cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8545289
title: Supplementary Material for: Changing Protein Permeability with Nephron Loss: Evidence for a Human Remnant Nephron Effect

description: <b><i>Background:</i></b> If loss of functioning nephrons predisposes to glomerular barotrauma (a “remnant nephron” effect), then glomerular permeability should increase as glomerular filtration rate (GFR) falls, as is observed in animal models of nephron loss. <b><i>Methods:</i></b> Changes in net renal protein permeability, defined as proteinuria or albuminuria per mL/min of GFR, were measured in the setting of nephron loss due to kidney donation (Assessing Long Term Outcomes in Living Kidney Donors cohort) or progressive chronic kidney disease (CKD; Modification of Diet in Renal Disease [MDRD], African American Study of Kidney Disease [AASK], and Chronic Renal insufficiency Cohort [CRIC] studies). <b><i>Results:</i></b> Following kidney donation, renal albumin permeability increased by 31% from predonation levels (<i>p</i> &lt; 0.001). With progression of CKD, a 50% loss of residual GFR was accompanied by increases in proteinuria per mL/min GFR of 1.8-, 2.1-, and 1.6-fold in the MDRD, AASK, and CRIC cohorts, respectively (<i>p</i> &lt; 0.001 for all), independent of changes in systolic blood pressure and ACEi/ARB use. A 70% reduction in GFR was associated with permeability increases of 3.1-, 4.4-, and 2.6-fold in the same cohorts. Among MDRD participants with progression of nonglomerular primary disease, the 75th percentile of final permeability was 141 mg/24 h proteinuria per mL/min GFR. This degree of permeability would have resulted in nephrotic range proteinuria had it been present at the baseline mean GFR of 40 mL/min, implying the development of de novo glomerular pathology as GFR fell. Increasing permeability also accompanied CKD progression in participants with nephrotic syndrome at baseline. Consequently, these participants had little improvement in 24 h proteinuria or serum albumin, despite substantial loss of functioning nephron mass across which the protein leak occurred. In the absence of a fall in GFR, there was no increase in permeability in any cohort. <b><i>Conclusion:</i></b> Nephron loss is accompanied by an increase in renal protein permeability, even in the absence of a primary glomerular disease. This is consistent with a remnant nephron effect in human CKD.
DOI: 10.6084/m9.figshare.8543132.v1
title: Supplementary Material for: Starting Renal Replacement Therapy: Is It About Time?

description: <b><i>Background:</i></b> Studies of the timing of end-stage renal disease (ESRD) have primarily defined “early” versus “late” initiation of dialysis using estimated glomerular filtration rate (eGFR)-based criteria. Our objective was to determine the theoretical <i>time</i> that could be spent in chronic kidney disease (CKD) stage 5 prior to reaching a conservative eGFR threshold of 5 mL/min/1.73 m<sup>2</sup> compared to the actual time spent in CKD stage 5 by risk factors of interest. <b><i>Methods:</i></b> Eight-hundred and seventy Chronic Renal Insufficiency Cohort participants with CKD stage 5 who started renal replacement therapy (RRT) were included for retrospective study. We used mixed models to estimate the person-specific trajectory of renal function. We then used these individual trajectories to estimate the amount of time that would be spent in CKD stage 5 (between eGFR of 15 and 5 mL/min/1.73 m<sup>2</sup>) and compared this estimate to the actual time spent in CKD stage 5 prior to ESRD (between eGFR of 15 mL/min/1.73 m<sup>2</sup> and ESRD). <b><i>Results:</i></b> We found the median observed time between eGFR of 15 mL/min/1.73 m<sup>2</sup> to RRT was 9.6 months, but the median predicted time between eGFR of 15 mL/min/1.73 m<sup>2</sup> to eGFR of 5 mL/min/1.73 m<sup>2</sup> was 17.7 months. Some of the largest differences between the predicted and actual amount of time spent in CKD stage 5 were noted among those with systolic blood pressure &lt;140 mm Hg (9.7 months longer predicted compared to actual), proteinuria &lt;1 g/g (9.1 months), and serum albumin ≥3.5 g/dL (9.0 months). <b><i>Conclusion:</i></b> We found marked differences between the actual and predicted time spent in CKD stage 5 based on risk factors of interest. We believe that placing timing of dialysis initiation in the perspective of time is novel and may identify subgroups of patients who may derive particular benefit from a more concerted effort to delay RRT.
DOI: 10.6084/m9.figshare.8538752
title: Dataset for: Temperature-cycle Electron Paramagnetic Resonance

description: This dataset is relative to the paper with the same name published in PCCP (DOI: 10.1039/D0CP00664E). It contains:- 275 GHz EPR spectra- oscilloscope timetracks- Python and Origin files used for data analysis and to generate the figures<br>All the experimental conditions are illustrated in detail in the paper.
DOI: 10.6084/m9.figshare.8549204.v1
title: Supplemental material for the Carpinus fangiana genome

description: This collection of files stems from the annotation (gene model predicted, repetitive elements, non-coding genes) of the Carpinus fangiana genome.
DOI: 10.6084/m9.figshare.8538752.v1
title: Dataset for: Temperature-cycle Electron Paramagnetic Resonance

description: This dataset is relative to the paper with the same name published in PCCP (DOI: 10.1039/D0CP00664E). It contains:- 275 GHz EPR spectra- oscilloscope timetracks- Python and Origin files used for data analysis and to generate the figures<br>All the experimental conditions are illustrated in detail in the paper.
DOI: 10.6084/m9.figshare.8538563
title: Nosocomials and Biogeography

description: Data from nosocomial microorganisms found in Hospitals.
DOI: 10.6084/m9.figshare.8549204.v2
title: Supplemental material for the Carpinus fangiana genome

description: This collection of files stems from the annotation (gene model predicted, annotation for repetitive elements and non-coding genes, nucleotide sequences for coding and non-coding genes, protein sequences for coding genes) of the Carpinus fangiana genome.
DOI: 10.6084/m9.figshare.8538563.v2
title: Nosocomials and Biogeography

description: Data from nosocomial microorganisms found in Hospitals.
DOI: 10.6084/m9.figshare.8549204.v3
title: Supplemental material for the Carpinus fangiana genome

description: Supplement_data 1: Information for the repetitive elements in Carpinus fangiana genome.Supplement_data 2: Information for the long treminal repeats (LTRs) in Carpinus fangiana genome.Supplement_data 3: Information for the predicted protein-coding gene models in Carpinus fangiana genome.Supplement_data 4: The CDS sequences of the predicted protein-coding gene models in Carpinus fangiana genome.Supplement_data 5: The protein sequences of the predicted protein-coding gene models in Carpinus fangiana genome.Supplement_data 6: Information for the predicted non-coding genes in Carpinus fangiana genome.Supplement_data 7: The sequences of the predicted non-coding genes in Carpinus fangiana genome.Supplement_data 8: Information for the predicted tRNA in Carpinus fangiana genome.Supplement_data 9: The sequences of the prediceted tRNA in Carpinus fangiana genome.Supplement_material 1: Perl script for the quality contral of pair-end Illumina sequencing data.Supplement_material 2: Perl script for computing heterozygosity of the Carpinus genome based on variant calling results.
DOI: 10.6084/m9.figshare.8538563.v1
title: Nosocomials

description: Data from nosocomial microorganisms found in Hospitals.
DOI: 10.6084/m9.figshare.8549204.v4
title: Supplemental files for the Carpinus fangiana genome

description: Supplement_data 1: Information for the repetitive elements in Carpinus fangiana genome.Supplement_data 2: Information for the long treminal repeats (LTRs) in Carpinus fangiana genome.Supplement_data 3: Information for the predicted protein-coding gene models in Carpinus fangiana genome.Supplement_data 4: The CDS sequences of the predicted protein-coding gene models in Carpinus fangiana genome.Supplement_data 5: The protein sequences of the predicted protein-coding gene models in Carpinus fangiana genome.Supplement_data 6: Information for the predicted non-coding genes in Carpinus fangiana genome.Supplement_data 7: The sequences of the predicted non-coding genes in Carpinus fangiana genome.Supplement_data 8: Information for the predicted tRNA in Carpinus fangiana genome.Supplement_data 9: The sequences of the prediceted tRNA in Carpinus fangiana genome.Supplement_material 1: Perl script for the quality contral of pair-end Illumina sequencing data.Supplement_material 2: Perl script for computing heterozygosity of the Carpinus genome based on variant calling results.
DOI: 10.6084/m9.figshare.8527148
title: Decentralized Gathering of Stochastic, Oblivious Agents on a Grid: A Case Study with 3D M-Blocks

description: In the attachment, one can find:- Optimized stochastic control policy paramater table (CSV file)- Multimedia material (MP4 video)
DOI: 10.6084/m9.figshare.8549204.v5
title: Data and material for the Carpinus fangiana genome

description: Supplement_data 1: Information for the repetitive elements in Carpinus fangiana genome.Supplement_data 2: Information for the long treminal repeats (LTRs) in Carpinus fangiana genome.Supplement_data 3: Information for the predicted protein-coding gene models in Carpinus fangiana genome.Supplement_data 4: The CDS sequences of the predicted protein-coding gene models in Carpinus fangiana genome.Supplement_data 5: The protein sequences of the predicted protein-coding gene models in Carpinus fangiana genome.Supplement_data 6: Information for the predicted non-coding genes in Carpinus fangiana genome.Supplement_data 7: The sequences of the predicted non-coding genes in Carpinus fangiana genome.Supplement_data 8: Information for the predicted tRNA in Carpinus fangiana genome.Supplement_data 9: The sequences of the prediceted tRNA in Carpinus fangiana genome.Supplement_material 1: Perl script for the quality contral of pair-end Illumina sequencing data.Supplement_material 2: Perl script for computing heterozygosity of the Carpinus genome based on variant calling results.
DOI: 10.6084/m9.figshare.8527148.v1
title: Decentralized Gathering of Stochastic, Oblivious Agents on a Grid: A Case Study with 3D M-Blocks

description: In the attachment, one can find:- Optimized stochastic control policy paramater table (CSV file)- Multimedia material (MP4 video)
DOI: 10.6084/m9.figshare.8527148.v2
title: Decentralized Gathering of Stochastic, Oblivious Agents on a Grid: A Case Study with 3D M-Blocks

description: In the attachment, one can find:- Optimized stochastic control policy paramater table (CSV file)- Multimedia material (MP4 video)
DOI: 10.6084/m9.figshare.8527148.v3
title: Decentralized Gathering of Stochastic, Oblivious Agents on a Grid: A Case Study with 3D M-Blocks

description: In the attachment, one can find:- Optimized stochastic control policy paramater table (CSV file)- Multimedia material (MP4 video)
DOI: 10.6084/m9.figshare.8523554
title: Diaa RDF plan.pdf

description: My RDF plan
DOI: 10.6084/m9.figshare.8527148.v5
title: Decentralized Gathering of Stochastic, Oblivious Agents on a Grid: A Case Study with 3D M-Blocks

description: In the attachment, one can find:- Optimized stochastic control policy paramater table (CSV file)- Multimedia material (MP4 video)
DOI: 10.6084/m9.figshare.8527148.v4
title: Decentralized Gathering of Stochastic, Oblivious Agents on a Grid: A Case Study with 3D M-Blocks

description: In the attachment, one can find:- Optimized stochastic control policy paramater table (CSV file)- Multimedia material (MP4 video)
DOI: 10.6084/m9.figshare.8523554.v2
title: Diaa RDF plan.pdf

description: My RDF plan
DOI: 10.6084/m9.figshare.8523554.v1
title: Diaa RDF plan.pdf

description: My RDF plan
DOI: 10.6084/m9.figshare.8514155
title: Supplementary Material for: Protocol for the Connected Speech Transcription of Children with Speech Disorders: An Example from Childhood Apraxia of Speech

description: <b><i>Objective:</i></b> While it is known that connected speech has different features to single-word speech, there are currently few recommendations regarding connected speech transcription. This research therefore aimed to develop a clinically feasible protocol for connected speech transcription. The protocol was then used to assist with description of the connected speech of children with childhood apraxia of speech (CAS), as little is known about their connected speech characteristics. <b><i>Participants and Methods:</i></b> Following a literature review, the Connected Speech Transcription Protocol (CoST-P) was iteratively developed and trialled. The CoST-P was then used to transcribe 50 connected utterances produced by 12 children (aged 6–13 years) with CAS. The characteristics of participants’ connected speech were analysed to capture independent and relational analyses. <b><i>Results:</i></b> The CoST-P was developed, trialled, and determined to have adequate reliability and fidelity. The frequency of inter-word segregation (mean = 29) was higher than intra-word segregation (mean = 4). Juncture accuracy was correlated with intelligibility metrics such as percentage of consonants correct. <b><i>Conclusion:</i></b> Connected speech transcription is challenging. The CoST-P may be a useful resource for speech-language pathologists and clinical researchers. Use of the CoST-P assisted in displaying CAS speech characteristics unique to connected speech (e.g., inter-word segregation and juncture).
DOI: 10.6084/m9.figshare.8493302
title: Rewiring of transcriptional networks as a major event leading to the diversity of asexual multicellularity in fungi

description: Complex multicellularity (CM) is characterized by the generation of three-dimensional structures that follow a genetically controlled program. CM emerged at least five times in evolution, one of them in fungi. There are two types of CM programs in fungi, leading, respectively, to the formation of sexual or asexual spores. Asexual spores foment the spread of mycoses, as they are the main vehicle for dispersion. In spite of this key dependence, there is great morphological diversity of asexual multicellular structures in fungi. To advance the understanding of the mechanisms that control initiation and progression of asexual CM and how they can lead to such a remarkable morphological diversification, we studied 503 fungal proteomes, representing all phyla and subphyla, and most known classes. Conservation analyses of 33 regulators of asexual development suggest stepwise emergence of transcription factors. While velvet proteins constitute one of the most ancient systems, the central regulator BrlA emerged late in evolution (with the class Eurotiomycetes). Some factors, such as MoConX4, seem to be species-specific. These observations suggest that the emergence and evolution of transcriptional regulators rewire transcriptional networks. This process could reach the species level, resulting in a vast diversity of morphologies.
DOI: 10.6084/m9.figshare.8493302.v2
title: Rewiring of transcriptional networks as a major event leading to the diversity of asexual multicellularity in fungi

description: Complex multicellularity (CM) is characterized by the generation of three-dimensional structures that follow a genetically controlled program. CM emerged at least five times in evolution, one of them in fungi. There are two types of CM programs in fungi, leading, respectively, to the formation of sexual or asexual spores. Asexual spores foment the spread of mycoses, as they are the main vehicle for dispersion. In spite of this key dependence, there is great morphological diversity of asexual multicellular structures in fungi. To advance the understanding of the mechanisms that control initiation and progression of asexual CM and how they can lead to such a remarkable morphological diversification, we studied 503 fungal proteomes, representing all phyla and subphyla, and most known classes. Conservation analyses of 33 regulators of asexual development suggest stepwise emergence of transcription factors. While velvet proteins constitute one of the most ancient systems, the central regulator BrlA emerged late in evolution (with the class Eurotiomycetes). Some factors, such as MoConX4, seem to be species-specific. These observations suggest that the emergence and evolution of transcriptional regulators rewire transcriptional networks. This process could reach the species level, resulting in a vast diversity of morphologies.
DOI: 10.6084/m9.figshare.8493302.v1
title: Rewiring of transcriptional networks as a major event leading to the diversity of asexual multicellularity in fungi

description: Complex multicellularity (CM) is characterized by the generation of three-dimensional structures that follow a genetically controlled program. CM emerged at least five times in evolution, one of them in fungi. There are two types of CM programs in fungi, leading, respectively, to the formation of sexual or asexual spores. Asexual spores foment the spread of mycoses, as they are the main vehicle for dispersion. In spite of this key dependence, there is great morphological diversity of asexual multicellular structures in fungi. To advance the understanding of the mechanisms that control initiation and progression of asexual CM and how they can lead to such a remarkable morphological diversification, we studied 503 fungal proteomes, representing all phyla and subphyla, and most known classes. Conservation analyses of 33 regulators of asexual development suggest stepwise emergence of transcription factors. While velvet proteins constitute one of the most ancient systems, the central regulator BrlA emerged late in evolution (with the class Eurotiomycetes). Some factors, such as MoConX4, seem to be species-specific. These observations suggest that the emergence and evolution of transcriptional regulators rewire transcriptional networks. This process could reach the species level, resulting in a vast diversity of morphologies.
DOI: 10.6084/m9.figshare.8490134
title: Knowledge Graph Consolidation by Unifying Synonymous Relationships

description: The datasets for reproducing the results of the paper "Knowledge Graph Consolidation by Unifying Synonymous Relationships" published at ISWC 2019.
DOI: 10.6084/m9.figshare.8490137
title: Transition of deformation mechanisms in nanotwinned single crystalline SiC

description: The ability to experimentally synthesise ceramic materials to incorporate nanotwinned microstructures can drastically affect the underlying deformation mechanisms and mechanics through the complex interaction between stress state, crystallographic orientation, and twin orientation. In this study, molecular dynamics simulations are used to examine the transition in deformation mechanisms and mechanical responses of nanotwinned zinc-blende SiC ceramics subjected to different stress states (uniaxial compressive, uniaxial tensile, and shear deformation) by employing various twin spacings and loading/crystallographic orientations in nanotwinned structures, as compared to their single crystal counterparts. The simulation results show that different combinations of stress states and crystal/twin orientation, and twin spacing trigger different deformation mechanisms: (i) shear localised deformation and shear-induced fracture, preceded by point defect formation and dislocation slip, in the vicinity of the twin lamellae, shear band formation, and dislocation (emission) avalanche; (ii) cleavage and fracture without dislocation plasticity, weakening the nanotwinned ceramics compared to their twin-free counterpart; (iii) severe localised deformation, generating a unique zigzag microstructure between twins without any structural phase transformations or amorphisation, and (iv) atomic disordering localised in the vicinity of coherent twin boundaries, triggering dislocation nucleation and low shearability compared to twin-free systems.
DOI: 10.6084/m9.figshare.8490134.v2
title: Knowledge Graph Consolidation by Unifying Synonymous Relationships

description: The datasets for reproducing the results of the paper "Knowledge Graph Consolidation by Unifying Synonymous Relationships" published at ISWC 2019.
DOI: 10.6084/m9.figshare.8490137.v2
title: Transition of deformation mechanisms in nanotwinned single crystalline SiC

description: The ability to experimentally synthesise ceramic materials to incorporate nanotwinned microstructures can drastically affect the underlying deformation mechanisms and mechanics through the complex interaction between stress state, crystallographic orientation, and twin orientation. In this study, molecular dynamics simulations are used to examine the transition in deformation mechanisms and mechanical responses of nanotwinned zinc-blende SiC ceramics subjected to different stress states (uniaxial compressive, uniaxial tensile, and shear deformation) by employing various twin spacings and loading/crystallographic orientations in nanotwinned structures, as compared to their single crystal counterparts. The simulation results show that different combinations of stress states and crystal/twin orientation, and twin spacing trigger different deformation mechanisms: (i) shear localised deformation and shear-induced fracture, preceded by point defect formation and dislocation slip, in the vicinity of the twin lamellae, shear band formation, and dislocation (emission) avalanche; (ii) cleavage and fracture without dislocation plasticity, weakening the nanotwinned ceramics compared to their twin-free counterpart; (iii) severe localised deformation, generating a unique zigzag microstructure between twins without any structural phase transformations or amorphisation, and (iv) atomic disordering localised in the vicinity of coherent twin boundaries, triggering dislocation nucleation and low shearability compared to twin-free systems.
DOI: 10.6084/m9.figshare.8490137.v1
title: Transition of deformation mechanisms in nanotwinned single crystalline SiC

description: The ability to experimentally synthesise ceramic materials to incorporate nanotwinned microstructures can drastically affect the underlying deformation mechanisms and mechanics through the complex interaction between stress state, crystallographic orientation, and twin orientation. In this study, molecular dynamics simulations are used to examine the transition in deformation mechanisms and mechanical responses of nanotwinned zinc-blende SiC ceramics subjected to different stress states (uniaxial compressive, uniaxial tensile, and shear deformation) by employing various twin spacings and loading/crystallographic orientations in nanotwinned structures, as compared to their single crystal counterparts. The simulation results show that different combinations of stress states and crystal/twin orientation, and twin spacing trigger different deformation mechanisms: (i) shear localised deformation and shear-induced fracture, preceded by point defect formation and dislocation slip, in the vicinity of the twin lamellae, shear band formation, and dislocation (emission) avalanche; (ii) cleavage and fracture without dislocation plasticity, weakening the nanotwinned ceramics compared to their twin-free counterpart; (iii) severe localised deformation, generating a unique zigzag microstructure between twins without any structural phase transformations or amorphisation, and (iv) atomic disordering localised in the vicinity of coherent twin boundaries, triggering dislocation nucleation and low shearability compared to twin-free systems.
DOI: 10.6084/m9.figshare.8490134.v1
title: Knowledge Graph Consolidation by Unifying Synonymous Relationships

description: The datasets for reproducing the results of the paper "Knowledge Graph Consolidation by Unifying Synonymous Relationships" published at ISWC 2019.
DOI: 10.6084/m9.figshare.8486822
title: The neck sensor signals from Neck sensor-supported hyoid bone movement tracking during swallowing

description: The original signals acquired by the neck sensors.