cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5841207
title: Is the accuracy of preoperative MRI stage in rectal adenocarcinoma influenced by tumour height?

description: <b>Aim:</b> To our knowledge, no prior studies have addressed the possible effects of tumour height on the accuracy of preoperative magnetic resonance imaging (MRI)-based staging relative to postoperative histopathological assessments in patients with adenocarcinoma of the rectum (RC). This study aimed to investigate whether the accuracy of preoperative MRI stage in RC is influenced by tumour height. <b>Methods:</b> A total of 489 consecutive RC patients scheduled for curative treatment between 2009 and 2013 were included. Of the 489 patients, 133 patients had preoperative chemoradiotherapy (CRT), and 356 patients underwent primary surgery. Low, mid and high RC were defined as a tumour &lt;5 cm, 5–10 cm and &gt;10 cm from the anal verge, respectively. Diagnostic MRI and, for patients with CRT, re-staging MRI features including tumour T-stage (mrT), distance between the tumour border and the distance to the mesorectal fascia (mrMRF), extramural tumour depth (mrEMD), extramural vascular invasion (mrEMVI) and nodal involvement (mrN) were correlated with the corresponding postoperative histopathological findings. <b>Results:</b> There were 115, 186 and 188 patients with low RC, mid RC and high RC, respectively. For all patients, the correlations between mrT and pT and between mrMRF and pCRM were not influenced by tumour height. None of the correlations between mrEMD, mrEMVI and mrN and the corresponding postoperative histopathological findings significantly differed for tumours of different heights. For patients with CRT, a remarkable proportion with low RC were overstaged as ymrT3 compared to ypT0-2. <b>Conclusions:</b> The ability to preoperatively use MRI to accurately stage is not influenced by tumour height. For patients with preoperative CRT, low RC may be MRI overstaged due to post-radiation fibrosis. We found that mrEMD predicts pEMD reliably and should therefore be considered in treatment decisions. Although new MRI techniques are emerging, preoperative RC staging remains incompletely definitive in daily clinical practice.
DOI: 10.6084/m9.figshare.5841207.v1
title: Is the accuracy of preoperative MRI stage in rectal adenocarcinoma influenced by tumour height?

description: <b>Aim:</b> To our knowledge, no prior studies have addressed the possible effects of tumour height on the accuracy of preoperative magnetic resonance imaging (MRI)-based staging relative to postoperative histopathological assessments in patients with adenocarcinoma of the rectum (RC). This study aimed to investigate whether the accuracy of preoperative MRI stage in RC is influenced by tumour height. <b>Methods:</b> A total of 489 consecutive RC patients scheduled for curative treatment between 2009 and 2013 were included. Of the 489 patients, 133 patients had preoperative chemoradiotherapy (CRT), and 356 patients underwent primary surgery. Low, mid and high RC were defined as a tumour &lt;5 cm, 5–10 cm and &gt;10 cm from the anal verge, respectively. Diagnostic MRI and, for patients with CRT, re-staging MRI features including tumour T-stage (mrT), distance between the tumour border and the distance to the mesorectal fascia (mrMRF), extramural tumour depth (mrEMD), extramural vascular invasion (mrEMVI) and nodal involvement (mrN) were correlated with the corresponding postoperative histopathological findings. <b>Results:</b> There were 115, 186 and 188 patients with low RC, mid RC and high RC, respectively. For all patients, the correlations between mrT and pT and between mrMRF and pCRM were not influenced by tumour height. None of the correlations between mrEMD, mrEMVI and mrN and the corresponding postoperative histopathological findings significantly differed for tumours of different heights. For patients with CRT, a remarkable proportion with low RC were overstaged as ymrT3 compared to ypT0-2. <b>Conclusions:</b> The ability to preoperatively use MRI to accurately stage is not influenced by tumour height. For patients with preoperative CRT, low RC may be MRI overstaged due to post-radiation fibrosis. We found that mrEMD predicts pEMD reliably and should therefore be considered in treatment decisions. Although new MRI techniques are emerging, preoperative RC staging remains incompletely definitive in daily clinical practice.
DOI: 10.6084/m9.figshare.5841105
title: Supplementary Material for: Micro Integral Membrane Protein (MIMP), a Newly Discovered Anti-Inflammatory Protein of Lactobacillus Plantarum, Enhances the Gut Barrier and Modulates Microbiota and Inflammatory Cytokines

description: <b><i>Background/Aims:</i></b> Recent studies have demonstrated that the manipulation of the gut microbiome represents a promising treatment for inflammatory bowel disease (IBD). We previously identified micro integral membrane protein (MIMP) as the smallest domain of surface layer protein from Lactobacillus Plantarum. However, the therapeutic relevance of MIMP in IBD remains unknown. <b><i>Methods:</i></b> We initially employed a dextran sodium sulphate (DSS)-induced colitis model and evaluated the effect of MIMP on the inflammation response, intestinal barrier and gut microbiota using histological examination, Fluorescein isothiocyanate-Dextran detection and pyrosequencing analysis respectively. We then established peripheral blood mononuclear cells (PBMCs) and an epithelial CaCO-2 co-culture model to investigate the regulatory role of MIMP in inflammatory cytokines. The level changes of inflammatory cytokines were detected using Enzyme-linked immunosorbent and real-time polymerase chain reaction assay. The involved regulatory mechanisms were investigated mainly using dual luciferase reporter and chromatin immunoprecipitation assay. <b><i>Results:</i></b> In the DSS-induced colitis model, we observed that MIMP intervention effectively improved the body weight loss, increased the colon length and decreased disease activity index. Consistently, the inflammation scores in the MIMP treatment group were significantly lower than those in the DSS treatment group. Furthermore, MIMP intervention was found to successfully neutralize DSS treatment by decreasing the expression of pro-inflammatory cytokines (IFN-γ, IL-17 and IL-23) and increasing the expression of anti-inflammatory cytokines (IL-4 and IL-10). Notably, the permeability assay demonstrated that the MIMP treatment group was remarkably lower than that in the DSS treatment group. We also showed that MIMP improved gut microbiota dysbiosis caused by DSS-induced inflammation. Additionally, in PBMCs and the CaCO-2 co-culture model, MIMP showed an obvious suppressive effect on lipopolysaccharide-induced inflammation in a time- and dose-dependent manner. Furthermore, we revealed that MIMP could modulate inflammatory cytokine expression through the toll-like receptor 4 pathway and histone acetylation. <b><i>Conclusions:</i></b> Our results suggested that MIMP showed a significant anti-inflammatory effect through regulating the gut barrier, microbiota and inflammatory cytokines. MIMP may have translational relevance as clinically relevant therapy for IBD patients.
DOI: 10.17028/rd.lboro.5841084
title: Supplementary figures for "Process development of human multipotent stromal cell microcarrier culture using an automated high-throughput microbioreactor"

description: Supplementary information files for "Process development of human multipotent stromal cell microcarrier culture using an automated high-throughput microbioreactor"<br><b>Figure S1</b>. Growth kinetics of hMSCs donor 2 cells using serum-free (SFM) and fetal bovine serum (FBS)-based media in both the ambr15 and spinner flasks with data showing the viable cell density.<br><b>Figure S2</b>. Nutrient and metabolite flux for hMSC donor 1 cells expanded on microcarriers in the serum-based and serum-free cultures in both the ambr and spinner flasks.<br><b>Figure S3</b>. Functional characterisation of hMSCs from donor 1 harvested from the serum-free ambr15 bioprocess.<br>ABSTRACTMicrobioreactors play a critical role in process development as they reduce reagent requirements and can facilitate high-throughput screening of process parameters and culture conditions. Here, we have demonstrated and explained in detail, for the first time, the amenability of the automated ambr15 cell culture microbioreactor system for the development of scalable adherent human mesenchymal multipotent stromal/stem cell (hMSC) microcarrier culture processes. This was achieved by first improving suspension and mixing of the microcarriers and then improving cell attachment thereby reducing the initial growth lag phase. The latter was achieved by using only 50% of the final working volume of medium for the first 24 h and using an intermittent agitation strategy. These changes resulted in &gt;150% increase in viable cell density after 24 h compared to the original process (no agitation for 24 h and 100% working volume). Using the same methodology as in the ambr15, similar improvements were obtained with larger scale spinner flask studies. Finally, this improved bioprocess methodology based on a serum-based medium was applied to a serum-free process in the ambr15, resulting in &gt;250% increase in yield compared to the serum-based process. At both scales, the agitation used during culture was the minimum required for microcarrier suspension, N<sub>JS</sub>. The use of the ambr15, with its improved control compared to the spinner flask, reduced the coefficient of variation on viable cell density in the serum containing medium from 7.65% to 4.08%, and the switch to serum free further reduced these to 1.06–0.54%, respectively. The combination of both serum-free and automated processing improved the reproducibility more than 10-fold compared to the serum-based, manual spinner flask process. The findings of this study demonstrate that the ambr15 microbioreactor is an effective tool for bioprocess development of hMSC microcarrier cultures and that a combination of serum-free medium, control, and automation improves both process yield and consistency.
DOI: 10.17028/rd.lboro.5841084.v1
title: Supplementary figures for "Process development of human multipotent stromal cell microcarrier culture using an automated high-throughput microbioreactor"

description: Supplementary information files for "Process development of human multipotent stromal cell microcarrier culture using an automated high-throughput microbioreactor"<br><b>Figure S1</b>. Growth kinetics of hMSCs donor 2 cells using serum-free (SFM) and fetal bovine serum (FBS)-based media in both the ambr15 and spinner flasks with data showing the viable cell density.<br><b>Figure S2</b>. Nutrient and metabolite flux for hMSC donor 1 cells expanded on microcarriers in the serum-based and serum-free cultures in both the ambr and spinner flasks.<br><b>Figure S3</b>. Functional characterisation of hMSCs from donor 1 harvested from the serum-free ambr15 bioprocess.<br>ABSTRACTMicrobioreactors play a critical role in process development as they reduce reagent requirements and can facilitate high-throughput screening of process parameters and culture conditions. Here, we have demonstrated and explained in detail, for the first time, the amenability of the automated ambr15 cell culture microbioreactor system for the development of scalable adherent human mesenchymal multipotent stromal/stem cell (hMSC) microcarrier culture processes. This was achieved by first improving suspension and mixing of the microcarriers and then improving cell attachment thereby reducing the initial growth lag phase. The latter was achieved by using only 50% of the final working volume of medium for the first 24 h and using an intermittent agitation strategy. These changes resulted in &gt;150% increase in viable cell density after 24 h compared to the original process (no agitation for 24 h and 100% working volume). Using the same methodology as in the ambr15, similar improvements were obtained with larger scale spinner flask studies. Finally, this improved bioprocess methodology based on a serum-based medium was applied to a serum-free process in the ambr15, resulting in &gt;250% increase in yield compared to the serum-based process. At both scales, the agitation used during culture was the minimum required for microcarrier suspension, N<sub>JS</sub>. The use of the ambr15, with its improved control compared to the spinner flask, reduced the coefficient of variation on viable cell density in the serum containing medium from 7.65% to 4.08%, and the switch to serum free further reduced these to 1.06–0.54%, respectively. The combination of both serum-free and automated processing improved the reproducibility more than 10-fold compared to the serum-based, manual spinner flask process. The findings of this study demonstrate that the ambr15 microbioreactor is an effective tool for bioprocess development of hMSC microcarrier cultures and that a combination of serum-free medium, control, and automation improves both process yield and consistency.
DOI: 10.6084/m9.figshare.5840991
title: RestMule Submission Artefact

description: Sanitised version of the tool for review purposes.
DOI: 10.6084/m9.figshare.5840991.v2
title: RestMule Submission Artefact

description: Sanitised version of the tool for review purposes.
DOI: 10.6084/m9.figshare.5840991.v1
title: RestMule Submission Artefact

description: Sanitised version of the tool for review purposes.
DOI: 10.17028/rd.lboro.5840979
title: Supplementary information files for "A comparison of azimuthal and axial oscillation microfiltration using surface and matrix types of microfilters with a cake-slurry shear plane exhibiting non-Newtonian behaviour"

description: Supplementary information files for "A comparison of azimuthal and axial oscillation microfiltration using surface and matrix types of microfilters with a cake-slurry shear plane exhibiting non-Newtonian behaviour"<br>AbstractThe mode of application of oscillation, axial or azimuthal, did not influence filtration performance, when filtering a calcite mineral with a d<sub>32</sub> value of 2.7 µm. The equilibrium flux and deposit thickness correlated with shear stress, regardless of: filter type (metal slotted surface filter or homogeneous sintered filter); and mode of oscillation. Shear stress values up to 240 Pa were used and the particle compact believed to be at, or near, the deposited solids showed non-Newtonian flow behaviour described by the Herschel-Bulkley equation. The shear was computed using Comsol® to model the shear at, and near, the oscillating surface. The peak shear (maximum value) was used in the correlation for flux, which appeared to fit the data well and provide a realistic prediction for sustainable flux using a force balance model.The existence of a yield stress in the compact appeared to limit the internal fouling of the matrix (homogeneous) type of filter, which had a membrane thickness of 8 mm, but did not demonstrate significant internal fouling over time, nor between filtrations. Thus, the results were similar to those obtained for the surface filters, and the resistance to filtration was dominated by the deposit formed.
DOI: 10.17028/rd.lboro.5840979.v1
title: Supplementary information files for "A comparison of azimuthal and axial oscillation microfiltration using surface and matrix types of microfilters with a cake-slurry shear plane exhibiting non-Newtonian behaviour"

description: Supplementary information files for "A comparison of azimuthal and axial oscillation microfiltration using surface and matrix types of microfilters with a cake-slurry shear plane exhibiting non-Newtonian behaviour"<br>AbstractThe mode of application of oscillation, axial or azimuthal, did not influence filtration performance, when filtering a calcite mineral with a d<sub>32</sub> value of 2.7 µm. The equilibrium flux and deposit thickness correlated with shear stress, regardless of: filter type (metal slotted surface filter or homogeneous sintered filter); and mode of oscillation. Shear stress values up to 240 Pa were used and the particle compact believed to be at, or near, the deposited solids showed non-Newtonian flow behaviour described by the Herschel-Bulkley equation. The shear was computed using Comsol® to model the shear at, and near, the oscillating surface. The peak shear (maximum value) was used in the correlation for flux, which appeared to fit the data well and provide a realistic prediction for sustainable flux using a force balance model.The existence of a yield stress in the compact appeared to limit the internal fouling of the matrix (homogeneous) type of filter, which had a membrane thickness of 8 mm, but did not demonstrate significant internal fouling over time, nor between filtrations. Thus, the results were similar to those obtained for the surface filters, and the resistance to filtration was dominated by the deposit formed.
DOI: 10.6084/m9.figshare.5840970
title: Capture-Mark-Recapture (CMR) datasets of Serengeti spotted hyenas infected with CDV

description: This excel table contains 4 sheets: 2 with the CMR datasets associated with the manuscript by Marescot et al. 2018 Functional ecology (Social status mediates the fitness costs of infection with canine distemper virus in Serengeti spotted hyenas) and 2 other sheets defining the variables included in the datasets.
DOI: 10.6084/m9.figshare.5840970.v1
title: Capture-Mark-Recapture (CMR) datasets of Serengeti spotted hyenas infected with CDV

description: This excel table contains 4 sheets: 2 with the CMR datasets associated with the manuscript by Marescot et al. 2018 Functional ecology (Social status mediates the fitness costs of infection with canine distemper virus in Serengeti spotted hyenas) and 2 other sheets defining the variables included in the datasets.
DOI: 10.6084/m9.figshare.5840856
title: The datasets supporting are uploaded at DRYAD and will be available if the manuscript is accepted (doi:10.5061/dryad.8h439). from Isotopic niche reflects stress-induced variability in physiological status

description: Excel work book containing five excel sheets with data on all individuals used in the two experiments. see sheet "read me" for instructions.
DOI: 10.6084/m9.figshare.5840856.v1
title: The datasets supporting are uploaded at DRYAD and will be available if the manuscript is accepted (doi:10.5061/dryad.8h439). from Isotopic niche reflects stress-induced variability in physiological status

description: Excel work book containing five excel sheets with data on all individuals used in the two experiments. see sheet "read me" for instructions.
DOI: 10.6084/m9.figshare.5840832
title: Supplementary Material for: Responsiveness of Infrapatellar Fat Pad Volume Change to Body Weight Loss or Gain: Data from the Osteoarthritis Initiative

description: Obesity is a potent risk factor for knee osteoarthritis (OA) that is driven by mechanical and potentially endocrine mechanisms, and it affects women more frequently than men. The infrapatellar fat pat (IPFP) represents a potential link between obesity, intra-articular inflammation and structural pathology. Here we investigate whether the IPFP is responsive to body weight loss/gain in women and how its responsiveness to weight change compares to that of subcutaneous fat (SCF) of the thigh. All female participants of the Osteoarthritis Initiative (OAI) with ≥10% weight loss/gain between baseline and a 2-year follow-up were included. Within-subject changes in IPFP volume and SCF cross-sectional areas (CSA) were determined from 3-T magnetic resonance imaging. Linear regression was used to assess the association between change in weight, IPFP volume, and SCF CSA. In the 38 participants with ≥10% weight loss over 2 years (age 59.3 ± 9.1 years, mean loss = 15.9%), there was a significant reduction in IPFP volume (-2.2%, <i>p</i> = 0.02) as well as in SCF CSA (-22%, <i>p</i> &lt; 0.001). In the 34 participants with ≥10% gain (age 61.5 ± 8.7 years, mean gain = 15.9%), there was a significant increase in SCF CSA (+26%, <i>p</i> &lt; 0.001) but not in IPFP volume (0.2%, <i>p</i> = 0.87). Weight change was significantly associated with SCF CSA change (<i>r</i> = 0.76, <i>p</i> &lt; 0.001) but not with IPFP volume change (<i>r</i> = 0.11, <i>p</i> = 0.37). In this first longitudinal, observational study investigating the responsiveness of IPFP and SCF to weight change, IPFP morphology was found responsive to weight loss but not to weight gain. Overall, the responsiveness of the IPFP was substantially less than that of the SCF.
DOI: 10.6084/m9.figshare.5840826.v1
title: 资料采集.xlsx

description: We talked about gastric-filling enhanced CT in the experimental group and control group raw data.
DOI: 10.6084/m9.figshare.5840802
title: 3D models of Early Jurassic tridactyl traces from the Dolomitic Formation of the Malaval Cave (Lozère)

description: Moreau J.-D., Trincal V., André D., Baret L., Jacquet A. and Wienin M., 2018. Underground dinosaur tracksite inside a karst of southern France: Early Jurassic tridactyl traces from the Dolomitic Formation of the Malaval Cave (Lozère). International Journal of Speleology, 47 (1), 29-42. Tampa, FL (USA) ISSN 0392-6672 https://doi.org/10.5038/1827-806X.47.1.2149 <br><br>
DOI: 10.6084/m9.figshare.5840802.v1
title: 3D models of Early Jurassic tridactyl traces from the Dolomitic Formation of the Malaval Cave (Lozère)

description: Moreau J.-D., Trincal V., André D., Baret L., Jacquet A. and Wienin M., 2018. Underground dinosaur tracksite inside a karst of southern France: Early Jurassic tridactyl traces from the Dolomitic Formation of the Malaval Cave (Lozère). International Journal of Speleology, 47 (1), 29-42. Tampa, FL (USA) ISSN 0392-6672 https://doi.org/10.5038/1827-806X.47.1.2149 <br><br>
DOI: 10.6084/m9.figshare.5840784
title: Dung-beetle networks

description: This folder contains datasets from studies on the distribution of dung beetle species across two or more types of dung (trophic networks). Each file is named by the reference. For an overview of references and additional information, see ELEblüthgenST1.xlsx<br>Reference:Frank K, Krell FT, Walter P, Slade EM, Raine EH, Chiew LY, Vairappan CS, Schmitt T, Blüthgen N (2018) Global dung webs: high trophic generalism of dung beetles along the latitudinal diversity gradient. Ecology Letters, in press.
DOI: 10.6084/m9.figshare.5840712
title: Experimental Data M1-M31.pdf

description: Data contains full PhD study experimental data of XRF analysis.
DOI: 10.6084/m9.figshare.5840712.v1
title: Experimental Data M1-M31.pdf

description: Data contains full PhD study experimental data of XRF analysis.
DOI: 10.6084/m9.figshare.5840706
title: Molecular dynamics of DSB in nucleosome

description: These files contain the coordinate files (.gro) and compact trajectory files (.xtc) from the GROMACS runs of the nucleosome models O (experimental 1kx5), M1-M4 (model O with double strand breaks at various positions). Trajectories are compacted from the .trr files, by excluding water molecules and ions. Frames are stored each 40 ps for ~1 microsecond trajectories (~25,000 frames per .xtc file, ~2 Gb each).<br>PLOS submitted manuscript "Mechanical evolution of DNA double strand breaks in the nucleosome", by F. Cleri, F. Landuzzi and R. Blossey<br><br>
DOI: 10.6084/m9.figshare.5840706.v1
title: M1.gro

description: These files contain the coordinate files (.gro) and compact trajectory files (.xtc) from the GROMACS runs of the nucleosome models O (experimental 1kx5), M1-M4 (model O with double strand breaks at various positions). Trajectories are compacted from the .trr files, by excluding water molecules and ions. Frames are stored each 40 ps for 1 microsecond trajectories (25,000 frames per .xtc file, about 2 Gb each).<br>PLOS submitted manuscript "Mechanical evolution of DNA double strand breaks in the nucleosome", by F. Cleri, F. Landuzzi and R. Blossey<br><br>