cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5353708
title: Supplementary Information from Designing the optimal bit: balancing energetic cost, speed and reliability

description: We consider the challenge of operating a reliable bit that can be rapidly erased. We find that both erasing and reliability times are non-monotonic in the underlying friction, leading to a trade-off between erasing speed and bit reliability. Fast erasure is possible at the expense of low reliability at moderate friction, and high reliability comes at the expense of slow erasure in the underdamped and overdamped limits. Within a given class of bit parameters and control strategies, we define ‘optimal’ designs of bits that meet the desired reliability and erasing time requirements with the lowest operational work cost. We find that optimal designs always saturate the bound on the erasing time requirement, but can exceed the required reliability time if critically damped. The non-trivial geometry of the reliability and erasing time-scales allows us to exclude large regions of parameter space as suboptimal. We find that optimal designs are either critically damped or close to critical damping under the erasing procedure.
DOI: 10.6084/m9.figshare.5353711
title: PRSA20170295_files Files pertaining to the data sets

description: Data files pertaining to the analysis of the ADV dataset
DOI: 10.6084/m9.figshare.5353705
title: Dataset for: EGF Regulation of Proximal Tubule Cell Proliferation and VEGF-A Secretion

description: Proximal tubule cell (PTC) proliferation is critical for tubular regeneration and recovery from acute kidney injury. Epidermal growth factor (EGF) and vascular endothelial growth factor (VEGF-A) are important for the maintenance of tubulointerstitial integrity and can stimulate PTC proliferation. We utilized HK-2 cells, an immortalized human PTC line, to characterize the EGF-dependent regulation of VEGF-A secretion and proliferation in PTCs. We demonstrate that EGF stimulates VEGF-A secretion via the EGF receptor (EGFR) and stimulates cell proliferation via activation of the VEGF receptor, VEGFR-2. EGFR activation promotes MAPK (ERK1/2) activation and HIF-1α expression, which are required for basal and EGF-stimulated VEGF-A secretion. EGF also stimulates the phosphorylation of P70S6 kinase (p70S6K), the downstream target of mTORC1. Rapamycin decreased basal and EGF stimulated HIF-1α and enhanced MAPK (ERK1/2) activation, while MAPK (ERK/12) inhibition downregulated HIF-1α expression and the phosphorylation of p70S6K. EGF stimulation of p70S6K was also independent of p-AKT. Inhibition of the mTORC1 pathway with rapamycin abolished phosphorylation of p70S6K but had no effect on VEGF-A secretion, indicating that EGF-stimulated VEGF-A secretion did not require mTORC1 pathway activation. We demonstrate evidence of a complex crosstalk between the MAPK/ERK and mTORC1 pathways, wherein MAPK (ERK1/2) activation stimulates p-P70S6K, while p-P70S6K activation seems to inhibit MAPK (ERK1/2) in EGF-treated HK-2 cells. Our results suggest that EGF stimulates MAPK (ERK1/2) in HK-2 cells, which in turn increases HIF-1α expression and VEGF-A secretion, indicating that VEGF-A mediates EGF-stimulated cell proliferation as an autocrine proximal tubular epithelial cell growth factor.
DOI: 10.6084/m9.figshare.5353711.v1
title: PRSA20170295_files Files pertaining to the data sets

description: Data files pertaining to the analysis of the ADV dataset
DOI: 10.6084/m9.figshare.5353726.v1
title: Shock induced collapse of a bubble attached to aluminium with separation distance = 0.95 from Numerical studies of cavitation erosion on an elastic–plastic material caused by shock-induced bubble collapse

description: A clip showing the simulation result of a shock-induced collapse of a 40-micron bubble attached to an aluminium wall with separation distance of 0.95. The peak pressure of the lithotripter-type shock is 60MPa.
DOI: 10.6084/m9.figshare.5353702
title: Dataset for: Pregnancy-Adapted Uterine Artery Endothelial Cell Ca2+ Signaling and Its Relationship with Membrane Potential

description: Pregnancy-derived uterine artery endothelial cells (P-UAEC) express P2Y2 receptors and at high cell density show sustained and synchronous [Ca2+]i burst responses in response to ATP. Bursts in turn require coupling of transient receptor potential canonical type3 channel (TRPC3) and inositol 1,4,5-triphosphate receptor type 2 (IP3R2), which is upregulated in P-UAEC in a manner dependent on connexin 43 (Cx43) gap junctions. While there is no known direct interaction of TRPC3 with Cx43, early descriptions of TRPC3 function showed it may also be influenced by altered membrane potential (Vm). Herein we ask if enhanced TRPC3 Ca2+ bursting due to enhanced Cx43 coupling may be coupled via dynamic alterations in Vm in P-UAEC, as reported in some (HUVEC) but not all endothelial cells. Following basic electrical characterization of UAEC we employed a high sensitivity cell imaging system to simultaneously monitor cell Vm and [Ca2+]i in real time in continuous monolayers of UAEC. Our findings show that while acute and sustained phase [Ca2+]i bursting occur dose dependently in response to ATP, Vm is not co-regulated with any periodicity related to [Ca2+]i bursting. Only a small but significant progressive change in Vm is seen, and this is more closely related to overall mobilization of Ca2+. Surprisingly, this is also most apparent in NP-UAEC &gt; P-UAEC. In contrast [Ca2+]i bursting is more synchronous in P-UAEC and even achieves [Ca2+]i waves passing through the P-UAEC monolayer. The relevance of these findings to mechanisms of pregnancy adaptation and its failure in hypertensive pregnancy are discussed.
DOI: 10.6084/m9.figshare.5353705.v1
title: Dataset for: EGF Regulation of Proximal Tubule Cell Proliferation and VEGF-A Secretion

description: Proximal tubule cell (PTC) proliferation is critical for tubular regeneration and recovery from acute kidney injury. Epidermal growth factor (EGF) and vascular endothelial growth factor (VEGF-A) are important for the maintenance of tubulointerstitial integrity and can stimulate PTC proliferation. We utilized HK-2 cells, an immortalized human PTC line, to characterize the EGF-dependent regulation of VEGF-A secretion and proliferation in PTCs. We demonstrate that EGF stimulates VEGF-A secretion via the EGF receptor (EGFR) and stimulates cell proliferation via activation of the VEGF receptor, VEGFR-2. EGFR activation promotes MAPK (ERK1/2) activation and HIF-1α expression, which are required for basal and EGF-stimulated VEGF-A secretion. EGF also stimulates the phosphorylation of P70S6 kinase (p70S6K), the downstream target of mTORC1. Rapamycin decreased basal and EGF stimulated HIF-1α and enhanced MAPK (ERK1/2) activation, while MAPK (ERK/12) inhibition downregulated HIF-1α expression and the phosphorylation of p70S6K. EGF stimulation of p70S6K was also independent of p-AKT. Inhibition of the mTORC1 pathway with rapamycin abolished phosphorylation of p70S6K but had no effect on VEGF-A secretion, indicating that EGF-stimulated VEGF-A secretion did not require mTORC1 pathway activation. We demonstrate evidence of a complex crosstalk between the MAPK/ERK and mTORC1 pathways, wherein MAPK (ERK1/2) activation stimulates p-P70S6K, while p-P70S6K activation seems to inhibit MAPK (ERK1/2) in EGF-treated HK-2 cells. Our results suggest that EGF stimulates MAPK (ERK1/2) in HK-2 cells, which in turn increases HIF-1α expression and VEGF-A secretion, indicating that VEGF-A mediates EGF-stimulated cell proliferation as an autocrine proximal tubular epithelial cell growth factor.
DOI: 10.6084/m9.figshare.5353708.v1
title: Supplementary Information from Designing the optimal bit: balancing energetic cost, speed and reliability

description: We consider the challenge of operating a reliable bit that can be rapidly erased. We find that both erasing and reliability times are non-monotonic in the underlying friction, leading to a trade-off between erasing speed and bit reliability. Fast erasure is possible at the expense of low reliability at moderate friction, and high reliability comes at the expense of slow erasure in the underdamped and overdamped limits. Within a given class of bit parameters and control strategies, we define ‘optimal’ designs of bits that meet the desired reliability and erasing time requirements with the lowest operational work cost. We find that optimal designs always saturate the bound on the erasing time requirement, but can exceed the required reliability time if critically damped. The non-trivial geometry of the reliability and erasing time-scales allows us to exclude large regions of parameter space as suboptimal. We find that optimal designs are either critically damped or close to critical damping under the erasing procedure.
DOI: 10.6084/m9.figshare.5353702.v1
title: Dataset for: Pregnancy-Adapted Uterine Artery Endothelial Cell Ca2+ Signaling and Its Relationship with Membrane Potential

description: Pregnancy-derived uterine artery endothelial cells (P-UAEC) express P2Y2 receptors and at high cell density show sustained and synchronous [Ca2+]i burst responses in response to ATP. Bursts in turn require coupling of transient receptor potential canonical type3 channel (TRPC3) and inositol 1,4,5-triphosphate receptor type 2 (IP3R2), which is upregulated in P-UAEC in a manner dependent on connexin 43 (Cx43) gap junctions. While there is no known direct interaction of TRPC3 with Cx43, early descriptions of TRPC3 function showed it may also be influenced by altered membrane potential (Vm). Herein we ask if enhanced TRPC3 Ca2+ bursting due to enhanced Cx43 coupling may be coupled via dynamic alterations in Vm in P-UAEC, as reported in some (HUVEC) but not all endothelial cells. Following basic electrical characterization of UAEC we employed a high sensitivity cell imaging system to simultaneously monitor cell Vm and [Ca2+]i in real time in continuous monolayers of UAEC. Our findings show that while acute and sustained phase [Ca2+]i bursting occur dose dependently in response to ATP, Vm is not co-regulated with any periodicity related to [Ca2+]i bursting. Only a small but significant progressive change in Vm is seen, and this is more closely related to overall mobilization of Ca2+. Surprisingly, this is also most apparent in NP-UAEC &gt; P-UAEC. In contrast [Ca2+]i bursting is more synchronous in P-UAEC and even achieves [Ca2+]i waves passing through the P-UAEC monolayer. The relevance of these findings to mechanisms of pregnancy adaptation and its failure in hypertensive pregnancy are discussed.
DOI: 10.6084/m9.figshare.5353738.v2
title: Ultra-early apparent diffusion coefficient change indicates irradiation and predicts radiotherapy outcome in brain metastases

description: Ultra-early apparent diffusion coefficient change indicates irradiation and predicts radiotherapy outcome in brain metastases
DOI: 10.6084/m9.figshare.5353738.v4
title: Ultra-early apparent diffusion coefficient change indicates irradiation and predicts radiotherapy outcome in brain metastases

description: Ultra-early apparent diffusion coefficient change indicates irradiation and predicts radiotherapy outcome in brain metastases
DOI: 10.6084/m9.figshare.5353738.v3
title: Ultra-early apparent diffusion coefficient change indicates irradiation and predicts radiotherapy outcome in brain metastases

description: Ultra-early apparent diffusion coefficient change indicates irradiation and predicts radiotherapy outcome in brain metastases
DOI: 10.6084/m9.figshare.5353639
title: Dataset for: The transcription factor ATF7 mediates in vitro fertilization-induced gene expression changes in mouse liver

description: Assisted reproductive technologies, including in vitro fertilization (IVF), are now frequently used, and increasing evidence indicates that IVF causes gene expression changes in children and adolescents that increase the risk of metabolic diseases. Although such gene expression changes are thought to be due to IVF-induced epigenetic changes, the mechanism remains elusive. We tested whether the transcription factor ATF7, – which mediates stress-induced changes in histone H3K9 tri- and di-methylation, typical marks of epigenetic silencing – is involved in the IVF-induced gene expression changes. IVF up- and down-regulated the expression of 688 and 204 genes, respectively, in the liver of 3-week-old wild-type (WT) mice, whereas 87% and 68% of these were not changed, respectively, by IVF in ATF7-deficient (Atf7<sup>—/—</sup>) mice. The genes, which are involved in metabolism, such as pyrimidine and purine metabolism, were up-regulated in WT mice but not in Atf7<sup>—/—</sup> mice. Of the genes whose expression was up-regulated by IVF in WT mice, 37% were also up-regulated by a loss of ATF7. These results indicate that ATF7 is a key factor in establishing the memory of IVF effects on metabolic pathways.
DOI: 10.6084/m9.figshare.5353630
title: Dataset 1: Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam

description: <b>Respiratory Viral Diagnostic Result from 442 patient swabs of the Luminex and reference assays.</b><b><br></b>- Site: Abbreviation of provinces where hospitals involved in the study, where patients were recruited. (DlK: Daklak, DT: Dong Thap, H: Hue, and KH: Khanh Hoa) - Gender: patient sex, 1: Male, 2: Female - DateCollection: Date when patient samples were collected - Flu A type (CDC): Results of influenza A and types from the reference assay: CDC Realtime RTPCR assay - Flu B (CDC): Results of influenza B from the reference assay: CDC Realtime RTPCR assay - RSV type: Results of RSV A and RSV B from in-house reference PCR assay - detected by 4tube multiplexPCR: Results of other 10 viruses from reference assay: in-house 4-tube multiplex PCR - Luminex result: Results from Luminex assay - Diagnose: Final diagnosis based on Luminex and reference assays, it was defined “pos” if sample was positive with any of reference assays or Luminex assay, "undiagnosed” if sample was negative with all reference assays and the Luminex assay
DOI: 10.6084/m9.figshare.5353627
title: Muscle co-contraction and postural sway during altered proprioceptive conditions

description: This dataset is associated with a project examining changes in postural sway and muscle co-contraction in young and older adults when exposed to altered proprioceptive information.<br>The 'contraction_data' file contains the mean co-contraction index (CCI) values for each 30s window during three postural phases; a stable baseline phase (120s), a sway-referenced adaptation phase (180s) and a stable reintegration phase (180s). CCI values were calculated between the tibialis anterior and gastrocnemius medialis in both legs. The data for the left (sheet 1), right (sheet 2) and averaged legs (sheet 3) are presented in the dataset.<br>The 'pathlength_data' file contains the mean anterior-posterior path length data from the waist marker for each 30s time window of the same three postural phases in both young and older adults.
DOI: 10.6084/m9.figshare.5353639.v1
title: Dataset for: The transcription factor ATF7 mediates in vitro fertilization-induced gene expression changes in mouse liver

description: Assisted reproductive technologies, including in vitro fertilization (IVF), are now frequently used, and increasing evidence indicates that IVF causes gene expression changes in children and adolescents that increase the risk of metabolic diseases. Although such gene expression changes are thought to be due to IVF-induced epigenetic changes, the mechanism remains elusive. We tested whether the transcription factor ATF7, – which mediates stress-induced changes in histone H3K9 tri- and di-methylation, typical marks of epigenetic silencing – is involved in the IVF-induced gene expression changes. IVF up- and down-regulated the expression of 688 and 204 genes, respectively, in the liver of 3-week-old wild-type (WT) mice, whereas 87% and 68% of these were not changed, respectively, by IVF in ATF7-deficient (Atf7<sup>—/—</sup>) mice. The genes, which are involved in metabolism, such as pyrimidine and purine metabolism, were up-regulated in WT mice but not in Atf7<sup>—/—</sup> mice. Of the genes whose expression was up-regulated by IVF in WT mice, 37% were also up-regulated by a loss of ATF7. These results indicate that ATF7 is a key factor in establishing the memory of IVF effects on metabolic pathways.
DOI: 10.6084/m9.figshare.5353615
title: Mathematica Notebook for 4 dimensional Schrödinger evolution from Quantum-like dynamics applied to cognition: a consideration of available options

description: This notebook provides the necessary Mathematica code to render the time-dependent outcome probabilities for the 4 dimensional problem with Schrödinger evolution.
DOI: 10.6084/m9.figshare.5353615.v1
title: Mathematica Notebook for 4 dimensional Schrödinger evolution from Quantum-like dynamics applied to cognition: a consideration of available options

description: This notebook provides the necessary Mathematica code to render the time-dependent outcome probabilities for the 4 dimensional problem with Schrödinger evolution.
DOI: 10.6084/m9.figshare.5353630.v1
title: Dataset 1: Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam

description: <b>Respiratory Viral Diagnostic Result from 442 patient swabs of the Luminex and reference assays.</b><b><br></b>- Site: Abbreviation of provinces where hospitals involved in the study, where patients were recruited. (DlK: Daklak, DT: Dong Thap, H: Hue, and KH: Khanh Hoa) - Gender: patient sex, 1: Male, 2: Female - DateCollection: Date when patient samples were collected - Flu A type (CDC): Results of influenza A and types from the reference assay: CDC Realtime RTPCR assay - Flu B (CDC): Results of influenza B from the reference assay: CDC Realtime RTPCR assay - RSV type: Results of RSV A and RSV B from in-house reference PCR assay - detected by 4tube multiplexPCR: Results of other 10 viruses from reference assay: in-house 4-tube multiplex PCR - Luminex result: Results from Luminex assay - Diagnose: Final diagnosis based on Luminex and reference assays, it was defined “pos” if sample was positive with any of reference assays or Luminex assay, "undiagnosed” if sample was negative with all reference assays and the Luminex assay
DOI: 10.6084/m9.figshare.5353612
title: Datasets from Breeding decisions and output are correlated with both temperature and rainfall in an arid-region passerine, the sociable weaver

description: Datasets for all analyses in Mares et al. Breeding decisions in sociable weavers
DOI: 10.6084/m9.figshare.5353612.v1
title: Datasets from Breeding decisions and output are correlated with both temperature and rainfall in an arid-region passerine, the sociable weaver

description: Datasets for all analyses in Mares et al. Breeding decisions in sociable weavers
DOI: 10.6084/m9.figshare.5353603
title: Supplementary Data - Fatigue from Rate-based structural health monitoring using permanently installed sensors

description: Raw fatigue data summarised in Table 2.
DOI: 10.6084/m9.figshare.5353594
title: Empirical data for biotic indicators from Using multiple lines of evidence to assess the risk of ecosystem collapse

description: Empirical validation data for benthic and consumer groups
DOI: 10.6084/m9.figshare.5353600
title: Mathematica Notebook for 2 dimensional Schrödinger evolution from Quantum-like dynamics applied to cognition: a consideration of available options

description: This notebook provides the necessary Mathematica code to render the time-dependent outcome probabilities for the 2 dimensional problem with Schrödinger evolution.
DOI: 10.6084/m9.figshare.5353627.v1
title: CCD_co-contraction_data.xlsx

description: This dataset contains the mean co-contraction index (CCI) values for each 30s window during three postural phases; a stable baseline phase (120s), a sway-referenced adaptation phase (180s) and a stable reintegration phase (180s). CCI values were calculated between the tibialis anterior and gastrocnemius medialis in both legs. The data for the left (sheet 1), right (sheet 2) and averaged legs (sheet 3) are presented in the dataset.
DOI: 10.6084/m9.figshare.5353600.v1
title: Mathematica Notebook for 2 dimensional Schrödinger evolution from Quantum-like dynamics applied to cognition: a consideration of available options

description: This notebook provides the necessary Mathematica code to render the time-dependent outcome probabilities for the 2 dimensional problem with Schrödinger evolution.
DOI: 10.6084/m9.figshare.5353594.v1
title: Empirical data for biotic indicators from Using multiple lines of evidence to assess the risk of ecosystem collapse

description: Empirical validation data for benthic and consumer groups
DOI: 10.6084/m9.figshare.5353603.v1
title: Supplementary Data - Fatigue from Rate-based structural health monitoring using permanently installed sensors

description: Raw fatigue data summarised in Table 2.
DOI: 10.6084/m9.figshare.5353573
title: Dataset for: Complex restitution behavior and reentry in a cardiac tissue model for neonatal mice

description: Spatio-temporal dynamics in cardiac tissue emerging from the coupling of individual cardiomyocytes underlie the heart’s normal rhythm as well as undesired and possibly life-threatening arrhythmias. While single cells and their transmembrane currents have been studied extensively, systematically investigating spatio-temporal dynamics is complicated by the non-trivial relationship between single-cell and emergent tissue properties. Mathematical models have been employed to bridge this gap and contribute to a deepened understanding of the onset, development and termination of arrhythmias. However, no such tissue-level model currently exists for neonatal mice. Here, we build on a recent single-cell model of neonatal mouse cardiomyocytes by Wang & Sobie (40) to predict properties that are commonly used to gauge arrhythmogenicity of cardiac substrates. We modify the model to yield well-defined behavior for common experimental protocols and construct a spatially extended version to study emergent tissue dynamics. We find a complex action potential duration (APD) restitution behavior characterized by a non-monotonic dependence on pacing frequency. Electrotonic coupling in tissue leads not only to changes in action potential morphology but can also induce spatially concordant and discordant alternans not observed in the single-cell model. In two-dimensional tissue, our results show that the model supports stable functional reentry, whose frequency is in good agreement with that observed in adult mice. Our results can be used to further constrain and validate the mathematical model of neonatal mouse cardiomyocytes with future experiments.