p><strong>(1) Data used for the Michaelis Menten Kinetics.</strong></p> <p><strong>HPLC-based assay.</strong> Steady-state kinetic measurements of LRRK2-mediated GTP hydrolysis were performed as previously described (Ahmadian et al., 1997). Briefly, 0.1 µM of full-length LRRK2 was incubated with different amounts of GTP (0, 25, 75, 150, 250, 500, 1000, 2000, 3000 and 5000 µM) and production of GDP was monitored by reversed phase C18 HPLC. To this end, the samples (10 µl) were directly injected on a reversed-phase C18 column (pre-column: Hypersil Gold, 3µm particle size, 4.6x10mm; main column: Hypersil Gold, 5µm particle size, 4.6x250mm, Thermo Scientific) using an Ultimate 3000 HPLC system (Thermo Scientific, Waltham, MA, USA) in HPLC-buffer containing 50 mM KH<sub>2</sub>PO<sub>4</sub>/K<sub>2</sub>HPO<sub>4</sub> pH 6.0, 10 mM tetrabutylammonium bromide and 10-15% acetonitrile. Subsequently, samples were analyzed using the HPLC integrator (Chromeleon 7.2, Thermo Scientific, Waltham, MA, USA). Initial rates of GDP production were plotted against the GTP concentration using GraFit5 (v.5.0.13, Erithacus Software). The number of experiments is indicated in the graph and data point is the average (±s.e.m.) of indicated repetitions. The Michaelis-Menten equation was fitted to determine K<sub>M</sub> (±s.e.) and k<sub>cat</sub> (±s.e.). Excel sheets used for the calculation of means are provided. No values are reported if the HPLC separation failed (e.g. unstable baseline).</p> <p><strong>Charcoal GTP hydrolysis assay. </strong>The [γ-32P]GTP charcoal assay was performed as previously described (Bollag and McCormick, 1995). Briefly, 0.1 µM full-length LRRK2 or 0.5 µM 6xHIS-MBP-RocCOR was incubated with different GTP concentrations, ranging from 75 µM to 8 mM, in the presence of [γ-<sup>32</sup>P] GTP in GTPase assay buffer (30 mM Tris pH 8, 150 mM NaCl, 10 mM MgCl<sub>2</sub>, 5% (v/v) Glycerol and 3 mM DTT). Samples were taken at different time-points and immediately quenched with 5% activated charcoal in 20 mM phosphoric acid. All non-hydrolyzed GTP and proteins were stripped by the activated charcoal and sedimented by centrifugation. The radioactivity of the isolated inorganic phosphates was then measured by scintillation counting. The initial rates of γ-phosphate release and the Michaelis-Menten kinetics were calculated as described above.</p> <p><strong>(2) Profile plots (Raw data) obtained for the Mass photometry analysis for T1343A vs WT LRRK2.</strong></p> <p>MP was performed as described in (Guaitoli et al., 2023).<strong> </strong>Briefly, the dimer ratio of LRRK2 was determined on a Refeyn Two MP instrument (Refeyn). Prior to the experiment, a standard curve relating particle contrasts to molecular weight was established using a Native molecular weight standard (Invitrogen, 1:200 dilution in HEPES-based elution buffer: 50 mM HEPES [pH 8.0], 150 mM NaCl supplemented with 200 µM desthiobiotin). Prior to mass photometry, the proteins, either WT or T1343A LRRK2, were incubated with 0.5 mM ATP or buffer (control) for 30 min at 30 ℃. The LRRK2 protein was diluted to 2x of the final concentration (end concentrations: 75 nM and 100 nM) in elution buffer. The optical setup was focused in 10 μl elution buffer before adding 10 µl of the adjusted protein sample. Depending on the obtained count numbers, acquisition times were chosen between 20 s to 1 min. The dimer ratio in each measurement was normalize according to the equation. The measurement was perfomed in triplicates.</p> <p><strong>(3) AlphaFold3 model of LRRK2-pT1343 either bound to GDP/Mg or GTP/Mg.</strong></p> <p>Using AlphaFold3 (Abramson et al., 2024), we modeled and compared the GDP vs the GTP-state of phospho-T1343 LRRK2. Interestingly, the AlphaFold3 model suggests, that the phosphate group of the pT1343 residue is orientated inwards thereby substituting the gamma phosphate of the GTP in the GDP-bound state of LRRK2. This finding is in well agreement with MD simulations published recently (Stormer et al., 2023).</p> <p><strong>(4) Western blot RAW files for the cell-based phospho Rab asssay (RAW data for Figure 6 supplement 2/ Supplemental Figure 4 in the preprint version, Gilsbach et al, 2024)</strong></p> <p>Cell-based LRRK2 activity assays were performed as previously described (Singh et al., 2022). Briefly,<strong> </strong>HEK293T cells were cultured in DMEM (supplemented with 10% Fetal Bovine Serum and 0.5% Pen/Strep). For the assay, the cells were seeded onto six-well plates and transfected at a confluency of 50-70% with SF-tagged LRRK2 variants using PEI-based lipofection. After 48 hours cells were lysed in lysis buffer [30 mM Tris-HCl (pH7.4), 150 mM NaCl, 1% NonidentP-40 substitute, complete protease inhibitor cocktail, PhosStop phosphatase inhibitors (Roche)]. Lysates were cleared by centrifugation at 10,000 x g and adjusted to a protein concentration of 1 µg/µl in 1x Laemmli Buffer. Samples were subsequently subjected to SDS PAGE and Western Blot analysis to determine LRRK2 pS935 and Rab10 T73 phosphorylation levels, as described below. Total LRRK2 and Rab10 levels were determined as a reference for normalization. For Western blot analysis, protein samples were separated by SDS–PAGE using NuPAGE 10% Bis-Tris gels (Invitrogen) and transferred onto PVDF membranes (Thermo Fisher). To allow simultaneous probing for LRRK2 on the one hand and Rab10 on the other hand, membranes were cut horizontally at the 140 kDa MW marker band. After blocking non-specific binding sites with 5% non-fat dry milk in TBST (1 h, RT) (25 mM Tris, pH 7.4, 150 mM NaCl, 0.1% Tween-20), membranes were incubated overnight at 4°C with primary antibodies at dilutions specified below. Phospho-specific antibodies were diluted in TBST/ 5% BSA (Roth GmbH). Non-phospho-specific antibodies were diluted in TBST/ 5% non-fat dry milk powder (BioRad). Phospho-Rab10 levels were determined by the site-specific rabbit monoclonal antibody anti-pRAB10(pT73) (Abcam, ab230261) and LRRK2 pS935 was determined by the site-specific rabbit monoclonal antibody UDD2 (Abcam, ab133450), both at a dilution of 1:2,000. Total LRRK2 levels were determined by the in-house rat monoclonal antibody anti-pan-LRRK2 (clone 24D8; 1:10,000) (Carrion et al., 2017). Total Rab10 levels were determined by the rabbit monoclonal antibody anti-RAB10/ERP13424 (Abcam, ab181367) at a dilution of 1:5,000. For detection, goat anti-rat IgG or anti-rabbit IgG HRP-coupled secondary antibodies (Jackson ImmunoResearch) were used at a dilution of 1:15,000 in TBST/ 5% non-fat dry milk powder. Antibody–antigen complexes were visualized using the ECL plus chemiluminescence detection system (GE Healthcare) using the Stella imaging system (Raytest) for detection and quantification.</p> <p><strong>Figure 6 Source Data 1:</strong> <span>Images generated by the Stella system are shown which were used for quantification. The annotation file equals Figure6-figure supplement 2 (Gilsbach et al., eLife 2024, doi:10.7554/eLife.91083). The lines corresponding to </span>LRRK2 pS935, total LRRK2, Rab10 pT73 and total Rab10 were <span>used for the quantification shown in Figure 6.</span></p>
FIG. 5 in Early illustrations of Aepyornis eggs (1851 - 1887): from popular science to Marco Polo's roc bird
FIG. 5. — Comparative dimensions of various bird eggs. From Capus (1885). Aepyornis egg (4) compared with eggs of an ostrich (3), a hen (2) and a hummingbird (1). Photo E. Buffetaut.
FIG. 4 in Early illustrations of Aepyornis eggs (1851 - 1887): from popular science to Marco Polo's roc bird
FIG. 4. — "The Ruc's egg". Colour lithograph, frontispiece of The Book of Ser Marco Polo, the Venetian, Concerning the Kingdoms and Marvels of the East. Volume 2 (Yule 1871). Photo E. Buffetaut.
FIG. 6 in Early illustrations of Aepyornis eggs (1851 - 1887): from popular science to Marco Polo's roc bird
FIG. 6. — "Egg of the Epiornis" [sic]. From Scientific American, March 12, 1887. Photo E. Buffetaut.
FIG. 1 in Early illustrations of Aepyornis eggs (1851 - 1887): from popular science to Marco Polo's roc bird
FIG. 1. – Egg of Aepyornis maximus Geoffroy Saint-Hilaire, 1851, from Rowley (1878). The original plate shows the egg (from Rowley's collection) at its actual size. This appears to be the first illustration of an Aepyornis egg in a scientific paper. Photo E. Buffetaut.
FIG. 3 in Early illustrations of Aepyornis eggs (1851 - 1887): from popular science to Marco Polo's roc bird
FIG. 3. — Egg of Aepiornis [sic] maximus, compared with a hen's egg. From Ward (1866). Photo E. Buffetaut.
Figure 1. The comparison of the Area Under the ROC Curve (AUC) for fuzzy Diagnosis, KNN and NB-Comparison of Fuzzy Diagnosis with K-Nearest Neighbor and Naïve Bayes Classifiers in Disease Diagnosis
<p>The area under the receiver operating characteristic (ROC) curve (AUC) is used to measure<br> the performance of fuzzy diagnosis, KNN and NB. In order to show the difference between AUC<br> for the three methods, a single figure which combines the three AUC for the three methods was<br> used for comparison as shown in figure 1 below.</p>
TA B L E 1 Summary of model fit, based on the area under the curve (AUC) of the receiver operating characteristic (ROC) for training data, and the most important bioclimatic variables in past, present, and future (2070) Maxent models of 13 bat species included in this study. in Southern Africa's Great Escarpment as an amphitheater of climate-driven diversification and a buffer against future climate change in bats
TA B L E 1 Summary of model fit, based on the area under the curve (AUC) of the receiver operating characteristic (ROC) for training data, and the most important bioclimatic variables in past, present, and future (2070) Maxent models of 13 bat species included in this study.
ROC_all SINTEF workflow results with consensus steady state from CCLE
<p>This dataset has the input data + result dataset that was the product of using the <strong>DrugLogics</strong> computational pipeline with the <strong>rbbt</strong> workflow system to predict synergistic drug combinations across 8 cell lines that were also tested in SINTEF. The <strong>atopo topology</strong> was used and the logical models were trained to a <strong>consensus steady state derived from ~1000 cell lines from CCLE</strong>.</p>
ROC_all SINTEF workflow results with Atopo topology
<p>This dataset has the input data + result dataset that was the product of using the <strong>DrugLogics</strong> computational pipeline with the <strong>rbbt</strong> workflow system to predict synergistic drug combinations across 8 cell lines that were also tested in SINTEF. <strong>An automated generated Signor-based topology</strong> was used and the logical models were trained to a <strong>steady state activity profile </strong>that was derived using the <strong>PARADIGM tool</strong> and input from the<strong> CCLE</strong>.</p>
ROC_all SINTEF workflow results with CASCADE topology
<p>This dataset has the input data + result dataset that was the product of using the <strong>DrugLogics</strong> computational pipeline with the <strong>rbbt</strong> workflow system to predict synergistic drug combinations across 8 cell lines that were also tested in SINTEF. The <strong>CASCADE topology</strong> was used and the logical models were trained to a <strong>steady state activity profile </strong>that was derived using the <strong>PARADIGM tool</strong> and input from the<strong> CCLE</strong>.</p>
РИС. 4. ROC-кривые и плоЩадь под ROC-кривой (AUC) для раЗных моделей. А. РеЗультаты для Xeropicta derbentina. B. РеЗультаты для Brephulopsis cylindrica. Красная кривая иллюстрирует покаЗатели модели для обучаюЩего набора, бледно-голубые линии — для тестовых наборов и отдельных моделей, толстая синяя линия — обЩие покаЗатели всех моделей. in Land snails Brephulopsis cylindrica and Xeropicta derbentina (Gastropoda: Stylommatophora): case study of invasive species distribution modelling
РИС. 4. ROC-кривые и плоЩадь под ROC-кривой (AUC) для раЗных моделей. А. РеЗультаты для Xeropicta derbentina. B. РеЗультаты для Brephulopsis cylindrica. Красная кривая иллюстрирует покаЗатели модели для обучаюЩего набора, бледно-голубые линии — для тестовых наборов и отдельных моделей, толстая синяя линия — обЩие покаЗатели всех моделей.
Retaule de Sant Roc. BRL
Retaule Ceràmic de Sant Roc (Alzira, carrer Sant Roc 14) 0,75x0,64 metres Data / fecha 1770 - 1780. Bé de rellevància local (BRL). Autor: Inocencio V. Pérez Guillén VAL: El Sant de peu amb la túnica alçada per a quede visible la nafra de la cuixa dreta; amb vestimenta de pelegrí, capa, gaiat amb la carabassa, petxines... Hi ha un gos amb el pà del sant a la dreta i als fons arbres i un ermitori. ES: El Santo de pie con la túnica levantada para quedo visible la llaga del muslo derecho; con vestimenta de peregrino, capa, bastón, con la calabaza, conchas... Hay un perro con el pan del santo a la dercecha y en el fondo, árbles y ermita. Inscripción: "ROCUS NOSTER CUSTODIT Á PESTE" Tipologia: panell ceràmic - panells ceràmics rituals. Font: inventari general patrimoni cultural valencià. Source: Objaverse 1.0 / Sketchfab
100 Hz ROCS microscopy correlated with fluorescence reveals cellular dynamics on different spatiotemporal scales
<p>Image Datasets to 100 Hz ROCS microscopy correlated with fluorescence reveals cellular dynamics on different spatiotemporal scales</p>
Souvenir Du Moulin Du Roc
Statuette d'environ 1.20 m de hauteur en fonte peinte située au niveau de la terrasse ombragée de l'hôtel-restaurant " Le Moulin du Roc" à Champagnac de Belair en bordure de la Dronne (Périgord Vert-France). Petit souvenir d'un merveilleux séjour en septembre 2019 Source: Objaverse 1.0 / Sketchfab
Roc relief with a boat and the inscription
Roman ' Roc relief with a boat and the inscription ' , CIL X - 8399 ' , inserted into the masonry of the walls . Rif. Bibl: 'C.I.L., X - 8399' M.R. De La Blanchère - 'Bas-relief du Tombeau d'un fabricant de voiles (Terracine)', in 'RA', 1884, s.III, t.III, pp. 137-140 G. Lugli - 'Forma Italiae, Regio I, I, pars prima, Anxur-Tarracina', Roma, 1926, c.46 (n.1 Source: Objaverse 1.0 / Sketchfab
Confocal microsscope and sharp force trauma (Roc de les Orenetes)
<p>3D scans obtained with confocal microscopy (Sensofar S-Neox 3D Optical Profiler (SSN09000)) on the Roc de les Orenetes (Queralbs, Girona, Spain) cut marks. The scans were obtained with SensoScan software, which can be opened and edited with SensoView, and the folder also contains some of the processed images used in this study. This is a supplementary material of the paper "Death in the high mountains: Evidence of interpersonal violence during Late Chalcolithic and Early Bronze Age at Roc de les Orenetes" (Moreno-Ibáñez et al., 2023: submitted). It is divided into two main folders: chop marks and slice marks. The cut marks of each bone have been grouped in folders with their corresponding labels, and in the case of a bone having more than one clearly distinguishable cut mark, these have also been divided into sub-folders, indicating “cut mark 1”, “cut mark 2”, etc. The file names also indicate the label code of the bone, the magnification at which the image was taken (5x, 10x, or 20x), and the type of visualization used in the form of acronyms, which are listed hereafter:</p> <p>ST: stack (conventional confocal display, black and white).</p> <p>FC: false color (visualization of the topography of the bone surface in a range of colors, without texture).</p> <p>FCST: false color + stack (combination of the two aforementioned visualizations, false color topography plus surface texture).</p> <p>FR: form removal (the inclination or concavity of the bone is flattened with SensoView software to better observe the surface topography in false color, without the curvature of the bone hindering the cut mark).</p> <p>VD: viridis (viridis false color range, from yellow to blue through green, used in cases where the desired features of the cut mark were best viewed in this mode).</p> <p>3D: three-dimensional movable scans.</p> <p>2D: two-dimensional images.</p>
Resuscitation Outcomes Consortium (ROC) Prehospital Resuscitation Using an Impedance Valve
ClinicalTrials.gov study NCT00394706. IPD Sharing: Not stated. Countries: 2. Publications: 8.
The Effect of Pretreatment With Roc on Succinylcholine Myalgias
ClinicalTrials.gov study NCT04581395. IPD Sharing: NO. Countries: 1. Publications: 8.
Data from: Establishing detection thresholds for environmental DNA using receiver operator characteristic (ROC) curves
Environmental DNA (eDNA) detection is increasingly being used to assess the potential presence of aquatic species. Setting defensible thresholds for qPCR assays are necessary to differentiate "detection" from "non-detection", but threshold rationales are rarely reported in eDNA studies. Detection thresholds for data inclusion and exclusion have implications for downstream data analysis; uncritical acceptance could result in false positive results (Type I error), whereas overly conservative thresholds could result in high false negative interpretation (Type II error). We assessed the use of the receiver operator characteristics (ROC) framework to identify a detection threshold for balancing sensitivity and specificity of eDNA data. The ROC framework was tested using empirical eDNA data from redside dace (Clinostomus elongatus), an endangered freshwater fish in southwestern Ontario. Based on negative controls, positive controls, and quality assurance guidelines, a minimum concentration of 1 copy reaction−1 was identified as the most appropriate threshold for this study. Although optimal thresholds will likely vary between studies and labs based on empirical data, the ROC framework provides a statistical method for establishing defensible thresholds for data acceptance or rejection as well as tradeoffs between the sensitivity and specificity of eDNA data.
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International Brain Laboratory public data
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OpenNeuro
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