cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12595178
title: Perivascular pumping in the mouse brain: Realistic boundary conditions reconcile theory, simulation, and experiment

description: Raw data used to generate the Figure 3 for Ladrón-de-Guevara et al. 2020 PNAS "Perivascular pumping in the mouse brain: Realistic boundary conditions reconcile theory, simulation, and experiment".<br>We measured hydraulic resistance and compliance using bolus injection, an approach introduced by Marmarou et al. (1). We injected fluid briefly and rapidly, measuring the resulting change in intracranial pressure (ICP), to estimate an impulse response, approximating the CSF pathway as a linear RC system. All experiments were approved by the University Committee on Animal Resources of the University of Rochester Medical Center (Protocol No. 2011-023), and an effort was made to minimize the number of animals used. We used 8- to 12-week-old male C57BL/6 mice acquired from Charles River Laboratories (Wilmington, MA, USA). In all experiments, animals were anesthetized with a combination of ketamine (100 mg/kg) and xylazine (10 mg/kg) administered intraperitoneally. Depth of anesthesia was determined by the pedal reflex test. Body temperature was maintained at 37.5C with a rectal probe-controlled heated platform, and ECG and respiratory rate were monitored using a small animal physiological monitoring system (Harvard Apparatus). Anesthetized mice were fixed in a stereotaxic frame, and two cannulae were implanted into the right lateral ventricle (0.85 mm lateral, 2.10 mm ventral and 0.22 mm caudal to bregma) and the cisterna magna, as previously described (2). Using a computer-controlled syringe pump (Harvard Apparatus Pump 11 Elite), we injected V = 5 μL of artificial CSF (126 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 2 mM MgSO4, 2 mM CaCl2, 10 mM glucose, 26 mM NaHCO3; pH 7.4 when gassed with 95% O2 and 5% CO2) at 1 μL/s into the right lateral ventricle. We monitored ICP via the cisterna magna cannulation connected to a transducer attached to a pressure monitor (BP-1, World Precision Instruments Inc., Sarasota, FL). We have verified that the results do not change appreciably if we instead inject into the cisterna magna and measure ICP in the ventricle.We calculated the compliance C from the pressure-volume index (PVI): C = 0.4343·PVI/P0. The PVI is defined as the volume of fluid required to cause a tenfold pressure increase during bolus injection:<pre><code>PVI=V/(log10⁡[P_max/P_0])</code></pre>The resistance R can be estimated as:<pre><code>R=(t·P_0)/(PVI·log10[P(t)·(P_max-P_0 )/(P_max·(P(t)-P_0))]) </code></pre>where P(t) is the pressure measured at time t. We expect R to be nearly constant, but to increase accuracy, we estimate R for each animal by averaging the results of the above equation to five evenly-spaced times during the experiment.<br><br>1. Marmarou A, Shulman K, Rosende RM (1978) A nonlinear analysis of the cerebrospinal fluid system and intracranial pressure dynamics. J Neurosurg 48(3):332–344.<br>2. Xavier AL, et al. (2018) Cannula implantation into the cisterna magna of rodents. JoVE (Journal of Visualized Experiments) (135):e57378.<br>
DOI: 10.6084/m9.figshare.12597084.v6
title: Table S7 from Brain microRNAs among social and solitary bees

description: Final miRNA sets for each species. Descriptions for each sheet and column header are provided in the ‘Metadata’ sheet.
DOI: 10.6084/m9.figshare.12595067
title: Source Data

description: Excel files allowing for the reproduction of figures of the paper
DOI: 10.6084/m9.figshare.12597084.v5
title: Table S8 from Brain microRNAs among social and solitary bees

description: Predicted targets and orthogroup ages of lineage-specific microRNAs in each species. Descriptions for each sheet and column header are provided in the ‘Metadata’ sheet.
DOI: 10.6084/m9.figshare.12595178.v1
title: Perivascular pumping in the mouse brain: Realistic boundary conditions reconcile theory, simulation, and experiment

description: Raw data used to generate the Figure 3 for Ladrón-de-Guevara et al. 2020 PNAS "Perivascular pumping in the mouse brain: Realistic boundary conditions reconcile theory, simulation, and experiment".<br>We measured hydraulic resistance and compliance using bolus injection, an approach introduced by Marmarou et al. (1). We injected fluid briefly and rapidly, measuring the resulting change in intracranial pressure (ICP), to estimate an impulse response, approximating the CSF pathway as a linear RC system. All experiments were approved by the University Committee on Animal Resources of the University of Rochester Medical Center (Protocol No. 2011-023), and an effort was made to minimize the number of animals used. We used 8- to 12-week-old male C57BL/6 mice acquired from Charles River Laboratories (Wilmington, MA, USA). In all experiments, animals were anesthetized with a combination of ketamine (100 mg/kg) and xylazine (10 mg/kg) administered intraperitoneally. Depth of anesthesia was determined by the pedal reflex test. Body temperature was maintained at 37.5C with a rectal probe-controlled heated platform, and ECG and respiratory rate were monitored using a small animal physiological monitoring system (Harvard Apparatus). Anesthetized mice were fixed in a stereotaxic frame, and two cannulae were implanted into the right lateral ventricle (0.85 mm lateral, 2.10 mm ventral and 0.22 mm caudal to bregma) and the cisterna magna, as previously described (2). Using a computer-controlled syringe pump (Harvard Apparatus Pump 11 Elite), we injected V = 5 μL of artificial CSF (126 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 2 mM MgSO4, 2 mM CaCl2, 10 mM glucose, 26 mM NaHCO3; pH 7.4 when gassed with 95% O2 and 5% CO2) at 1 μL/s into the right lateral ventricle. We monitored ICP via the cisterna magna cannulation connected to a transducer attached to a pressure monitor (BP-1, World Precision Instruments Inc., Sarasota, FL). We have verified that the results do not change appreciably if we instead inject into the cisterna magna and measure ICP in the ventricle.We calculated the compliance C from the pressure-volume index (PVI): C = 0.4343·PVI/P0. The PVI is defined as the volume of fluid required to cause a tenfold pressure increase during bolus injection:<pre><code>PVI=V/(log10⁡[P_max/P_0])</code></pre>The resistance R can be estimated as:<pre><code>R=(t·P_0)/(PVI·log10[P(t)·(P_max-P_0 )/(P_max·(P(t)-P_0))]) </code></pre>where P(t) is the pressure measured at time t. We expect R to be nearly constant, but to increase accuracy, we estimate R for each animal by averaging the results of the above equation to five evenly-spaced times during the experiment.<br><br>1. Marmarou A, Shulman K, Rosende RM (1978) A nonlinear analysis of the cerebrospinal fluid system and intracranial pressure dynamics. J Neurosurg 48(3):332–344.<br>2. Xavier AL, et al. (2018) Cannula implantation into the cisterna magna of rodents. JoVE (Journal of Visualized Experiments) (135):e57378.<br>
DOI: 10.6084/m9.figshare.12597082.v5
title: Table S1. from Higher temperatures lower rates of physiological and niche evolution

description: Physiological data for each species.
DOI: 10.6084/m9.figshare.12597079.v5
title: Data File from Sperm velocity in a promiscuous bird across experimental media of different viscosities

description: Data for Sperm velocity in a promiscuous bird across experimental media of different viscosities
DOI: 10.6084/m9.figshare.12595019
title: BCA Bootstrap in MS EXCEL

description: Data were collected through an online survey and processed to create 95% CI using the BCA bootstrap confidence interval algorithm in MS EXCEL. Construction of confidence interval in MS EXCEL using the BCA bootstrap confidence interval algorithm is earlier not presented in any studies. The macro capabilities of MS EXCEL was utilized for the purpose stated.
DOI: 10.6084/m9.figshare.12595067.v1
title: Excel Files

description: Excel files allowing for the reproduction of figures of the paper
DOI: 10.6084/m9.figshare.12597082.v7
title: Table S2. from Higher temperatures lower rates of physiological and niche evolution

description: Climatic data for each species.
DOI: 10.6084/m9.figshare.12594905
title: Figure 4 - CRESS Rep alignment (LINSi Leave Gap)

description: Figure 4 - CRESS Rep alignment (LINSi Leave Gap). <br>Three families.
DOI: 10.6084/m9.figshare.12594806
title: Figure 4 - CRESS Rep Treefile

description: Figure 4 - CRESS Rep Treefile (three families)<br>
DOI: 10.6084/m9.figshare.12594905.v1
title: Figure 4 - CRESS Rep alignment (LINSi Leave Gap)

description: Figure 4 - CRESS Rep alignment (LINSi Leave Gap). <br>Three families.
DOI: 10.6084/m9.figshare.12597079.v7
title: Schmoll Proc B ESM ASReml Code_as.txt from Sperm velocity in a promiscuous bird across experimental media of different viscosities

description: Electronic supplementary Tables and Figures;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 0% cellulose;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 1% cellulose;Representative video recordings of willow warbler Phylloscopus trochilus spermatozoa swimming in 2% cellulose;Data for Sperm velocity in a promiscuous bird across experimental media of different viscosities
DOI: 10.6084/m9.figshare.12594806.v1
title: Figure 4 - CRESS Rep Treefile

description: Figure 4 - CRESS Rep Treefile (three families)<br>
DOI: 10.6084/m9.figshare.12594749
title: Figure 2 - CRESS Rep alignment (LINSi Leave Gap)

description: CRESS Rep alignment (LINSi Leave Gap) - For figure 2
DOI: 10.6084/m9.figshare.12597082.v8
title: Datafile S3: from Higher temperatures lower rates of physiological and niche evolution

description: Phylogeny used for birds
DOI: 10.6084/m9.figshare.12594749.v1
title: Figure 2 - CRESS Rep alignment (LINSi Leave Gap)

description: CRESS Rep alignment (LINSi Leave Gap) - For figure 2
DOI: 10.6084/m9.figshare.12594680
title: Figure 2 - CRESS Rep Treefile

description: CRESS Rep Treefile (figure 2)<br>Open using a tree visualizsation programme, for example FigTree.
DOI: 10.6084/m9.figshare.12594680.v1
title: Figure 2 - CRESS Rep Treefile

description: CRESS Rep Treefile (figure 2)<br>Open using a tree visualizsation programme, for example FigTree.
DOI: 10.6084/m9.figshare.12594638
title: Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

description: The archive contains the simulated data used in Barba-Montoya et al. 2020. Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated. <i>Bioinformatics.</i>
DOI: 10.6084/m9.figshare.12597082.v10
title: Datafile S2: from Higher temperatures lower rates of physiological and niche evolution

description: Phylogeny used for squamates
DOI: 10.6084/m9.figshare.12597082.v11
title: Datafile S7: from Higher temperatures lower rates of physiological and niche evolution

description: Alternative phylogeny used for birds
DOI: 10.6084/m9.figshare.12597082.v12
title: Datafile S8: from Higher temperatures lower rates of physiological and niche evolution

description: Alternative phylogeny used for mammals
DOI: 10.6084/m9.figshare.12597082.v13
title: Datafile S5: from Higher temperatures lower rates of physiological and niche evolution

description: Alternative phylogeny used for amphibians
DOI: 10.6084/m9.figshare.12597082.v15
title: Datafile S6: from Higher temperatures lower rates of physiological and niche evolution

description: Alternative phylogeny used for squamates
DOI: 10.6084/m9.figshare.12597082.v14
title: Table S5. from Higher temperatures lower rates of physiological and niche evolution

description: Physiological and climatic data for matched localities
DOI: 10.6084/m9.figshare.12594464
title: Supplementary Material for: Circulatory CD4-Positive T-Lymphocyte Imbalance Mediated by Homocysteine-Induced AIM2 and NLRP1 Inflammasome Upregulation and Activation Is Associated with Human Abdominal Aortic Aneurysm

description: <b><i>Introduction:</i></b> CD4-positive T lymphocytes (CD4 cells) play a significant role in human abdominal aortic aneurysm (AAA). However, we know little about the role of the different CD4 subtypes. <b><i>Objective:</i></b> We aimed to discover the circulatory CD4 phenotypic marker profile and the roles of the newly found T helper cell 9 (Th9) and follicular helper T cells (Tfh) and that of inflammasomes in CD4 cells from AAA patients. <b><i>Methods:</i></b> We extracted CD4 cells from 30 AAA patients and 21 age-matched controls. Phenotype-specific transcription factors (TFs) and inflammasomes were analyzed with qRT-PCR. <b><i>Results:</i></b> Th17-, Th1-, Th9-, and Tfh-specific TFs and inflammasome components <i>NLRP1</i> (NLR family pyrin domain-containing 1), <i>NLRP3</i>, <i>NLRC4</i>, <i>AIM2</i> (absent in melanoma 2), <i>PYCARD</i> (apoptosis speck-like protein containing a CARD), and <i>CASP1</i> (caspase 1) were upregulated, and T regulatory cell- and Th2-specific TFs were downregulated in the patients’ peripheral blood CD4 cells. Homocysteine was involved in Tfh and Th17 imbalance by <i>AIM2</i> and <i>NLRP1</i> inflammasome upregulation. Blood total cholesterol level correlated positively with <i>NLRP1</i> expression, and blood low-density lipoprotein level correlated negatively with <i>FOXP3</i> expression. <b><i>Conclusions:</i></b> Inflammasome-induced CD4 cell imbalance was involved in AAA. We thought that AAA might be a consequence of synergism between systemic immune imbalance and local autoimmunity.
DOI: 10.6084/m9.figshare.12594449
title: Supplementary Material for: Sub-Staging-Specific Differences in Recurrence-Free, Progression-Free, and Cancer-Specific Survival for Patients with T1 Bladder Cancer: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> The efficiency of the T1 sub-staging system on categorizing bladder cancer (BC) patients into subgroups with different clinical outcomes was unclear. We summarized relevant evidences, including recurrence-free survival (RFS), progression-free survival (PFS), and cancer-specific survival (CSS), to analyze the prognostic significance of T1 sub-stage. <b><i>Methods:</i></b> Systematic literature searches of MEDLINE, EMBASE, and the Cochrane Library were performed. We pooled data on recurrence, progression, and CSS from 35 studies. <b><i>Results:</i></b> The pooled hazard ratios (HRs) and 95% confidence intervals (CIs) indicated the difference in RFS between T1a sub-stage and T1b sub-stage (HR 1.28, 95% CI 1.14–1.43, <i>p</i> &lt; 0.001). The significant difference was observed in PFS between the 2 arms (HR 2.18, 95% CI 1.95–2.44, <i>p</i> &lt; 0.001). Worse CSS was found in T1b patients than in T1a patients (HR 1.36, 95% CI 1.21–1.54, <i>p</i> &lt; 0.001). <b><i>Conclusions:</i></b> T1 sub-staging system based on the invasion depth into muscularis mucosae can be a significant prognostic factor for RFS, PFS, and CSS of patients with T1 BC. Urologists and pathologists are encouraged to work together to give a precise sub-stage classification of T1 BC, and T1 sub-staging system should be a routine part of any histopathological report when possible. Different treatment strategies need to be developed for both T1a BC and T1b BC.
DOI: 10.6084/m9.figshare.12594470
title: Metadata record for: A high-content image-based drug screen of clinical compounds against cell transmission of adenovirus

description: This dataset contains key characteristics about the data described in the Data Descriptor A high-content image-based drug screen of clinical compounds against cell transmission of adenovirus. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12594455
title: Frequency of "reversion" and "atavism"

description: The brief analysis here plots the relative appearance of the terms "reversion" and "atavism" in the journals <i>Nature</i> and <i>Proceedings of the Royal Society B: Biological Sciences.</i> In the paper, only the "strict" dataset was used, and only to make the rough claim that the rate of appearance of these two terms between 1870 and 1910 was roughly 1.5%, and after 1910 was roughly 0.5%.<br>
DOI: 10.6084/m9.figshare.12594464.v1
title: Supplementary Material for: Circulatory CD4-Positive T-Lymphocyte Imbalance Mediated by Homocysteine-Induced AIM2 and NLRP1 Inflammasome Upregulation and Activation Is Associated with Human Abdominal Aortic Aneurysm

description: <b><i>Introduction:</i></b> CD4-positive T lymphocytes (CD4 cells) play a significant role in human abdominal aortic aneurysm (AAA). However, we know little about the role of the different CD4 subtypes. <b><i>Objective:</i></b> We aimed to discover the circulatory CD4 phenotypic marker profile and the roles of the newly found T helper cell 9 (Th9) and follicular helper T cells (Tfh) and that of inflammasomes in CD4 cells from AAA patients. <b><i>Methods:</i></b> We extracted CD4 cells from 30 AAA patients and 21 age-matched controls. Phenotype-specific transcription factors (TFs) and inflammasomes were analyzed with qRT-PCR. <b><i>Results:</i></b> Th17-, Th1-, Th9-, and Tfh-specific TFs and inflammasome components <i>NLRP1</i> (NLR family pyrin domain-containing 1), <i>NLRP3</i>, <i>NLRC4</i>, <i>AIM2</i> (absent in melanoma 2), <i>PYCARD</i> (apoptosis speck-like protein containing a CARD), and <i>CASP1</i> (caspase 1) were upregulated, and T regulatory cell- and Th2-specific TFs were downregulated in the patients’ peripheral blood CD4 cells. Homocysteine was involved in Tfh and Th17 imbalance by <i>AIM2</i> and <i>NLRP1</i> inflammasome upregulation. Blood total cholesterol level correlated positively with <i>NLRP1</i> expression, and blood low-density lipoprotein level correlated negatively with <i>FOXP3</i> expression. <b><i>Conclusions:</i></b> Inflammasome-induced CD4 cell imbalance was involved in AAA. We thought that AAA might be a consequence of synergism between systemic immune imbalance and local autoimmunity.
DOI: 10.6084/m9.figshare.12594470.v1
title: Metadata record for: A high-content image-based drug screen of clinical compounds against cell transmission of adenovirus

description: This dataset contains key characteristics about the data described in the Data Descriptor A high-content image-based drug screen of clinical compounds against cell transmission of adenovirus. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12594449.v1
title: Supplementary Material for: Sub-Staging-Specific Differences in Recurrence-Free, Progression-Free, and Cancer-Specific Survival for Patients with T1 Bladder Cancer: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> The efficiency of the T1 sub-staging system on categorizing bladder cancer (BC) patients into subgroups with different clinical outcomes was unclear. We summarized relevant evidences, including recurrence-free survival (RFS), progression-free survival (PFS), and cancer-specific survival (CSS), to analyze the prognostic significance of T1 sub-stage. <b><i>Methods:</i></b> Systematic literature searches of MEDLINE, EMBASE, and the Cochrane Library were performed. We pooled data on recurrence, progression, and CSS from 35 studies. <b><i>Results:</i></b> The pooled hazard ratios (HRs) and 95% confidence intervals (CIs) indicated the difference in RFS between T1a sub-stage and T1b sub-stage (HR 1.28, 95% CI 1.14–1.43, <i>p</i> &lt; 0.001). The significant difference was observed in PFS between the 2 arms (HR 2.18, 95% CI 1.95–2.44, <i>p</i> &lt; 0.001). Worse CSS was found in T1b patients than in T1a patients (HR 1.36, 95% CI 1.21–1.54, <i>p</i> &lt; 0.001). <b><i>Conclusions:</i></b> T1 sub-staging system based on the invasion depth into muscularis mucosae can be a significant prognostic factor for RFS, PFS, and CSS of patients with T1 BC. Urologists and pathologists are encouraged to work together to give a precise sub-stage classification of T1 BC, and T1 sub-staging system should be a routine part of any histopathological report when possible. Different treatment strategies need to be developed for both T1a BC and T1b BC.
DOI: 10.6084/m9.figshare.12594455.v1
title: Frequency of "reversion" and "atavism"

description: The brief analysis here plots the relative appearance of the terms "reversion" and "atavism" in the journals <i>Nature</i> and <i>Proceedings of the Royal Society B: Biological Sciences.</i> In the paper, only the "strict" dataset was used, and only to make the rough claim that the rate of appearance of these two terms between 1870 and 1910 was roughly 1.5%, and after 1910 was roughly 0.5%.<br>
DOI: 10.6084/m9.figshare.12594377
title: SHS and preterm birth

description: SHS and preterm
DOI: 10.6084/m9.figshare.12594239
title: Supplementary Material for: Semaphorin-3C Is Upregulated in Polycystic Kidney Epithelial Cells and Inhibits Angiogenesis of Glomerular Endothelial Cells

description: <b><i>Background:</i></b> Polycystic kidney disease (PKD) is a hereditary disease characterized by cyst formation in the kidneys bilaterally. It has been observed that semaphorin-3C (SEMA3C) is overexpressed in polycystic kidney epithelial cells. It is hypothesized that upregulated SEMA3C would contribute to survival of polycystic kidney epithelial cells. Furthermore, as the kidney is a highly vascularized organ, the secreted SEMA3C from PKD epithelial cells will affect glomerular endothelial cells (GECs) in a paracrine manner. <b><i>Methods:</i></b> To evaluate the effect of SEMA3C on renal cells, siSEMA3C-treated PKD epithelial cells were used for further analysis, and GECs were exposed to recombinant SEMA3C (rSEMA3C). Also, co-culture and treatment of conditioned media were employed to confirm whether PKD epithelial cells could influence on GECs via SEMA3C secretion. <b><i>Results:</i></b> SEMA3C knockdown reduced proliferation of PKD epithelial cells. In case of GECs, exposure to rSEMA3C decreased angiogenesis, which resulted from suppressed migratory ability not cell proliferation. <b><i>Conclusions:</i></b> This study indicates that SEMA3C is the aggravating factor in PKD. Thus, it is proposed that targeting SEMA3C can be effective to mitigate PKD.