cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8015489.v1
title: Uptake of adenine by purine permeases of <i>Coffea canephora</i>

description: Purine permeases (PUPs) mediate the proton-coupled uptake of nucleotide bases and their derivatives into cytosol. PUPs facilitate uptake of adenine, cytokinins and nicotine. Caffeine, a purine alkaloid derived from xanthosine, occurs in only a few eudicot species, including coffee, cacao, and tea. Although caffeine is not an endogenous metabolite in Arabidopsis and rice, AtPUP1 and OsPUP7 were suggested to transport caffeine. In this study, we identified 15 PUPs in the genome of <i>Coffea canephora</i>. Direct uptake measurements in yeast demonstrated that CcPUP1 and CcPUP5 facilitate adenine – but not caffeine – transport. Adenine uptake was pH-dependent, with increased activity at pH 3 and 4, and inhibited by nigericin, a potassium–proton ionophore, suggesting that CcPUP1 and CcPUP5 function as proton-symporters. Furthermore, adenine uptake was not competitively inhibited by an excess amount of caffeine, which implies that PUPs of <i>C. canephora</i> have evolved to become caffeine-insensitive to promote efficient uptake of adenine into cytosol. CcPUP1 & CcPUP5 distinguish adenine from caffeine. The adenine uptake activity of AtPUP1 is inhibited by caffeine.
DOI: 10.6084/m9.figshare.8015372
title: When is <i>n</i> large enough? Looking for the right sample size to estimate proportions

description: The central limit theorem indicates that when the sample size goes to infinite, the sampling distribution of means tends to follow a normal distribution; it is the basis for the most usual confidence interval and sample size formulas. This study analyzes what sample size is large enough to assume that the distribution of the estimator of a proportion follows a Normal distribution. Also, we propose the use of a correction factor in sample size formulas to ensure a confidence level even when the central limit theorem does not apply for these distributions.
DOI: 10.6084/m9.figshare.8015378
title: Model selection in high-dimensional noisy data: a simulation study

description: In many practical applications, high-dimensional regression analyses have to take into account measurement error in the covariates. It is thus necessary to extend regularization methods, that can handle the situation where the number of covariates <i>p</i> largely exceed the sample size <i>n</i>, to the case in which covariates are also mismeasured. A variety of methods are available in this context, but many of them rely on knowledge about the measurement error and the structure of its covariance matrix. In this paper, we set the goal to compare some of these methods, focusing on situations relevant for practical applications. In particular, we will evaluate these methods in setups in which the measurement error distribution and dependence structure are not known and have to be estimated from data. Our focus is on variable selection, and the evaluation is based on extensive simulations.
DOI: 10.6084/m9.figshare.8015354
title: Mueller report terms and count

description: A scrape and clean up all unique terms in Mueller Reports using rstats. https://cjlortie.github.io/Mueller_Report/<br>Updated version without numbers in word column.
DOI: 10.6084/m9.figshare.8015372.v1
title: When is <i>n</i> large enough? Looking for the right sample size to estimate proportions

description: The central limit theorem indicates that when the sample size goes to infinite, the sampling distribution of means tends to follow a normal distribution; it is the basis for the most usual confidence interval and sample size formulas. This study analyzes what sample size is large enough to assume that the distribution of the estimator of a proportion follows a Normal distribution. Also, we propose the use of a correction factor in sample size formulas to ensure a confidence level even when the central limit theorem does not apply for these distributions.
DOI: 10.6084/m9.figshare.8015378.v1
title: Model selection in high-dimensional noisy data: a simulation study

description: In many practical applications, high-dimensional regression analyses have to take into account measurement error in the covariates. It is thus necessary to extend regularization methods, that can handle the situation where the number of covariates <i>p</i> largely exceed the sample size <i>n</i>, to the case in which covariates are also mismeasured. A variety of methods are available in this context, but many of them rely on knowledge about the measurement error and the structure of its covariance matrix. In this paper, we set the goal to compare some of these methods, focusing on situations relevant for practical applications. In particular, we will evaluate these methods in setups in which the measurement error distribution and dependence structure are not known and have to be estimated from data. Our focus is on variable selection, and the evaluation is based on extensive simulations.
DOI: 10.6084/m9.figshare.8015198
title: Sinonasal Microbiotypes Dataset Two

description: This is "Dataset Two" for the manuscript "Microbiotyping the sinonasal microbiome".<br>Middle meatus swabs were collected from participants' sinuses for 16S rRNA gene sequencing (V3-V4 hypervariable region) on the Illumina MiSeq platform.<br>
DOI: 10.6084/m9.figshare.12871805
title: Photoacoustic Microscopy Dataset

description: Dataset for deep learning project that aims to upsample undersampled PAM images.
DOI: 10.6084/m9.figshare.8015354.v1
title: Mueller report terms and count

description: A scrape and clean up all unique terms in Mueller Reports using rstats. https://cjlortie.github.io/Mueller_Report/
DOI: 10.6084/m9.figshare.8015354.v3
title: Mueller report terms and count

description: A scrape and clean up all unique terms in Mueller Reports using rstats. https://cjlortie.github.io/Mueller_Report/<br>Updated version without numbers in word column.
DOI: 10.6084/m9.figshare.8015354.v2
title: Mueller report terms and count

description: A scrape and clean up all unique terms in Mueller Reports using rstats. https://cjlortie.github.io/Mueller_Report/<br>Updated version without numbers in word column.
DOI: 10.6084/m9.figshare.8015036
title: Sub-mesoscale Fronts modify Elephant Seals foraging behavior.

description: We analyzed data from 12 bio-logged female elephant seals in 2011, 2012 and 2013 during their post breeding voyages. This dataset contains mainly time, GPS positions, temperature, depth and accelerometer measurements. <br> This fileset includes the following data: <br> The 12 .mat files, each one containing all the data for 1 individual.A metadata form that provides tables explaining the data included here as part of the manuscript submitted to L&O Letters.<br>
DOI: 10.6084/m9.figshare.8015033
title: Channel modeling for IEEE 802.11ad indoor links in the 60 GHz band

description: In this work, we analyze the empirical power losses and the power distribution with angle when an indoor base station serves indoor users, emulating the operation of an IEEE 802.11ad high-speed wireless LAN at 60 GHz. To this end, we performed a measurement campaign in an office environment, with and without pedestrian movement in the vicinity of the wireless terminals. We observed that useful lobes exist even in obstructed links, allowing the use of angular combiners or beamformers to increase link availability and data rate. Our results are relevant for the proper calibration of PHY or network simulators by including propagation constraints, and to validate the results of theoretical studies.
DOI: 10.6084/m9.figshare.8015036.v2
title: Sub-mesoscale Fronts modify Elephant Seals foraging behavior. P., Rivière, T. Jaud, L. Siegelman, P. Klein, C. Cotte, J. Le Sommer, G. Dencausse, C. Guinet. 2019

description: We analyzed data from 12 bio-logged female elephant seals in 2011, 2012 and 2013 during their post breeding voyages. This dataset contains mainly time, GPS positions, temperature, depth and accelerometer measurements. <br> This fileset includes the following data: <br> The 12 .mat files, each one containing all the data for 1 individual.A metadata form that provides tables explaining the data included here as part of the manuscript submitted to L&O Letters.<br>
DOI: 10.6084/m9.figshare.8014997
title: Patient 1 Structure Sets

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.8015033.v2
title: Channel modeling for IEEE 802.11ad indoor links in the 60 GHz band

description: In this work, we analyze the empirical power losses and the power distribution with angle when an indoor base station serves indoor users, emulating the operation of an IEEE 802.11ad high-speed wireless LAN at 60 GHz. To this end, we performed a measurement campaign in an office environment, with and without pedestrian movement in the vicinity of the wireless terminals. We observed that useful lobes exist even in obstructed links, allowing the use of angular combiners or beamformers to increase link availability and data rate. Our results are relevant for the proper calibration of PHY or network simulators by including propagation constraints, and to validate the results of theoretical studies.
DOI: 10.6084/m9.figshare.8015036.v1
title: Sub-mesoscale Fronts modify Elephant Seals foraging behavior

description: We analyzed data from 12 bio-logged female elephant seals in 2011, 2012 and 2013 during their post breeding voyages. This dataset contains mainly time, GPS positions, temperature, depth and accelerometer measurements. <br> This fileset includes the following data: <br> The 12 .mat files, each one containing all the data for 1 individual.A metadata form that provides tables explaining the data included here as part of the manuscript submitted to L&O Letters.<br>
DOI: 10.6084/m9.figshare.8015033.v1
title: Untitled Item

description: In this work, we analyze the empirical power losses and the power distribution with angle when an indoor base station serves indoor users, emulating the operation of an IEEE 802.11ad high-speed wireless LAN at 60 GHz. To this end, we performed a measurement campaign in an office environment, with and without pedestrian movement in the vicinity of the wireless terminals. We observed that useful lobes exist even in obstructed links, allowing the use of angular combiners or beamformers to increase link availability and data rate. Our results are relevant for the proper calibration of PHY or network simulators by including propagation constraints, and to validate the results of theoretical studies.
DOI: 10.6084/m9.figshare.8014991
title: Patient 1 MRI

description: CTs and MRIs were both acquired under radiotherapy immobilization protocols with patients in the treatment position.<br>CT scans were acquired on one of four machine models (LightSpeed RT16, GE Medical Systems, Waukesha, WI, USA; Brilliance 64 or Brilliance Big Bore, Philips Healthcare, Cambridge, MA, USA; SOMATOM Definition Edge, Siemens, Washington D.C., USA) using x-ray tube currents between 208 – 434 mA at 120 kVp. All scans have slice thicknesses of either 2.5 or 3 mm, with 2.5 or 3 mm of space between slices. Sections are displayed in 512 x 512 pixel matrices and were reconstructed in diameters between 500 – 600 mm. <br>MRI scans were acquired in one of two machine models (Discovery MR750, GE Medical Systems, Waukesha, WI, USA; Ingenia, Philips Healthcare, Cambridge, MA, USA) in 3 Tesla magnetic fields with echo times between 97.72 – 101.82 milliseconds. All scans have slice thicknesses of 2.5 mm, with 2.5 or 4 mm of space between slices. Sections are displayed in 512 x 512 pixel matrices and were reconstructed in 256 mm diameters.
DOI: 10.6084/m9.figshare.8015000.v3
title: Soleus and Tibialis Anterior Motor Axon Excitability

description: These are data files to accompany the paper "Nerve Excitability Differences in Slow and Fast Motor Axons of the Rat: more than just I_h". There are 4 separate files containing the nerve excitability tests on motor axons to two different muscles (soleus and tibialis anterior) using two different anaesthetics (ketamine-xylazine and sodium pentobarbital). The experiments were done using QTrac software and the raw data files were exported to Excel for sharing. There are an additional 2 PDF files, one of which is a research note with data complimentary to the published manuscript.
DOI: 10.6084/m9.figshare.8014919
title: Mueller report as a dataframe

description: Code and source of pdf to this data format here:https://github.com/cjlortie/Mueller_Report<br>
DOI: 10.6084/m9.figshare.8014973
title: Patient 1 CT

description: CTs and MRIs were both acquired under radiotherapy immobilization protocols with patients in the treatment position.<br>CT scans were acquired on one of four machine models (LightSpeed RT16, GE Medical Systems, Waukesha, WI, USA; Brilliance 64 or Brilliance Big Bore, Philips Healthcare, Cambridge, MA, USA; SOMATOM Definition Edge, Siemens, Washington D.C., USA) using x-ray tube currents between 208 – 434 mA at 120 kVp. All scans have slice thicknesses of either 2.5 or 3 mm, with 2.5 or 3 mm of space between slices. Sections are displayed in 512 x 512 pixel matrices and were reconstructed in diameters between 500 – 600 mm. <br>MRI scans were acquired in one of two machine models (Discovery MR750, GE Medical Systems, Waukesha, WI, USA; Ingenia, Philips Healthcare, Cambridge, MA, USA) in 3 Tesla magnetic fields with echo times between 97.72 – 101.82 milliseconds. All scans have slice thicknesses of 2.5 mm, with 2.5 or 4 mm of space between slices. Sections are displayed in 512 x 512 pixel matrices and were reconstructed in 256 mm diameters.
DOI: 10.6084/m9.figshare.8015000
title: Soleus and Tibialis Anterior Motor Axon Excitability

description: These are data files to accompany the paper "Nerve Excitability Differences in Slow and Fast Motor Axons of the Rat: more than just I_h". There are 4 separate files containing the nerve excitability tests on motor axons to two different muscles (soleus and tibialis anterior) using two different anaesthetics (ketamine-xylazine and sodium pentobarbital). The experiments were done using QTrac software and the raw data files were exported to Excel for sharing. There are an additional 2 PDF files, one of which is a research note with data complimentary to the published manuscript.
DOI: 10.6084/m9.figshare.8014919.v1
title: Mueller report as a dataframe

description: Code and source of pdf to this data format here:https://github.com/cjlortie/Mueller_Report<br>
DOI: 10.6084/m9.figshare.8014868
title: Human shadowing events in the 60 GHz band: modeling the effect of multiple pedestrians

description: We modeled human-induced shadowing events, when 1-7 pedestrians block the line-of-sight (LOS) in an access point (AP) to user station (STA), operating at 60 GHz, for two types of scenarios: controlling the trajectories of pedestrians, and a non-controlled case. Deep shadowing events only occurred when pedestrians crossed the LOS in both cases, which means that the effect of blocking reflected or scattered signals was negligible. For the controlled scenario (when multiple pedestrians crossed the LOS simultaneously) we observed that once the closest positions to the STA were blocked, the effect of blocking the rest of the link were only marginal. We also tested two antenna-aiming strategies at the STA. We observed that once the antenna gain is normalized and oriented towards the AP, there are no significant penalties by aligning the antenna in the horizontal plane only. We also report results to parameterize single and sequences of shadow fades, that are useful for simulation purposes and to validate theoretical models
DOI: 10.6084/m9.figshare.8014889
title: high resolution run

description: high resolution run
DOI: 10.6084/m9.figshare.8014868.v1
title: Human shadowing events in the 60 GHz band: modeling the effect of multiple pedestrians

description: We modeled human-induced shadowing events, when 1-7 pedestrians block the line-of-sight (LOS) in an access point (AP) to user station (STA), operating at 60 GHz, for two types of scenarios: controlling the trajectories of pedestrians, and a non-controlled case. Deep shadowing events only occurred when pedestrians crossed the LOS in both cases, which means that the effect of blocking reflected or scattered signals was negligible. For the controlled scenario (when multiple pedestrians crossed the LOS simultaneously) we observed that once the closest positions to the STA were blocked, the effect of blocking the rest of the link were only marginal. We also tested two antenna-aiming strategies at the STA. We observed that once the antenna gain is normalized and oriented towards the AP, there are no significant penalties by aligning the antenna in the horizontal plane only. We also report results to parameterize single and sequences of shadow fades, that are useful for simulation purposes and to validate theoretical models
DOI: 10.6084/m9.figshare.8014820
title: Dataset of Natural Parasitism Behaviour of Microcharops anticarsiae

description: This is a dataset to describe the results on "Natural Parasitism Behaviour of<i> Microcharops anticarsiae</i> Gupta and its Sex Ratio in the Field and Laboratory".<br>
DOI: 10.6084/m9.figshare.8014823
title: CCDB_3950.jpg

description: Serial tomographic reconstruction from four serial tomograms showing a large number of HTLV-1 particles in the space between a chronically infected MS9 cell (top) and a potential Jurkat cell (bottom). Viral particles are characterized by an electron-dense core surrounded by a less dense area and bounded by a viral membrane.
DOI: 10.6084/m9.figshare.8014817
title: CCDB_3949.jpg

description: Tomographic reconstruction from two serial tomograms showing a virological synapse formed between a chronically HTLV-1 infected MS9 cell (lower right) and Jurkat cell (upper left).
DOI: 10.6084/m9.figshare.8014814
title: CCDB_3948.jpg

description: Virological synapse formed between HTLV-1 infected CD4+ T-cell (PBMC) and an autologous uninfected CD4+ T-cell as a target cell. These cells were stained against HTLV-1 Gag p19 matrix protein with a specific monoclonal antibody (GIN7). A large immunolabeled HTLV-1 particle is visible between the two cell membranes. See Figure 4D of Majorovits et al., 2008.
DOI: 10.6084/m9.figshare.8014817.v1
title: CCDB_3949.jpg

description: Tomographic reconstruction from two serial tomograms showing a virological synapse formed between a chronically HTLV-1 infected MS9 cell (lower right) and Jurkat cell (upper left).
DOI: 10.6084/m9.figshare.8014823.v1
title: CCDB_3950.jpg

description: Serial tomographic reconstruction from four serial tomograms showing a large number of HTLV-1 particles in the space between a chronically infected MS9 cell (top) and a potential Jurkat cell (bottom). Viral particles are characterized by an electron-dense core surrounded by a less dense area and bounded by a viral membrane.
DOI: 10.6084/m9.figshare.8014772
title: CCDB_3939.jpg

description: Electron micrograph of cultured Drosophila Dl1 cells infected with flock house virus, prepared using chemical fixation and high pressure freezing followed by freeze substitution. This cell was prepared as part of an experiment to investigate different protocols for high pressure freezing.
DOI: 10.6084/m9.figshare.8014802
title: CCDB_3947.jpg

description: Single computed slice through a tomographic reconstruction of virus particles that budded from a naturally HTLV-1 infected CD4+ T cell into the synaptic cleft of the virological synapse. Viral particles are characterized by an electron-dense core surrounded by a less dense area and the viral membrane.
DOI: 10.6084/m9.figshare.8014814.v1
title: CCDB_3948.jpg

description: Virological synapse formed between HTLV-1 infected CD4+ T-cell (PBMC) and an autologous uninfected CD4+ T-cell as a target cell. These cells were stained against HTLV-1 Gag p19 matrix protein with a specific monoclonal antibody (GIN7). A large immunolabeled HTLV-1 particle is visible between the two cell membranes. See Figure 4D of Majorovits et al., 2008.
DOI: 10.6084/m9.figshare.8014799
title: CCDB_3946.jpg

description: Single computed slice through a tomographic reconstruction of a virological synapse formed between naturally HTLV-1 infected CD4+ T cells and autologous uninfected CD4+ target cells. HTLV-1 particles in the synaptic cleft were identified by immunolabeling using anti-Gag p19 labeling and peroxidase-DAB detection.
DOI: 10.6084/m9.figshare.8014772.v1
title: CCDB_3939.jpg

description: Electron micrograph of cultured Drosophila Dl1 cells infected with flock house virus, prepared using chemical fixation and high pressure freezing followed by freeze substitution. This cell was prepared as part of an experiment to investigate different protocols for high pressure freezing.
DOI: 10.6084/m9.figshare.8014802.v1
title: CCDB_3947.jpg

description: Single computed slice through a tomographic reconstruction of virus particles that budded from a naturally HTLV-1 infected CD4+ T cell into the synaptic cleft of the virological synapse. Viral particles are characterized by an electron-dense core surrounded by a less dense area and the viral membrane.
DOI: 10.6084/m9.figshare.8014724
title: CD8 Gag-reactive TCR repertoire file

description: CD8 Gag-reactive TCR repertoire for all subjects
DOI: 10.6084/m9.figshare.8014727
title: Subject data

description: Clinical, TCR and viral data of the cohort
DOI: 10.6084/m9.figshare.8014799.v1
title: CCDB_3946.jpg

description: Single computed slice through a tomographic reconstruction of a virological synapse formed between naturally HTLV-1 infected CD4+ T cells and autologous uninfected CD4+ target cells. HTLV-1 particles in the synaptic cleft were identified by immunolabeling using anti-Gag p19 labeling and peroxidase-DAB detection.
DOI: 10.6084/m9.figshare.8014709
title: CCDB_3938.jpg

description: Electron micrograph of a cultured Drosophila DL1 cell infected with flock house virus, prepared by high pressure freezing followed by freeze substitution. This cell was prepared as part of an experiment to investigate different protocols for high pressure freezing.
DOI: 10.6084/m9.figshare.8014721
title: CD4 Gag-reactive TCR repertoire files

description: CD4 Gag-reactive TCR repertoires
DOI: 10.6084/m9.figshare.8014706
title: CCDB_3937.jpg

description: Electron micrograph of a cultured Drosophila DL1 cell infected with flock house virus, prepared using chemical fixation followed by routine embedding for electron microscopy. This specimen was prepared as a control to compare different high pressure freezing protocols.
DOI: 10.6084/m9.figshare.8014706.v1
title: CCDB_3937.jpg

description: Electron micrograph of a cultured Drosophila DL1 cell infected with flock house virus, prepared using chemical fixation followed by routine embedding for electron microscopy. This specimen was prepared as a control to compare different high pressure freezing protocols.
DOI: 10.6084/m9.figshare.8014721.v1
title: CD4 Gag-reactive TCR repertoire files

description: CD4 Gag-reactive TCR repertoires
DOI: 10.6084/m9.figshare.8014724.v1
title: CD8 Gag-reactive TCR repertoire file

description: CD8 Gag-reactive TCR repertoire for all subjects
DOI: 10.6084/m9.figshare.8014709.v1
title: CCDB_3938.jpg

description: Electron micrograph of a cultured Drosophila DL1 cell infected with flock house virus, prepared by high pressure freezing followed by freeze substitution. This cell was prepared as part of an experiment to investigate different protocols for high pressure freezing.
DOI: 10.6084/m9.figshare.8014583
title: Artificial data - Probabilistic age sampling.xlsx

description: Artificial data spreadsheets representing the random sampling of ages from alluvial surfaces.
DOI: 10.6084/m9.figshare.8011544
title: ISS manual versus automatico.sav

description: Base de datos del artículo publicado en Plos One con doi:10.1371/journal.pone.0216206.