cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29815495
title: Unified framework for direct sensitivity analysis of smooth and non-smooth multibody systems

description: Sensitivity analysis of multibody systems is essential for quantifying the effect of design parameters on the dynamic output. The most straight-forward and often used approach to calculate dynamic sensitivities is through finite difference method. This procedure is computationally expensive when the number of parameters is large, and numerical errors can severely limit its accuracy. The current state-of-the-art has demonstrated efficient techniques for evaluating sensitivities of smooth multibody systems with ideal joints and friction. However, real-world applications have clearances within the joints where the dynamics is governed by intermittent formation of contacts. Though excluded in case of ideal joints, these clearances have substantial influence on the dynamic response of multibody systems. This article explores a general unified framework for evaluating direct sensitivities of ideal joints as well as joints with clearance using a non-smooth dynamics approach. The sensitivity equations are derived from the non-smooth dynamics formulation with half-implicit discretization scheme. The proposed methodology is demonstrated on a simple pendulum, and a control problem related to motorcycle’s gear-shifting mechanism. The results have been validated with central finite difference method (CFDM) for real valued perturbations. Limitation on CFDM’s accuracy, and noise content in the solution are emphasized, specially in case of systems with clearances. The sensitivities corresponding to a system with ideal joints were found to be independent on step-size as opposed to time-step varying sensitivities in system with joints with clearance. To the best of our knowledge, the results of such a study have not been reported in the literature.
DOI: 10.6084/m9.figshare.29815495.v1
title: Unified framework for direct sensitivity analysis of smooth and non-smooth multibody systems

description: Sensitivity analysis of multibody systems is essential for quantifying the effect of design parameters on the dynamic output. The most straight-forward and often used approach to calculate dynamic sensitivities is through finite difference method. This procedure is computationally expensive when the number of parameters is large, and numerical errors can severely limit its accuracy. The current state-of-the-art has demonstrated efficient techniques for evaluating sensitivities of smooth multibody systems with ideal joints and friction. However, real-world applications have clearances within the joints where the dynamics is governed by intermittent formation of contacts. Though excluded in case of ideal joints, these clearances have substantial influence on the dynamic response of multibody systems. This article explores a general unified framework for evaluating direct sensitivities of ideal joints as well as joints with clearance using a non-smooth dynamics approach. The sensitivity equations are derived from the non-smooth dynamics formulation with half-implicit discretization scheme. The proposed methodology is demonstrated on a simple pendulum, and a control problem related to motorcycle’s gear-shifting mechanism. The results have been validated with central finite difference method (CFDM) for real valued perturbations. Limitation on CFDM’s accuracy, and noise content in the solution are emphasized, specially in case of systems with clearances. The sensitivities corresponding to a system with ideal joints were found to be independent on step-size as opposed to time-step varying sensitivities in system with joints with clearance. To the best of our knowledge, the results of such a study have not been reported in the literature.
DOI: 10.6075/j0ff3r3j
title: CIL:13867, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: HA peptide tag; 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody; Cy3; Fluorescein (FITC)
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Cells (MATa cdc14::3HA-CDC14), grown in rich media with glucose, were fixed for 15 min in 3.7% formaldehyde and 0.1 M potassium phosphate buffer, pH 6.4. Cells were then washed twice with 0.1 M potassium phosphate buffer, pH 6.4, and resuspended in 1.2 M sorbitol in 0.12 M K2HPO4/0.033 M citric acid, pH 5.9. Fixed cells were digested with 0.1 mg/ml zymolyase-100T (US Biological) and 1/10 volume of glusulase (PerkinElmer) at 30C for 15 min, washed once, and resuspended in 1.2 M sorbitol in 0.12 M K2HPO4/0.033 M citric acid, pH 5.9. Primary antibodies were anti-HA monoclonal antibody (HA.11; 1:500) and anti-tubulin (Abcam; 1:500). Secondary antibodies were: anti-mouse Cy3 (for HA) and anti-rat FITC (for tubulin). Cells were resuspended in DAPI (1 mg/ml). Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (leica) and ImageJ software.
description: 3HA-Cdc14 (red) localization in metaphase. The protein is sequestered in the nucleolus. Metaphase is determined by spindle morphology (tubulin, green) and nuclear morphology (DAPI, blue). Image is Fig 3D, left panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig 3 include CIL# 13862, 13863, 13864, 13865, 13866, 13867.
DOI: 10.6075/j08k78kc
title: CIL: 52122, Homo sapiens. In Cell Image Library

description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
DOI: 10.6075/j0h993xz
title: CIL:13866, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: HA peptide tag; 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody; Cy3; Fluorescein (FITC)
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Cells (MATa cdc14::3HA-CDC14), grown in rich media with glucose, were fixed for 15 min in 3.7% formaldehyde and 0.1 M potassium phosphate buffer, pH 6.4. Cells were then washed twice with 0.1 M potassium phosphate buffer, pH 6.4, and resuspended in 1.2 M sorbitol in 0.12 M K2HPO4/0.033 M citric acid, pH 5.9. Fixed cells were digested with 0.1 mg/ml zymolyase-100T (US Biological) and 1/10 volume of glusulase (PerkinElmer) at 30C for 15 min, washed once, and resuspended in 1.2 M sorbitol in 0.12 M K2HPO4/0.033 M citric acid, pH 5.9. Primary antibodies were anti-HA monoclonal antibody (HA.11; 1:500) and anti-tubulin (Abcam; 1:500). Secondary antibodies were: anti-mouse Cy3 (for HA) and anti-rat FITC (for tubulin). Cells were resuspended in DAPI (1 mg/ml). Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (leica) and ImageJ software.
description: 3HA-Cdc14 (red) localization in early anaphase. The protein is partially released throughout the nucleus. Early anaphase is determined by spindle morphology (tubulin, green) and nuclear morphology (DAPI, blue). Image is Fig 3D, middle panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig 3 include CIL# 13862, 13863, 13864, 13865, 13866, 13867.
DOI: 10.6075/j0p55mms
title: CIL:12306, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Endoplasmic reticulum, mitochondria with their tubular cristae and a Golgi stack. Ribosomes are scattered in the cytosol. TEM taken on 3/13/69 by R. Allen with Philips 300 operating at 60kV. Neg. 20,500X. Bar = 0.5µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0z31xkb
title: CIL:35782, Saccharomyces cerevisiae. In Cell Image Library

description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Read the microscopy section of the referenced paper for details prior to image analysis.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Bck2, a Cln-independent activator of CLN1,2 expression. These phase and GFP images are part of a group that ranges from CIL:35780-35799. Note that there are additional groups of images monitoring the dynamics of other proteins involved in cell cycle regulation by the same authors in the Library.
DOI: 10.6075/j0513xfg
title: CIL:338, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: uranyl salt; lead salt
Visualization methods: detection of electrons
Processing history: unprocessed raw data
description: Thin section electron microscopy of gastrocnemius (skeletal) muscle from a wild type mouse.

Sample was viewed with a Hitachi 7600 electron microscope (accelerating voltage 80 KV) and imaged with an AMT digital camera. Image taken at 50,000X magnification.

This image is part of a set of wild type gastrocnemius muscle images that served as controls for the study of the delta-sarcoglycan knockout mouse. Both the set of wild-type and delta-sarcoglycan knockout mouse images are part of The CELL: an image library.

Reference: Nat Med. 2008 Apr;14(4):442-7. 
Genetic and pharmacologic inhibition of mitochondrial-dependent necrosis attenuates muscular dystrophy.
Millay DP, Sargent MA, Osinska H, Baines CP, Barton ER, Vuagniaux G, Sweeney HL, Robbins J, Molkentin JD (tissue preparation described in Fewell JG, et al. A treadmill exercise regimen for identifying cardiovascular phenotypes in transgenic mice. Am J Physiol. 1997;273:H1595–H1605)
DOI: 10.6075/j00p0xt8
title: CIL:10924, Felis catus, myelinating Schwann cell, peripheral neuron. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide
Data qualification: Processed
description: This electron micrograph shows a cross section through an axon, its myelin wrap, and the associated myelin-producing Schwann cell from the the cochlear nerve of the cat. The external mesaxon is the location where the wrapping edges of the Schwann cell meet, as the cell extends membrane that encircles the axon. This image, by Enrico Mugnaini, is Figure 14 from Chapter 1 (The Cell Surface) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0zc82cq
title: CIL: 52305, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=4, y=2, z=7 from BL_024216_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j07d2tbx
title: CIL:12312, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Contractile vacuole of Nassula sp. Parts of the single CV appear on two sides of the CV pore. Fields of spongiome abut the filled portions of the CV. TEM taken on 3/27/69 by R. Allen with Philips 300 operating at 60kV. Neg. 3,120X. Bar = 2µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis.Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0nz86t8
title: CIL:11846, Haemanthus katharinae, endosperm. In Cell Image Library

description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 0.5 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of interphase, the grid was tilted to 45 degrees. A similar micrograph tilted to 55 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0cr5sq8
title: CIL:39754, Mus musculus, cardiac muscle cell. In Cell Image Library

description: Transmission electron micrograph of mouse cardiac muscle. Transport is visible in the ventricle across a space from one muscle cell to the adjacent muscle cell.
description: Primary fixation included: 2.5 % glutaraldehyde, 2% formaldehyde in 0.1 M Na-phosphate buffer, pH 7.4. Post-fixed in 2% OSO4 in 0.1 M Na-phosphate buffer, pH 7.4. Stained en bloc in 1% uranyl acetate. The tissue was then dehydrated in a graded series of ethanol and infiltrated with Spurr's resin. Thin sections of 70 nm were trimmed using a diamond knife and post-stained in uranyl acetate and lead citrate. This micrograph image was taken using a Phillips CM 100 transmission electron microscope at an accelerating voltage of 80kV.
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; tissue in epoxy resin embedment; ethanol dehydration
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt
Processing history: unprocessed raw data
DOI: 10.6075/j06m36p3
title: CIL: 54767, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Epifluorescent imaging
description: DAPI staining
DOI: 10.6075/j0hx1csn
title: CIL:40255, Rattus norvegicus, peripheral neuron. In Cell Image Library

description: Single computed slice through a tomographic volume of mitochondria at the Node of Ranvier in rat peripheral nerve root. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information, see: Perkins et al. Mitochondrial configurations in peripheral nerve suggest differential ATP production. J. Struct. Biol. (2010), doi:10.1016/j.jsb.2010.06.017 http://www.ncbi.nlm.nih.gov/pubmed/20600951
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
description: Chemical fixation with 2% paraformaldehyde and 2.5% glutaraldehyde via vascular perfusion in 0.15M cacodylate buffer (pH 7.4) at 37 degrees C followed by high pressure freezing and freeze substitution using a Bal Tec HPM010 high pressure freezer (from Perkins et al., J. Structural Biology 161, 469, 2008).
DOI: 10.5281/zenodo.17482747
title: Building components from underutilised wood stocks

description: Supplementary table to WoodStock Deliverable 5.3. 'Review of zero-waste product concepts'. List of over 150 products and prototypes based on one or more of the four underutilised wood streams: low-quality wood, damaged wood, hardwoods, post-consumer and residual wood. Projects range from conceptual designs to market-ready solutions, developed in academia and by industry. Information included: Name of the project, authors, affiliation, access link, location, wood stream, wood species, type of building component.
DOI: 10.5281/zenodo.17482746
title: Building components from underutilised wood stocks

description: Supplementary table to WoodStock Deliverable 5.3. 'Review of zero-waste product concepts'. List of over 150 products and prototypes based on one or more of the four underutilised wood streams: low-quality wood, damaged wood, hardwoods, post-consumer and residual wood. Projects range from conceptual designs to market-ready solutions, developed in academia and by industry. Information included: Name of the project, authors, affiliation, access link, location, wood stream, wood species, type of building component.
DOI: 10.5281/zenodo.17491776
title: Total number of tRNA gene copies and their location within the genome of Yellowfin tuna (Thunnus albacares) as obtained from GenBank.
DOI: 10.5281/zenodo.17491777
title: Total number of tRNA gene copies and their location within the genome of Yellowfin tuna (Thunnus albacares) as obtained from GenBank.
DOI: 10.5281/zenodo.17168306
title: Early-life high-dose sodium butyrate supplementation inhibits growth via sterol metabolism in 15-month-old dairy cattle: insights from gastrointestinal microbiota and host metabolism

description: Sodium butyrate is a common calf feed additive, but its long-term effects are unknown. This study found that feeding high doses in milk before weaning had a negative programming effect, stunting growth in heifers at 15 months of age. This was caused by disrupting rumen microbes and cholesterol metabolism. Our results provide dairy farmers and nutritionists with crucial guidance: optimizing butyrate dosage is essential to avoid unintended losses in growth and productivity, ensuring sustainable and economical dairy production.
DOI: 10.5281/zenodo.17168307
title: Early-life high-dose sodium butyrate supplementation inhibits growth via sterol metabolism in 15-month-old dairy cattle: insights from gastrointestinal microbiota and host metabolism

description: Sodium butyrate is a common calf feed additive, but its long-term effects are unknown. This study found that feeding high doses in milk before weaning had a negative programming effect, stunting growth in heifers at 15 months of age. This was caused by disrupting rumen microbes and cholesterol metabolism. Our results provide dairy farmers and nutritionists with crucial guidance: optimizing butyrate dosage is essential to avoid unintended losses in growth and productivity, ensuring sustainable and economical dairy production.
DOI: 10.15468/dl.6yqpvx
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Succochlea"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009530-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gexjtj
title: Occurrence Download

description: A dataset containing 7063 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tradescantia zebrina"
 ]
}

 The dataset includes 7063 records from 336 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009529-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13566347
title: Daily Public Opinion on Israel-Palestine War
DOI: 10.5281/zenodo.17491780
title: Open Data_Rekapitulasi Responden
DOI: 10.5281/zenodo.17491781
title: Open Data_Rekapitulasi Responden