cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7284/136358
title: Radiometer data collected during research cruise TN373 using a Eppley RAD instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136365
title: Singlebeam Echosounder data collected during research cruise TN373 using a Knudsen 3260 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.6963338
title: Additional file 4: of Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean

description: CheckM analysis of the genomes sequenced in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6963338.v1
title: Additional file 4: of Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean

description: CheckM analysis of the genomes sequenced in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6963332
title: Additional file 3: of Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean

description: Ks analysis on 100 CDS presenting characteristics unique to CBB agents. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.6963332.v1
title: Additional file 3: of Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean

description: Ks analysis on 100 CDS presenting characteristics unique to CBB agents. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.6963323
title: Additional file 2: of Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean

description: OrthoMCL matrix. (XLSX 10182 kb)
DOI: 10.6084/m9.figshare.6963323.v1
title: Additional file 2: of Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean

description: OrthoMCL matrix. (XLSX 10182 kb)
DOI: 10.6084/m9.figshare.6962948
title: Whipple Data Deidentified.xlsx

description: Single institution data about implementing a clinical care pathway for post-operative care after pancreaticoduodenectomy
DOI: 10.6084/m9.figshare.6962933
title: Dataset for: Traits of criticality in membrane potential fluctuations of pyramidal neurons in the CA1 region of rat hippocampus.

description: Evidence that neural circuits are operating near criticality has been provided at various levels of brain organization with a presumed role in maximizing information processing and multiscale activity association. Criticality has been linked to excitation at both the single cell and network levels, as action potential generation marks an obvious phase transition from a resting to an excitable state. Using in vitro intracellular recordings, we examine irregular, small amplitude membrane potential fluctuations from CA1 pyramidal neurons of Wistar male rats. We show that these fluctuations, confounded with noise, carry information relevant to the neuronal state. The underlying dynamics exhibit intermittent characteristics shown to describe the temporal fluctuations of the order parameter of a macroscopic system at its critical point even in the absence of firing. An externally applied stimulus serves as the control parameter, driving the system in and out of its critical state. Based on our experimental observations we calculate the equivalent of the isothermal critical exponent δ<sub>h</sub> finding a value which depends on the applied stimulus. For each neuron there is a stimulus amplitude for which the critical behavior becomes most pronounced. The corresponding mean value of δ<sub>h</sub> in the considered ensemble of neurons is δ<sub>h</sub> ≈ 1.89, close to theoretical predictions for critical networks. Finally, we show that the firing rate of a neuron decreases exponentially with δ<sub>h</sub>.
DOI: 10.6084/m9.figshare.6962933.v1
title: Dataset for: Traits of criticality in membrane potential fluctuations of pyramidal neurons in the CA1 region of rat hippocampus.

description: Evidence that neural circuits are operating near criticality has been provided at various levels of brain organization with a presumed role in maximizing information processing and multiscale activity association. Criticality has been linked to excitation at both the single cell and network levels, as action potential generation marks an obvious phase transition from a resting to an excitable state. Using in vitro intracellular recordings, we examine irregular, small amplitude membrane potential fluctuations from CA1 pyramidal neurons of Wistar male rats. We show that these fluctuations, confounded with noise, carry information relevant to the neuronal state. The underlying dynamics exhibit intermittent characteristics shown to describe the temporal fluctuations of the order parameter of a macroscopic system at its critical point even in the absence of firing. An externally applied stimulus serves as the control parameter, driving the system in and out of its critical state. Based on our experimental observations we calculate the equivalent of the isothermal critical exponent δ<sub>h</sub> finding a value which depends on the applied stimulus. For each neuron there is a stimulus amplitude for which the critical behavior becomes most pronounced. The corresponding mean value of δ<sub>h</sub> in the considered ensemble of neurons is δ<sub>h</sub> ≈ 1.89, close to theoretical predictions for critical networks. Finally, we show that the firing rate of a neuron decreases exponentially with δ<sub>h</sub>.
DOI: 10.6084/m9.figshare.6962867
title: First Draft genome for Pagrus major

description: The red sea bream (<i>Pagrus major</i>) belongs to the family of <i>Sparidea</i>, which includes 35 genera, 132 species and 10 subspecies. <i>Pagrus major</i> genome size was estimated as ~806 Mb using the <i>k-mer</i> method from 190.3 Gb of raw short read sequences, which were generated from Illumina sequencer . Furthermore, 73 Gb of long read sequences which were generated from PacBio sequencing method were assemble into 1657 contigs with the total size of 829.3 Mb with N50 &gt; 2.8 MB.
DOI: 10.6084/m9.figshare.6962816
title: CT data accompanying the paper "Ornithopod diversity in the Griman Creek Formation (Cenomanian), New South Wales, Australia." Part 2 of 3

description: Part 2 of 3. Part 2 includes micro CT data of the anterior half of the holotype dentary of the small ornithopod, <i>Weewarrasaurus pobeni</i> (LRF3067) from the Griman Creek Formation (Cretaceous) of New South Wales, Australia..
DOI: 10.6084/m9.figshare.6962621
title: Oil-Segmented-Water

description: Segmented water phase for image: Oil-Filtered Segmentation performed using Watershed segmentation in Avizo. Image Dimension: 1024×1024×845 Image Type: 8 bit
DOI: 10.6084/m9.figshare.6962624
title: Oil-Segmented-Oil

description: Segmented water phase for image: Oil-Filtered Segmentation performed using Watershed segmentation in Avizo. Image Dimension: 1024×1024×845 Image Type: 8 bit
DOI: 10.6084/m9.figshare.6962624.v1
title: Oil-Segmented-Oil

description: Segmented water phase for image: Oil-Filtered Segmentation performed using Watershed segmentation in Avizo. Image Dimension: 1024×1024×845 Image Type: 8 bit
DOI: 10.6084/m9.figshare.6962588
title: Clinical and laboratory characterization of dogs in different stages of chronic kidney disease and the importance of hyperphosphatemia

description: Chronic kidney disease (CKD) is a progressive and degenerative disorder that mainly affects elderly dogs. There is no cure for CKD, and since most patients are diagnosed late, when treatment will be ineffective, survival time is short. In order to standardize procedures for the detection and treatment of CKD, the International Renal Interest Society (IRIS) proposed a classification system based on serum creatinine concentration. Hyperphosphatemia is one of the major complications of CKD, which is correlated with high mortality in human patients with this disease. The present study followed 65 dogs with CKD and an average age greater than seven years. The mortality rate was 55%. According to the IRIS staging system of CKD for dogs, 6.2% were in stage 1, 13.8% in stage 2, 38.5% in stage 3, and 41.5% in stage 4 when the study beganAs their condition worsened, in most animals proteinuria and blood pressure increased, but urine density decreased. Most animals in the more severe stages of CKD presented proteinuria, arterial hypertension, and low urinary density. Hyperphosphatemia was associated with high rates of mortality, hypoalbuminemia, hypertension, proteinuria, and disease progression, and mainly occurred in IRIS stages 3 and 4. The use of a renal diet contributed to the control of hyperphosphatemia and increased the survival of dogs with CKD.
DOI: 10.6084/m9.figshare.6962618
title: Oil-Filtered

description: Filtered using Non-local means filter in Avizo software. Image Dimension: 1024×1024×845 Image Type: 8 bit
DOI: 10.6084/m9.figshare.6962465
title: Neuroticism related differences in working memory task.sav

description: These file includes data related to performance of high and low neurotic participants on working memory tasks. we used the Cambridge Neuropsychological Tasks Automated Battery (CANTAB) as our test tool and we selected three working memory tasks which tested the effect of neuroticism on both in the central executive system (CES) and the WM storage system (i.e. visuospatial sketchpad) in 21 low and 24 high neurotics.
DOI: 10.6084/m9.figshare.6962588.v1
title: Clinical and laboratory characterization of dogs in different stages of chronic kidney disease and the importance of hyperphosphatemia

description: Chronic kidney disease (CKD) is a progressive and degenerative disorder that mainly affects elderly dogs. There is no cure for CKD, and since most patients are diagnosed late, when treatment will be ineffective, survival time is short. In order to standardize procedures for the detection and treatment of CKD, the International Renal Interest Society (IRIS) proposed a classification system based on serum creatinine concentration. Hyperphosphatemia is one of the major complications of CKD, which is correlated with high mortality in human patients with this disease. The present study followed 65 dogs with CKD and an average age greater than seven years. The mortality rate was 55%. According to the IRIS staging system of CKD for dogs, 6.2% were in stage 1, 13.8% in stage 2, 38.5% in stage 3, and 41.5% in stage 4 when the study beganAs their condition worsened, in most animals proteinuria and blood pressure increased, but urine density decreased. Most animals in the more severe stages of CKD presented proteinuria, arterial hypertension, and low urinary density. Hyperphosphatemia was associated with high rates of mortality, hypoalbuminemia, hypertension, proteinuria, and disease progression, and mainly occurred in IRIS stages 3 and 4. The use of a renal diet contributed to the control of hyperphosphatemia and increased the survival of dogs with CKD.
DOI: 10.6084/m9.figshare.6962618.v1
title: Oil-Filtered

description: Filtered using Non-local means filter in Avizo software. Image Dimension: 1024×1024×845 Image Type: 8 bit
DOI: 10.6084/m9.figshare.6962465.v1
title: Neuroticism related differences in working memory task.sav

description: These file includes data related to performance of high and low neurotic participants on working memory tasks. we used the Cambridge Neuropsychological Tasks Automated Battery (CANTAB) as our test tool and we selected three working memory tasks which tested the effect of neuroticism on both in the central executive system (CES) and the WM storage system (i.e. visuospatial sketchpad) in 21 low and 24 high neurotics.
DOI: 10.6084/m9.figshare.6962465.v2
title: Neuroticism related differences in working memory task.sav

description: These file includes data related to performance of high and low neurotic participants on working memory tasks. we used the Cambridge Neuropsychological Tasks Automated Battery (CANTAB) as our test tool and we selected three working memory tasks which tested the effect of neuroticism on both in the central executive system (CES) and the WM storage system (i.e. visuospatial sketchpad) in 21 low and 24 high neurotics.
DOI: 10.6084/m9.figshare.6960998
title: A Friend in Need - Data and Analysis Code

description: Data and R code for "A Friend in Need is a Friend Indeed: Need-Based Sharing, Rather than Cooperative Assortment, Predicts Experimental Resource Transfers among Agta Hunter-Gatherers"
DOI: 10.6084/m9.figshare.6960998.v1
title: A Friend in Need - Data and Analysis Code

description: Data and R code for "A Friend in Need is a Friend Indeed: Need-Based Sharing, Rather than Cooperative Assortment, Predicts Experimental Resource Transfers among Agta Hunter-Gatherers"
DOI: 10.6084/m9.figshare.6960926
title: Supplementary Data 1 from A simple, high-resolution, non-destructive method for determining the spatial gradient of the elastic modulus of insect cuticle

description: MATLAB GUI. The GUI can be used to measure the Young's modulus of insect cuticle using a CLSM image.
DOI: 10.6084/m9.figshare.6960926.v1
title: Supplementary Data 1 from A simple, high-resolution, non-destructive method for determining the spatial gradient of the elastic modulus of insect cuticle

description: MATLAB GUI. The GUI can be used to measure the Young's modulus of insect cuticle using a CLSM image.
DOI: 10.6084/m9.figshare.6960863
title: Novel multiplex PCR-RFLP assay discriminates bovine, porcine and fish gelatin substitution in Asian pharmaceuticals capsule shells

description: Gelatin is widely used in pharmaceuticals as a protective coating, such as soft and hard capsule shells. However, the animal source of gelatin is a sensitive issue because certain gelatins such as porcine and bovine gelatins are not welcome in Halal, Kosher and Hindus’ consumer goods. Recently, we have documented DNA barcoding and multiplex PCR platforms for discriminating porcine, bovine and fish gelatins in various fish and confectionary products; but those assays were not self-authenticating and also not tested in highly refined pharmaceutical products. To address this knowledge gap, here we report a self-authenticating multiplex PCR-restriction fragment length polymorphism (RFLP) assay to identify animal sources of various gelatin in pharmaceutical capsules. Three different restriction enzymes, <i>BsaAI, Hpy188I</i> and <i>BcoDI</i> were used to yield distinctive RFLP patterns for gelatin-based bovine (26, 94 bp), fish (97, 198 bp) and porcine (17, 70 bp) DNA in control experiments. The specificity was cross-tested against 16 non-target species and the optimised assay was used to screen gelatin sources in 30 halal-branded pharmaceuticals capsule shells. Bovine and porcine DNA was found in 27 and 3 of the 30 different capsules products. The assay was suitable for detecting 0.1 to 0.01 ng total DNA extracted from pure and mixed gelatins. The study might be useful to authenticate and monitor halal, kosher, vegetarian and Hindu compliant pharmaceuticals, foods and cosmetics.
DOI: 10.6084/m9.figshare.6960863.v1
title: Novel multiplex PCR-RFLP assay discriminates bovine, porcine and fish gelatin substitution in Asian pharmaceuticals capsule shells

description: Gelatin is widely used in pharmaceuticals as a protective coating, such as soft and hard capsule shells. However, the animal source of gelatin is a sensitive issue because certain gelatins such as porcine and bovine gelatins are not welcome in Halal, Kosher and Hindus’ consumer goods. Recently, we have documented DNA barcoding and multiplex PCR platforms for discriminating porcine, bovine and fish gelatins in various fish and confectionary products; but those assays were not self-authenticating and also not tested in highly refined pharmaceutical products. To address this knowledge gap, here we report a self-authenticating multiplex PCR-restriction fragment length polymorphism (RFLP) assay to identify animal sources of various gelatin in pharmaceutical capsules. Three different restriction enzymes, <i>BsaAI, Hpy188I</i> and <i>BcoDI</i> were used to yield distinctive RFLP patterns for gelatin-based bovine (26, 94 bp), fish (97, 198 bp) and porcine (17, 70 bp) DNA in control experiments. The specificity was cross-tested against 16 non-target species and the optimised assay was used to screen gelatin sources in 30 halal-branded pharmaceuticals capsule shells. Bovine and porcine DNA was found in 27 and 3 of the 30 different capsules products. The assay was suitable for detecting 0.1 to 0.01 ng total DNA extracted from pure and mixed gelatins. The study might be useful to authenticate and monitor halal, kosher, vegetarian and Hindu compliant pharmaceuticals, foods and cosmetics.
DOI: 10.6084/m9.figshare.6960851
title: Measurement Invariance Tutorial Files

description: The files include input files for analyses and dataset used in tutorial.
DOI: 10.6084/m9.figshare.6960851.v1
title: Measurement Invariance Tutorial Files

description: The files include input files for analyses and dataset used in tutorial.
DOI: 10.6084/m9.figshare.6960800
title: Richardson_Sup Fig 1, 2, and 3

description: <b>Sup. Fig. 1: RU486 titration in amnion epithelial cells (AECs)</b> <b>A)</b> Documenting morphology of cultured primary AECs under control and RU486 titration conditions. Cells were contoured<b> </b>or puckered after 0.2 µM–0.8 µM RU486 treatment, indicating some form of cell stress. Crystal violet staining was used to show AEC viability (detected by the intensity of crystal violet dye excluded from cells).<b>B)</b> The number of crystal violet positive cells were reduced by half after 48 h with RU486 (≥ 0.2 µM) treatment compared to control (control: 2.8 RIU, 0.01 µM RU486: 2.9 RIU, 0.2 µM RU486: 1.4 RIU, 0.4 µM RU486: 1.4 RIU, 0.6 µM RU486: 1.2 RIU, 0.8 µM RU486: 0.8 RIU). Images were taken at 10X magnification<b>. </b> <b>C-D) </b>The three doses of RU486 that reduced cell viability by one-half after 48 h were added as co-treatments with Dex and cell proliferation and downstream signaling were tested. Co-treatment with Dex+RU486 led to the loss of cells and a stressed phenotype regardless of concentration when compared to control or Dex treatments. Dex+0.4 µM RU486 co-treatment maintained cell viability but was able to antagonize Dex-induced senescence. Due to these two factors, plus the current literature, 0.4 µM RU486 was chosen as the proper dose to antagonize Dex-induced responses. (<b>Proliferation:</b> control: 81.30% RIU, Dex: 78.10% RIU, 0.2 µM RU486: 64.78% RIU, 0.4 µM RU486: 80.36% RIU, 0.6 µM RU486: 57.05% RIU) (<b>Senescence-associated-β-galactosidase:</b> control: 17.47% RIU, Dex: 49.71% RIU, 0.2 µM RU486: 57.47% RIU, 0.4 µM RU486: 25.72% RIU, 0.6 µM RU486: 17.55% RIU). RIU = relative intensity unit.<br> <b> </b> <b>Sup. Fig. 2: Dexamethasone (Dex)- and RU486-induced signaling and cell fate</b> <b>A) </b>11β-hydroxysteroid dehydrogenase-1 (11β-HSD1) was not stimulated by Dex treatment in AECs after 48 h (control 0.28 ± 0.08 RFU, Dex 0.33 ± 0.08 RFU, Dex+RU486 0.37 ± 0.05 RFU) (N = 3). RFU = relative florescence units. <b> B) </b>Treatments with Dex did not induce necrosis in myometrial cells, while Dex+RU468 and RU486 alone increased necrosis when compared with control and Dex treatments (control 8.5±6.9 RFU, Dex 5.7±3.8 RFU, Dex+RU486 24.36±1 RFU, RU486 46.3±16.8 RFU) (Control vs RU486, p=0.005<i>) </i>(Dex vs RU486, p=0.003<i>)</i>. Neither Dex nor RU486 treatment of myometrial cells induced apoptosis (control 36.3±16 RFU, Dex 46.7±19.7 RFU, Dex+RU486 65.1±6 RFU, RU486 40.5±3.6 RFU)<i> </i>(N = 3). RFU = relative florescence units.<br> <br><b>Sup. Fig. 3: Dex does not induce transitions in AECs</b> <br>Morphology of primary AECs under normal cell culture, Dex, and Dex+RU486 conditions<b>.</b> Cells were contoured<b> </b>or puckered after Dex+RU486 but not with Dex alone, indicating some form of cell stress from RU486. Dex nor Dex+RU468 treatment of AECs did not induce cellular transitions measured by E-cadherin/N-cadherin ratio when compared with control (N=3). <br>
DOI: 10.6084/m9.figshare.6960776
title: Earth Analytics Bootcamp | Homework 3 Teaching Subset

description: This is a teaching data subset that contains data for average monthly temperature (Fahrenheit) and total precipitation (millimeters) for Boulder, CO. Data included:<br> 1. Average monthly temperature (Fahrenheit) between 2004 and 2009 (boulder-temp-2004-to-2009.csv): 6 rows (one for each year from 2004 through 2009) and 12 columns (one for each month from January through December) <br><br> 2. Average monthly temperature (Fahrenheit) between 2010 and 2014 (boulder-temp-2010-to-2014.csv): 5 rows (one for each year from 2010 through 2014) and 12 columns (one for each month from January through December) <br><br>3. Average monthly temperature (Fahrenheit) for 2015 (boulder-temp-2015.txt): 12 rows/records (one for each month from January through December) <br>4. Average monthly temperature (Fahrenheit) for 2016 (boulder-temp-2016.txt): 12 rows/records (one for each month from January through December) <br>5. Average monthly temperature (Fahrenheit) for 2017 (boulder-temp-2017.txt): 12 rows/records (one for each month from January through December) <br>6. Total monthly precipitation (mm) from 1996 to 2006 with month names (boulder-precip-1996-to-2006-months.csv): contains headers<br>7. Total monthly precipitation (mm) from 2007 to 2017 with month and season names (boulder-precip-2007-to-2017-months-seasons.csv): contains headers<br> Source: NOAA.<br> <br>
DOI: 10.6084/m9.figshare.6960746
title: Dataset for: Organochlorines, perfluoroalkyl substances, mercury and egg incubation temperature in an Arctic seabird: insight from data loggers

description: In birds, incubation-related behaviors and brood patch formation are influenced by hormonal regulation like prolactin secretion. Brood patch provides efficient heat transfer between the incubating parent and the developing embryo in the egg. Importantly, several environmental contaminants are already known to have adverse effects on avian reproduction. However, relatively little is known about the effect of contaminants on incubation temperature (Tinc) for wild birds. By using temperature thermistors placed into artificial eggs, we investigated whether the most contaminated parent birds are less able to provide appropriate egg warming and thus less committed in incubating their clutch. Specifically, we investigated the relationships between three groups of contaminants (organochlorines (OCs), perfluoroalkyl substances (PFASs), and mercury (Hg)) with Tinc and also with prolactin concentrations and brood patch size in incubating Arctic black-legged kittiwakes (Rissa tridactyla). Our results reveal that among the considered OCs, only blood levels of oxychlordane, the main metabolite of “chlordane”, a banned pesticide, were negatively related to the minimum incubation temperature in male kittiwakes. PFAS and Hg levels were unrelated to Tinc in kittiwakes. Moreover, our study suggests a possible underlying mechanism since we reported a significant and negative association between blood oxychlordane concentrations and the size of the brood patch in males. Finally, this reduced Tinc in the most oxychlordane-contaminated kittiwakes was associated with a lower egg hatching probability.