cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5048584.v1
title: Vibration data of the clamped-clamped beam from Nonlinear model identification and spectral submanifolds for multi-degree-of-freedom mechanical vibrations

description: This is a MATLAB file containing velocity time series that were used to calculate the three backbone curves in figure 4. The data is re-sampled with a relatively coarse sample rate as described in the article text. The file contains 4 matrices. The first row of each matrix is time, the second row is the velocity of the beam near its midpoint. There are four tracks of vibrations, but only three of them, ‘NNM1a’, ‘NNM2’ and ‘NNM3’ were used to calculate the backbone curves. ‘NNM1b’ is an alternative track for the first mode, which can be used in combination with the rest or can replace ‘NNM1a’.
DOI: 10.6084/m9.figshare.5048569
title: Data.tar from Extensional channel flow revisited: a dynamical systems perspective

description: Bifurcation curves data files.
DOI: 10.6084/m9.figshare.5048566
title: Table S1 from Body shape convergence driven by small size optimum in marine angelfishes

description: List of studied species and their maximum total length (TL). The number of used X-rays (n) and the Genbank accession numbers are also provided.
DOI: 10.6084/m9.figshare.5048569.v1
title: Data.tar from Extensional channel flow revisited: a dynamical systems perspective

description: Bifurcation curves data files.
DOI: 10.6084/m9.figshare.5048566.v1
title: Table S1 from Body shape convergence driven by small size optimum in marine angelfishes

description: List of studied species and their maximum total length (TL). The number of used X-rays (n) and the Genbank accession numbers are also provided.
DOI: 10.6084/m9.figshare.5048542
title: Matlab Code for Brownian dynamics from Macromolecular crowding directs the motion of small molecules inside cells

description: It is now well established that cell interiors are significantly crowded by macromolecules, which impede diffusion and enhance binding rates. However, it is not fully appreciated that levels of crowding are heterogeneous, and can vary substantially between subcellular regions. In this article, starting from a microscopic model, we derive coupled nonlinear partial differential equations for the concentrations of two populations of large and small spherical particles with steric volume exclusion. By performing an expansion in the ratio of the particle sizes, we find that the diffusion of a small particle in the presence of large particles obeys an advection–diffusion equation, with a reduced diffusion coefficient and a velocity directed towards less crowded regions. The interplay between advection and diffusion leads to behaviour that differs significantly from Brownian diffusion. We show that biologically plausible distributions of macromolecules can lead to highly non-Gaussian probability densities for the small particle position, including asymmetrical and multimodal densities. We confirm all our results using hard-sphere Brownian dynamics simulations.
DOI: 10.6084/m9.figshare.5048512
title: Supplementary material: Prognostic Interaction patterns in diabetes mellitus II network: A RMT relation

description: The article is a supplementary material of the published paper that includes the detailed functional information of the disease as well as the normal protiens, and details of random matrix techniques.
DOI: 10.6084/m9.figshare.5048518
title: Protocetid (Cetacea, Artiodactyla) bullae and petrosals from the middle Eocene locality of Kpogamé, Togo: new insights into the early history of cetacean hearing

description: Extant cetaceans are fully aquatic mammals with deep modifications of their sensory organs, notably of the sound perception pathway. Early diverging cetaceans, known as archaeocetes, show a diversity of morphologies of the petrotympanic complex and middle ear ossicles, documenting a variety of sound transmission mechanisms from a mostly terrestrial configuration to a fully aquatic layout. Protocetids are a paraphyletic assemblage of semi-aquatic archaeocetes known from the Eocene. The auditory region of these ‘transitional’ forms is only partly known. The middle Eocene locality of Kpogamé, Togo (46–43 Ma) has yielded abundant material of protocetid whales documenting the auditory region, including isolated bullae, one petrosal and a skull fragment preserving the petrotympanic complex. Detailed study of this material leads us to reassess the original taxonomic attribution of this material, first attributed to <i>Togocetus traversei</i>, and to recognize three different protocetid taxa on the basis of bullar and petrosal remains: ?<i>Carolinacetus</i> sp., <i>Togocetus traversei</i> and Protocetidae indeterminate (morphotype γ). Associating isolated petrosals or bullae with dental remains solely based on size criteria can be misleading and we show here that there is no correlation between the size of tympanic bulla and size of dental remains in protocetids. CT-scan investigation of the <i>in situ</i> petrotympanic complex reveals that Protocetidae retained a complete tympanic ring similar to that of terrestrial artiodactyls and that the involucrum could probably articulate with the medial side of the ventral surface of the petrosal. This bulla/petrosal articulation is absent in fully aquatic cetaceans. Finally, the close phylogenetic relationships between protocetids from Kpogamé and North American protocetids suggest successive dispersals of these non-fully aquatic archaeocetes from African coasts to North America.
DOI: 10.6084/m9.figshare.5048518.v1
title: Protocetid (Cetacea, Artiodactyla) bullae and petrosals from the middle Eocene locality of Kpogamé, Togo: new insights into the early history of cetacean hearing

description: Extant cetaceans are fully aquatic mammals with deep modifications of their sensory organs, notably of the sound perception pathway. Early diverging cetaceans, known as archaeocetes, show a diversity of morphologies of the petrotympanic complex and middle ear ossicles, documenting a variety of sound transmission mechanisms from a mostly terrestrial configuration to a fully aquatic layout. Protocetids are a paraphyletic assemblage of semi-aquatic archaeocetes known from the Eocene. The auditory region of these ‘transitional’ forms is only partly known. The middle Eocene locality of Kpogamé, Togo (46–43 Ma) has yielded abundant material of protocetid whales documenting the auditory region, including isolated bullae, one petrosal and a skull fragment preserving the petrotympanic complex. Detailed study of this material leads us to reassess the original taxonomic attribution of this material, first attributed to <i>Togocetus traversei</i>, and to recognize three different protocetid taxa on the basis of bullar and petrosal remains: ?<i>Carolinacetus</i> sp., <i>Togocetus traversei</i> and Protocetidae indeterminate (morphotype γ). Associating isolated petrosals or bullae with dental remains solely based on size criteria can be misleading and we show here that there is no correlation between the size of tympanic bulla and size of dental remains in protocetids. CT-scan investigation of the <i>in situ</i> petrotympanic complex reveals that Protocetidae retained a complete tympanic ring similar to that of terrestrial artiodactyls and that the involucrum could probably articulate with the medial side of the ventral surface of the petrosal. This bulla/petrosal articulation is absent in fully aquatic cetaceans. Finally, the close phylogenetic relationships between protocetids from Kpogamé and North American protocetids suggest successive dispersals of these non-fully aquatic archaeocetes from African coasts to North America.
DOI: 10.6084/m9.figshare.5048497
title: Supplementary Material for: MicroRNA-1185 Induces Endothelial Cell Apoptosis by Targeting UVRAG and KRIT1

description: <i>Background/Aims:</i> Atherosclerosis is a multifactorial chronic disease and is the main cause of death and impairment in the world. Endothelial injury and apoptosis play a crucial role in the onset and development of atherosclerosis. MicroRNAs (miRNAs) have been proven to be involved in the pathogenesis of atherosclerosis. However, studies of the functional role of apoptosis-related miRNAs in the endothelium during atherogenesis are limited. <i>Methods:</i> Cell injury and apoptosis were measured in five types of cells transfected with miR-1185 or co-transfected with miR-1185 and its inhibitor. Bioinformatics analysis and a luciferase reporter assay were used to confirm the targets of miR-1185. The effects of the targets of miR-1185 on endothelial apoptosis were determined using small-interfering RNA. <i>Results:</i> In this study, we first report that miR-1185 significantly promoted apoptosis in endothelial cells but not in vascular smooth muscle cells and macrophages. A mechanistic analysis showed that ultraviolet irradiation resistance-associated gene (UVRAG) and krev1 interaction trapped gene 1 (KRIT1), targets of miR-1185, mediated miR-1185-induced endothelial cell apoptosis. <i>Conclusion:</i> The results revealed the impact of miR-1185 on endothelial apoptosis, suggesting that miR-1185 may be a potential target for the prevention and treatment of atherosclerosis.
DOI: 10.6084/m9.figshare.5048485
title: Exploring disorder in the human charged biased proteins

description: A considerable interest has been put in the identification of biased regions in proteins. These regions are frequently associated with a structural role in the cell and particularly with protein disorder. Here, we have investigated the intrinsically disordered regions (IDRs) in the human charged biased proteins identified in our earlier work. We found that 65% of charged biased proteins contained significant IDRs involved particularly in DNA and RNA binding. Also, we have observed that these proteins are well conserved in metazoans and more particularly in mammalian. In addition, the IDRs are located largely in N-terminal, C-terminal sequence flanking the functional domains (FD) and slightly less in (FD) itself. Our work also supports the association between protein disorder and protein–protein/DNA interaction. An example will be described.
DOI: 10.6084/m9.figshare.5048479
title: Supplementary Material for: Quantitative Proteomics Analysis of Ischemia/Reperfusion Injury-Modulated Proteins in Cardiac Microvascular Endothelial Cells and the Protective Role of Tongxinluo

description: <i>Background:</i> The protection of endothelial cells (ECs) against reperfusion injury has received little attention. In this study, we used Tandem Mass Tag (TMT) labeling proteomics to investigate the modulated proteins in an <i>in vitro</i> model of cardiac microvascular endothelial cells (CMECs) subjected to ischemia/reperfusion (I/R) injury and their alteration by traditional Chinese medicine Tongxinluo (TXL). <i>Methods:</i> Human CMECs were subjected to 2 h of hypoxia followed by 2 h of reoxygenation with different concentrations of TXL Protein expression profiles of CMECs were determined using tandem mass spectrometry. We evaluated several proteins with altered expression in I/R injury and summarized some reported proteins related to I/R injury. <i>Results:</i> TXL dose-dependently decreased CMEC apoptosis, and the optimal concentration was 800 µg/mL. I/R significantly altered proteins in CMECs, and 30 different proteins were detected between a normal group and a hypoxia and serum deprivation group. In I/R injury, TXL treatment up-regulated 6 types of proteins including acyl-coenzyme A synthetase ACSM2B mitochondrial (ACSM2B), cyclin-dependent kinase inhibitor 1B (CDKN1B), heme oxygenase 1 (HMOX1), transcription factor SOX-17 (SOX17), sequestosome-1 isoform 1 (SQSTM1), and TBC1 domain family member 10B (TBC1D10B). Also, TXL down-regulated 5 proteins including angiopoietin-2 isoform c precursor (ANGPT2), cytochrome c oxidase assembly factor 5 (COA5), connective tissue growth factor precursor (CTGF), cathepsin L1 isoform 2 (CTSL), and eukaryotic elongation factor 2 kinase (LOC101930123). These types of proteins mainly had vital functions, including cell proliferation, stress response, and regulation of metabolic process. <i>Conclusions:</i> The study presented differential proteins upon I/R injury through a proteomic analysis. TXL modulated the expression of proteins in CMECs and has a protective role in response to I/R.
DOI: 10.6084/m9.figshare.5048449
title: Supplementary Material for: Emery-Dreifuss Muscular Dystrophy-Associated Mutant Forms of Lamin A Recruit the Stress Responsive Protein Ankrd2 into the Nucleus, Affecting the Cellular Response to Oxidative Stress

description: <i>Background:</i> Ankrd2 is a stress responsive protein mainly expressed in muscle cells. Upon the application of oxidative stress, Ankrd2 translocates into the nucleus where it regulates the activity of genes involved in cellular response to stress. Emery-Dreifuss Muscular Dystrophy 2 (EDMD2) is a muscular disorder caused by mutations of the gene encoding lamin A, <i>LMNA</i>. As well as many phenotypic abnormalities, EDMD2 muscle cells also feature a permanent basal stress state, the underlying molecular mechanisms of which are currently unclear. <i>Methods:</i> Experiments were performed in EDMD2-lamin A overexpressing cell lines and EDMD2-affected human myotubes. Oxidative stress was produced by H2O2 treatment. Co-immunoprecipitation, cellular subfractionation and immunofluorescence analysis were used to validate the relation between Ankrd2 and forms of lamin A; cellular sensibility to stress was monitored by the analysis of Reactive Oxygen Species (ROS) release and cell viability. <i>Results:</i> Our data demonstrate that oxidative stress induces the formation of a complex between Ankrd2 and lamin A. However, EDMD2-lamin A mutants were able to bind and mislocalize Ankrd2 in the nucleus even under basal conditions. Nonetheless, cells co-expressing Ankrd2 and EDMD2-lamin A mutants were more sensitive to oxidative stress than the Ankrd2-wild type lamin A counterpart. <i>Conclusions:</i> For the first time, we present evidence that in muscle fibers from patients affected by EDMD2, Ankrd2 has an unusual nuclear localization. By introducing a plausible mechanism ruling this accumulation, our data hint at a novel function of Ankrd2 in the pathogenesis of EDMD2-affected cells.
DOI: 10.6084/m9.figshare.5048458
title: Long-term livestock grazing increases the recruitment success of epigeal termites: insights from a &gt;75-year grazing experiment in the Karoo, South Africa

description: Epigeal termites alter ecosystem-level processes through foraging and mound building. These effects are proportional to density. Whilst much is known about the factors influencing mound density in natural settings, how termites respond to livestock grazing has been overlooked. We compared the characteristics and density of <i>Trinervitermes trinervoides</i> (Isoptera: Termitidae) mounds in the Karoo (South Africa) within an exclosure and continuously-grazed plot from a &gt;75-year grazing experiment. Specifically, we asked whether long-term livestock grazing impacted (1) termite mound density, volume, basal area and size, (2) mound occupancy and age, (3) vegetation characteristics and (4) soil properties. Long-term grazing increased mound density two-fold. This was coupled with a decrease in mean mound size, an increase in the size of the largest mounds and range of mound sizes, and an increase in the proportion and numbers of young, active mounds. However, these changes did not alter landscape-scale mound basal area or volume. Vegetation was unaffected by long-term grazing but it did cause soil phosphorus, magnesium and calcium depletion. We suggest that livestock grazing provides additional forage resources for termites through litter breakup and dung production, leading to greater mound recruitment and thus densities, whilst allowing mounds to achieve greater maximum size.
DOI: 10.6084/m9.figshare.5048458.v2
title: Long-term livestock grazing increases the recruitment success of epigeal termites: insights from a &gt;75-year grazing experiment in the Karoo, South Africa

description: Epigeal termites alter ecosystem-level processes through foraging and mound building. These effects are proportional to density. Whilst much is known about the factors influencing mound density in natural settings, how termites respond to livestock grazing has been overlooked. We compared the characteristics and density of <i>Trinervitermes trinervoides</i> (Isoptera: Termitidae) mounds in the Karoo (South Africa) within an exclosure and continuously-grazed plot from a &gt;75-year grazing experiment. Specifically, we asked whether long-term livestock grazing impacted (1) termite mound density, volume, basal area and size, (2) mound occupancy and age, (3) vegetation characteristics and (4) soil properties. Long-term grazing increased mound density two-fold. This was coupled with a decrease in mean mound size, an increase in the size of the largest mounds and range of mound sizes, and an increase in the proportion and numbers of young, active mounds. However, these changes did not alter landscape-scale mound basal area or volume. Vegetation was unaffected by long-term grazing but it did cause soil phosphorus, magnesium and calcium depletion. We suggest that livestock grazing provides additional forage resources for termites through litter breakup and dung production, leading to greater mound recruitment and thus densities, whilst allowing mounds to achieve greater maximum size.
DOI: 10.6084/m9.figshare.5048437
title: Supplementary Material for: Higher Ultrafiltration Rate Is Associated with Longer Dialysis Recovery Time in Patients Undergoing Conventional Hemodialysis

description: <i>Background:</i> Increased mortality and morbidity are reported in association with high ultrafiltration rate (UFR) and with long dialysis recovery time (DRT). We studied the association between UFR and DRT. <i>Methods:</i> This is a cross-sectional, observational study was conducted. Patients on thrice-weekly hemodialysis (HD) with self-reported DRT between August and December 2014 were included. We examined the association of 30-day average UFR with recovery time. <i>Results:</i> The total number of patients included in this study was 2,689. DRT in categories of immediate recovery, &gt;0-≤2, &gt;2-≤6, &gt;6-≤12, and &gt;12 h, were reported in 27, 28, 17, 9, and 20% of the patients respectively. In multivariable analysis, longer DRT was associated with female gender, non-black race, higher body weight, lower serum albumin, chronic heart failure, cerebrovascular disease, missed dialysis sessions, higher pre-dialysis systolic blood pressure, and larger UF volume. Compared to UFR of &lt;10, UFR ≥13 mL/kg/h was associated with longer DRT, OR of 1.16 (95% CI 0.99-1.36), and 1.28 (95% CI 1.06-1.54) in the unadjusted and the adjusted analyses respectively. Intradialytic hypotension was also associated with longer DRT in the unadjusted (per 10% higher frequency, OR 1.04 [95% CI 1.01-1.07]) and adjusted analyses (OR 1.03 [95% CI 1.00-1.07]). <i>Conclusion:</i>Long recovery time is common after HD. Rapid fluid removal is associated with longer DRT.
DOI: 10.6084/m9.figshare.5048425
title: ferroelectric search distortion and workflow data

description: These files contain details for each candidate from a search of the Materials Project database for ferroelectrics. These JSON files provide details of the symmetry analysis performed for each candidate and data generated by DFT calculations and post-processing from the workflow.
DOI: 10.6084/m9.figshare.5048425.v1
title: ferroelectric search distortion and workflow data

description: These files contain details for each candidate from a search of the Materials Project database for ferroelectrics. These JSON files provide details of the symmetry analysis performed for each candidate and data generated by DFT calculations and post-processing from the workflow.
DOI: 10.6084/m9.figshare.5048425.v3
title: ferroelectric search distortion and workflow data

description: These files contain details for each candidate from a search of the Materials Project database for ferroelectrics. These JSON files provide details of the symmetry analysis performed for each candidate and data generated by DFT calculations and post-processing from the workflow.
DOI: 10.6084/m9.figshare.5048425.v2
title: ferroelectric search distortion and workflow data

description: These files contain details for each candidate from a search of the Materials Project database for ferroelectrics. These JSON files provide details of the symmetry analysis performed for each candidate and data generated by DFT calculations and post-processing from the workflow.
DOI: 10.6084/m9.figshare.5048329
title: Review on Physically Flexible Nonvolatile Memory for Internet of Everything Electronics

description: Solid-state memory is an essential component of the digital age. With advancements in healthcare technology and the Internet of Things (IoT), the demand for ultra-dense, ultra-low-power memory is increasing. In this review, we present a comprehensive perspective on the most notable approaches to the fabrication of physically flexible memory devices. With the future goal of replacing traditional mechanical hard disks with solid-state storage devices, a fully flexible electronic system will need two basic devices: transistors and nonvolatile memory. Transistors are used for logic operations and gating memory arrays, while nonvolatile memory (NVM) devices are required for storing information in the main memory and cache storage. Since the highest density of transistors and storage structures is manifested in memories, the focus of this review is flexible NVM. Flexible NVM components are discussed in terms of their functionality, performance metrics, and reliability aspects, all of which are critical components for NVM technology to be part of mainstream consumer electronics, IoT, and advanced healthcare devices. Finally, flexible NVMs are benchmarked and future prospects are provided.
DOI: 10.6084/m9.figshare.5048326
title: Approximations of Steel Cased wells for a DC resistivity experiment

description: In this example, we examine the impact of upscaling the well using- the assumption that the well is a solid rod of steel- averaging conductivity such that the product of the electrical conductivity and cross sectional area is the same in both cases<br>These experiments are conducted at DC. The initial model we consider is based on that shown Um, 2015: Finite element modelling of transient electromagnetic fields near steel-cased wells (https://doi.org/10.1093/gji/ggv193)<br>For the full write-up, please see the notebook Approximating_Steel_Cased_Wells_DC.ipynb<br><b>Reproducing these results</b>To run these examples, please see requirements.txt for the required packages (`pip install -r requirements.txt`). If you run into issues, please make an issue on github: https://github.com/lheagy/casingNotebooks/issues/new <br>SimPEG and the implementation for electrical and electromagnetic methods is described in (Cockett et al., 2015: https://doi.org/10.1016/j.cageo.2015.09.015 and Heagy et al., 2017: https://arxiv.org/abs/1610.00804)