cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7579877
title: Composite biomaterial repair strategy to restore biomechanical function and reduce herniation risk in an ex vivo large animal model of intervertebral disc herniation with varying injury severity

description: Abstract: Back pain commonly arises from intervertebral disc (IVD) damage including annulus fibrosus (AF) defects and nucleus pulposus (NP) loss. Poor IVD healing motivates developing tissue engineering repair strategies. This study evaluated a composite injectable IVD biomaterial repair strategy using carboxymethylcellulose-methylcellulose (CMC-MC) and genipin-crosslinked fibrin (FibGen) that mimic NP and AF properties, respectively. Bovine ex vivo caudal IVDs were evaluated in cyclic compression-tension, torsion, and compression-to-failure tests to determine IVD biomechanical properties, height loss, and herniation risk following experimentally-induced severe herniation injury and discectomy (4 mm biopsy defect with 20% NP removed). FibGen with and without CMC-MC had failure strength similar to discectomy injury suggesting no increased risk compared to surgical procedures, yet no biomaterials improved axial or torsional biomechanical properties suggesting they were incapable of adequately restoring AF tension. FibGen had the largest failure strength and was further evaluated in additional discectomy injury models with varying AF defect types (2 mm biopsy, 4 mm cruciate, 4 mm biopsy) and NP removal volume (0%, 20%). All simulated discectomy defects significantly compromised failure strength and biomechanical properties. The 0% NP removal group had mean values of axial biomechanical properties closer to intact levels than defects with 20% NP removed but they were not statistically different and 0% NP removal also decreased failure strength. FibGen with and without CMC-MC failed at super-physiological stress levels above simulated discectomy suggesting repair with these tissue engineered biomaterials may perform better than discectomy alone, although restored biomechanical function may require additional healing with the potential application of these biomaterials as sealants and cell/drug delivery carriers. <br><br>Full article at https://doi.org/10.1371/journal.pone.0217357 <br>
DOI: 10.7284/129759
title: Multibeam Echosounder data collected during research cruise FK181005 using a Kongsberg EM302 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7579877.v1
title: Composite biomaterial repair strategy to restore biomechanical function and reduce herniation risk in an ex vivo large animal model of intervertebral disc herniation with varying injury severity

description: Abstract: Back pain commonly arises from intervertebral disc (IVD) damage including annulus fibrosus (AF) defects and nucleus pulposus (NP) loss. Poor IVD healing motivates developing tissue engineering repair strategies. This study evaluated a composite injectable IVD biomaterial repair strategy using carboxymethylcellulose-methylcellulose (CMC-MC) and genipin-crosslinked fibrin (FibGen) that mimic NP and AF properties, respectively. Bovine ex vivo caudal IVDs were evaluated in cyclic compression-tension, torsion, and compression-to-failure tests to determine IVD biomechanical properties, height loss, and herniation risk following experimentally-induced severe herniation injury and discectomy (4 mm biopsy defect with 20% NP removed). FibGen with and without CMC-MC had failure strength similar to discectomy injury suggesting no increased risk compared to surgical procedures, yet no biomaterials improved axial or torsional biomechanical properties suggesting they were incapable of adequately restoring AF tension. FibGen had the largest failure strength and was further evaluated in additional discectomy injury models with varying AF defect types (2 mm biopsy, 4 mm cruciate, 4 mm biopsy) and NP removal volume (0%, 20%). All simulated discectomy defects significantly compromised failure strength and biomechanical properties. The 0% NP removal group had mean values of axial biomechanical properties closer to intact levels than defects with 20% NP removed but they were not statistically different and 0% NP removal also decreased failure strength. FibGen with and without CMC-MC failed at super-physiological stress levels above simulated discectomy suggesting repair with these tissue engineered biomaterials may perform better than discectomy alone, although restored biomechanical function may require additional healing with the potential application of these biomaterials as sealants and cell/drug delivery carriers. <br><br>Full article at https://doi.org/10.1371/journal.pone.0217357 <br>
DOI: 10.7284/129760
title: Multibeam Echosounder data collected during research cruise FK181005 using a Kongsberg EM710 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129761
title: Multibeam Echosounder data collected during research cruise FK181005 using a Kongsberg EM710 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129753
title: Splitbeam Echosounder data collected during research cruise FK181005 using a Kongsberg EK60 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7578728
title: elfi_model.pdf

description: Figure S1: The ELFI model used in computing the posterior as visualized by ELFI. The grey node named sim is the simulator. It takes in the rate parameters that are transformed from the parameters of interest. The grey child nodes are summary statistics or quantities from which the summary statics are computed from (not all of the summaries in Table S1 were available as individual nodes but were computed in dist from obs times and clusters). Some other side information was also collected, such as the total simulated time and size of the compliant and non-compliant populations at the end of the simulation.
DOI: 10.7284/129755
title: SSV (Sound Speed Velocimeter) data collected during research cruise FK181005 using a Valeport MiniSVS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129757
title: TSG (Thermosalinograph) data collected during research cruise FK181005 using a Sea-Bird SBE-45 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7578623
title: Self-assembled tetrameric H<sub>2</sub>O clusters in the crystal lattice of [Cu(μ<sup>2</sup>-OH){Ph<sub>2</sub>P(O)NP(O)Ph<sub>2</sub>-κ<sup>1</sup><i>O,O′</i>}(1,10-phen-κ<sup>2</sup><i>N,N′</i>)]<sub>2</sub>·2H<sub>2</sub>O

description: The synthesis and characterization of the dinuclear Cu(II) complex [Cu(μ<sup>2</sup>-OH){Ph<sub>2</sub>P(O)NP(O)Ph<sub>2</sub>-κ<sup>1</sup><i>O,O′</i>}(1,10-phen-κ<sup>2</sup><i>N,N′</i>)]<sub>2</sub>·2H<sub>2</sub>O (<b>1</b>), 1,10-phen = 1,10-phenanthroline, is described. X-ray crystallographic studies reveal that the Cu(II) centers of <b>1</b> are bridged by two OH<sup>−</sup> groups and are coordinated by the (O,O) = Ph<sub>2</sub>P(O)NP(O)Ph<sub>2</sub><sup>−</sup> ligand in a monodentate fashion, unprecedented for Cu(II). The crystal lattice of <b>1</b> also contains H<sub>2</sub>O molecules, which are involved in the formation of a hydrogen bonding network with bridging OH<sup>−</sup> groups and noncoordinated O atoms of the (O,O) ligand. These H<sub>2</sub>O molecules are arranged in the crystal lattice of <b>1</b> as tetrameric clusters. The packing of molecules in the structure of <b>1</b> was investigated by Hirshfeld Surface analysis.
DOI: 10.7284/132910
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise FK181031 using a Hawaii UHDAS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132909
title: Expendable Probe data collected during research cruise FK181031 using a Turo Quoll instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7578596
title: Interviews.docx data set.docx

description: Sample of MATs for research into MAT communication with Communities
DOI: 10.6084/m9.figshare.7578593
title: tables of innovations in MATs.docx

description: Summary of innovations re board communication with school communities.
DOI: 10.6084/m9.figshare.7578596.v1
title: Interviews.docx data set.docx

description: Sample of MATs for research into MAT communication with Communities
DOI: 10.7284/132912
title: Fluorometer data collected during research cruise FK181031 using a WET Labs ECO-FLNTU instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7578593.v1
title: tables of innovations in MATs.docx

description: Summary of innovations re board communication with school communities.
DOI: 10.6084/m9.figshare.7578587
title: Identification of potential inhibitors for <i>Klebsiella pneumoniae</i> carbapenemase-3: a molecular docking and dynamics study

description: <i>Klebsiella pneumoniae</i> (<i>K. pneumoniae)</i> is a Gram-negative bacterium, which is a leading causal agent for nosocomial infections. Penicillin, cephalosporin and carbapenems along with the inhibitors such as tazobactam, sulbactam and clavulanic acid are prescribed for the treatment of <i>K. pneumoniae</i> infections. Prolonged exposure to β-lactam antibiotics leads to the development of resistance. The major reason for the β-lactam resistance in <i>K. pneumoniae</i> is the secretion of the enzyme <i>K. pneumoniae</i> carbapenemase (KPC). Secretion of KPC-2 and its variant KPC-3 by the <i>K. pneumoniae</i> strains causes resistance to both the substrate imipenem and the β-lactamase inhibitors. Hence, molecular docking and dynamics studies were carried out to analyze the resistance mechanism of KPC-2–imipenem and KPC-3–imipenem at the structural level. It reveals that KPC-3-imipenem has the highest <i>c</i>-score value of 4.03 with greater stability than the KPC-2–imipenem <i>c</i>-score value of 2.36. Greater the interaction between the substrate and the β-lactamase enzyme, higher the chances of hydrolysis of the substrate. Presently available β-lactamase inhibitors are also ineffective against KPC-3-expressing strains. This situation necessitates the need for development of novel and effective inhibitors for KPC-3. We have carried out the virtual screening process to identify more effective inhibitors for KPC-3, and this has resulted in ZINC48682523, ZINC50209041 and ZINC50420049 as the best binding energy compounds, having greater binding affinity and stability than KPC-3–tazobactam interactions. Our study provides a clear understanding of the mechanism of drug resistance and provides valuable inputs for the development of inhibitors against KPC-3 expressing <i>K. pneumoniae.</i> Communicated by Ramaswamy H. Sarma <b>HIGHLIGHTS</b>Molecular docking results in high binding energy between imipenem and KPC-3.Molecular dynamics results in higher stability of KPC-3-imipenem complex.Virtual screening was carried out to find novel inhibitors for KPC-3.Molecular dynamics reveals higher stability of novel inhibitors than tazobactam. Molecular docking results in high binding energy between imipenem and KPC-3. Molecular dynamics results in higher stability of KPC-3-imipenem complex. Virtual screening was carried out to find novel inhibitors for KPC-3. Molecular dynamics reveals higher stability of novel inhibitors than tazobactam.
DOI: 10.6084/m9.figshare.7578587.v1
title: Identification of potential inhibitors for <i>Klebsiella pneumoniae</i> carbapenemase-3: a molecular docking and dynamics study

description: <i>Klebsiella pneumoniae</i> (<i>K. pneumoniae)</i> is a Gram-negative bacterium, which is a leading causal agent for nosocomial infections. Penicillin, cephalosporin and carbapenems along with the inhibitors such as tazobactam, sulbactam and clavulanic acid are prescribed for the treatment of <i>K. pneumoniae</i> infections. Prolonged exposure to β-lactam antibiotics leads to the development of resistance. The major reason for the β-lactam resistance in <i>K. pneumoniae</i> is the secretion of the enzyme <i>K. pneumoniae</i> carbapenemase (KPC). Secretion of KPC-2 and its variant KPC-3 by the <i>K. pneumoniae</i> strains causes resistance to both the substrate imipenem and the β-lactamase inhibitors. Hence, molecular docking and dynamics studies were carried out to analyze the resistance mechanism of KPC-2–imipenem and KPC-3–imipenem at the structural level. It reveals that KPC-3-imipenem has the highest <i>c</i>-score value of 4.03 with greater stability than the KPC-2–imipenem <i>c</i>-score value of 2.36. Greater the interaction between the substrate and the β-lactamase enzyme, higher the chances of hydrolysis of the substrate. Presently available β-lactamase inhibitors are also ineffective against KPC-3-expressing strains. This situation necessitates the need for development of novel and effective inhibitors for KPC-3. We have carried out the virtual screening process to identify more effective inhibitors for KPC-3, and this has resulted in ZINC48682523, ZINC50209041 and ZINC50420049 as the best binding energy compounds, having greater binding affinity and stability than KPC-3–tazobactam interactions. Our study provides a clear understanding of the mechanism of drug resistance and provides valuable inputs for the development of inhibitors against KPC-3 expressing <i>K. pneumoniae.</i> Communicated by Ramaswamy H. Sarma <b>HIGHLIGHTS</b>Molecular docking results in high binding energy between imipenem and KPC-3.Molecular dynamics results in higher stability of KPC-3-imipenem complex.Virtual screening was carried out to find novel inhibitors for KPC-3.Molecular dynamics reveals higher stability of novel inhibitors than tazobactam. Molecular docking results in high binding energy between imipenem and KPC-3. Molecular dynamics results in higher stability of KPC-3-imipenem complex. Virtual screening was carried out to find novel inhibitors for KPC-3. Molecular dynamics reveals higher stability of novel inhibitors than tazobactam.
DOI: 10.7284/132908
title: GNSS (Global Navigation Satellite System) data collected during research cruise FK181031 using a C&C C-Nav 3050 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132907
title: Gyrocompass data collected during research cruise FK181031 using a Raytheon STD 22 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7578557
title: HEK293 nicastrin knockout NFKB-responsive luciferase assay

description: These data are the results of an NFKB-responsive luciferase assay of HEK293 wildtype cells and cells knocked out for nicastrin. Renilla luciferase was co-transfected as a transfection efficiency control.<br>
DOI: 10.6084/m9.figshare.7578560
title: Bash and R scripts used for the analyses

description: The purpose of this study is to characterize the Vδ1 + TCR repertoire in the thymus, namely by providing a detailed description of transcribed (mRNA) V(D)J recombination products in highly (FACS-)purified thymic Vδ1 + T cells.<br>These are the scripts used to obtain the tables of functional clonotypes available at https://figshare.com/s/0df2683ebb40ffba8f6e and used for the graphical representation of the data.<br>Raw data available at https://figshare.com/s/84ef2f6aaa48c2896228. <br>Raw <br>
DOI: 10.6084/m9.figshare.7578566
title: Raw background subtracted Illumina microarray of nicastrin knockdowns

description: HEK293 and HEK001 cells were both knocked down for either a nicastrin targeted shRNA or a control targeted luciferase. We profiled the transcriptomes using Illumina HT12 v4 microarrays. This is the background subtracted raw data.<br>
DOI: 10.6084/m9.figshare.7578560.v1
title: Bash and R scripts used for the analyses

description: The purpose of this study is to characterize the Vδ1 + TCR repertoire in the thymus, namely by providing a detailed description of transcribed (mRNA) V(D)J recombination products in highly (FACS-)purified thymic Vδ1 + T cells.<br>These are the scripts used to obtain the tables of functional clonotypes available at https://figshare.com/s/0df2683ebb40ffba8f6e and used for the graphical representation of the data.<br>Raw data available at https://figshare.com/s/84ef2f6aaa48c2896228. <br>Raw <br>
DOI: 10.6084/m9.figshare.7578566.v1
title: Raw background subtracted Illumina microarray of nicastrin knockdowns

description: HEK293 and HEK001 cells were both knocked down for either a nicastrin targeted shRNA or a control targeted luciferase. We profiled the transcriptomes using Illumina HT12 v4 microarrays. This is the background subtracted raw data.<br>
DOI: 10.7284/132914
title: INS (Inertial Navigation System) data collected during research cruise FK181031 using a Kongsberg Seapath 320 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7578539
title: HEK293 nicastrin knockout RT-qPCR

description: This is an RT-qPCR confirming the knockout (CRISPR-Cas9 mediated) of nicastrin in HEK293 cells.<br>
DOI: 10.6084/m9.figshare.7578548
title: supplementary materials from 'Identification of Novel Functional CpG-SNPs Associated with Type 2 Diabetes and Coronary Artery Disease'

description: Supplementary materials from title '<b>Identification of Novel Functional CpG-SNPs Associated with Type 2 Diabetes and Coronary Artery Disease</b>'<br>
DOI: 10.6084/m9.figshare.7578539.v1
title: HEK293 nicastrin knockout RT-qPCR

description: This is an RT-qPCR confirming the knockout (CRISPR-Cas9 mediated) of nicastrin in HEK293 cells.<br>
DOI: 10.6084/m9.figshare.7578548.v1
title: supplementary materials

description: Supplementary materials from title '<b>Identification of Novel Functional CpG-SNPs Associated with Type 2 Diabetes and Coronary Artery Disease</b>'<br>
DOI: 10.6084/m9.figshare.7578548.v3
title: supplementary materials from 'Identification of Novel Functional CpG-SNPs Associated with Type 2 Diabetes and Coronary Artery Disease'

description: Supplementary materials from title '<b>Identification of Novel Functional CpG-SNPs Associated with Type 2 Diabetes and Coronary Artery Disease</b>'<br>
DOI: 10.7284/132917
title: Multibeam Echosounder data collected during research cruise FK181031 using a Kongsberg EM302 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7578488
title: Nicastrin knockdown NFKB-responsive luciferase assay

description: These data are the luciferase assays of nicastrin knockdown cells with and without stimulation with TNF. The firefly luciferase was NFKB-responsive, and renilla luciferase was co-transfected as a transfection efficiency control.<br>
DOI: 10.6084/m9.figshare.7578548.v2
title: supplementary materials

description: Supplementary materials from title '<b>Identification of Novel Functional CpG-SNPs Associated with Type 2 Diabetes and Coronary Artery Disease</b>'<br>
DOI: 10.6084/m9.figshare.7578488.v1
title: Nicastrin knockdown NFKB-responsive luciferase assay

description: These data are the luciferase assays of nicastrin knockdown cells with and without stimulation with TNF. The firefly luciferase was NFKB-responsive, and renilla luciferase was co-transfected as a transfection efficiency control.<br>
DOI: 10.7284/132911
title: Splitbeam Echosounder data collected during research cruise FK181031 using a Kongsberg EK60 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7578443
title: Nicastrin knockdown RT-qPCR - transient knockdown shRNA test

description: These data are the real-time qPCR data from 5 separate shRNA constructs (A06-A10) targeting nicastrin.<br>
DOI: 10.6084/m9.figshare.7578428
title: Nicastrin knockdown RT-qPCR - stable knockdown

description: These data are the real-time qPCR of HEK001 and HEK293 cell lines stably knocked down for a nicastrin specific shRNA or a luciferase-specific shRNA.<br>
DOI: 10.7284/132913
title: SSV (Sound Speed Velocimeter) data collected during research cruise FK181031 using a Valeport MiniSVS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132915
title: TSG (Thermosalinograph) data collected during research cruise FK181031 using a Sea-Bird SBE-45 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133007
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise FK181210 using a Hawaii UHDAS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133005
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise FK181210 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133006
title: Expendable Probe data collected during research cruise FK181210 using a Turo Quoll instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133009
title: Fluorometer data collected during research cruise FK181210 using a WET Labs ECO-FLNTU instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7578350
title: The prognostic role of inflammation-scores on overall survival in lung cancer patients

description: <b>Objective:</b> Inflammation has been validated as a host-related prognostic marker in cancer. The Glasgow Prognostic score (GPS) and neutrophil-to-lymphocyte ratio (NLR) are suggested measures of inflammation. However, the allocation of patients has been questioned. Hence, optimized inflammation-scores has been developed, such as the combined NLR and GPS (CNG) system, and the Aarhus composite biomarker score (ACBS). So far, these optimized inflammation-scores have not been validated in lung cancer patients. We evaluated if the optimized inflammation-scores were prognostic markers of inferior survival in lung cancer patients. Furthermore, we tested which of the optimized inflammation-scores led to better patient-allocation. <b>Material and methods:</b> The cohort of this prospective study composed of 275 non-small cell lung cancer patients. We evaluated pre-diagnostic serum biomarkers for GPR, NLR, platelet-to-lymphocyte ratio as well as the optimized inflammation-scores CNG and ABCS as predictors of overall survival (OS), and we examined the patient-allocation derived from each inflammation-score. <b>Results:</b> Each of the evaluated inflammation-scores could predict the overall survival even when adjustments were made for comorbidity and clinicopathological characteristics. When comparing the scores, the optimized inflammation-scores CNG and ACBS led to a better and more balanced patient-allocation. In the early clinical stages I & II, the optimized scores could reveal a subgroup of patients with poorer survival that is similar to stage III. <b>Conclusion:</b> In this cohort of lung cancer patients, we demonstrate that inflammation-scores are prognostic markers of inferior survival. Furthermore, we demonstrate that the optimized inflammation-scores CNG and ACBS lead to better patient-allocation independently of the clinicopathological characteristics and comorbidity.