cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5454838.v1
title: Risk of chemotherapy-induced febrile neutropenia by day of pegfilgrastim prophylaxis in US clinical practice from 2010-2015

description: <b>Objective:</b> Pegfilgrastim prophylaxis (PP) is recommended 1-3 days following administration of chemotherapy during the cycle. Some patients, however, receive PP before or after the recommended timing. While evidence suggests that risk of febrile neutropenia (FN) may be lower when PP is administered per recommendation, such evidence is based on older data. We undertook a new study to compare FN risk between patients who received PP on the last day of chemotherapy (“Day 0”) or 4-5 days following chemotherapy (“Days 4-5”), versus 1-3 days following chemotherapy (“Days 1-3”), using recent data from US clinical practice. <b>Methods:</b> A retrospective cohort design and data from two US private healthcare claims repositories (2010-2016) were employed. Patients received intermediate/high-risk chemotherapy regimens for solid tumors or non-Hodgkin’s lymphoma, and PP in ≥1 cycle; all cycles with PP were pooled for analyses. Adjusted odds ratios (OR) for FN during the cycle were estimated for patients who received PP on Day 0 or Days 4-5, vs. Days 1-3, using generalized estimating equations. <b>Results:</b> The study population included 53,814 patients who received PP in 217,273 cycles; in 9% of cycles, patients received PP on Day 0 (8%) or Days 4-5 (&lt;1%). Odds of FN in cycle 1 were significantly higher among patients receiving PP on Day 0 (OR: 1.4 [95%CI: 1.2 - 1.7]) or Days 4-5 (1.9 [1.2 - 3.0]), vs. Days 1-3, in that cycle. Results for subsequent cycles of chemotherapy were comparable to those for the first cycle. <b>Conclusions:</b> In this large-scale retrospective evaluation of cancer chemotherapy patients receiving PP in recent US clinical practice, PP was administered before or after the recommended timing in 9% of cycles. FN incidence was significantly higher in these cycles providing additional real-world evidence that PP should be administered the day after chemotherapy in alignment with recently updated US practice guidelines.
DOI: 10.6084/m9.figshare.5454844.v1
title: Risk of chemotherapy-induced febrile neutropenia with early discontinuation of pegfilgrastim prophylaxis based on real-world data from 2010-2015

description: <b>Objective:</b> Evidence suggests that not all cancer chemotherapy patients who receive first-cycle pegfilgrastim prophylaxis (PP) continue to receive it in later cycles, and that these patients may be subsequently at higher risk of febrile neutropenia (FN). Available evidence, however, may not be reflective of current clinical practice. We undertook an evaluation to estimate the odds of FN, beginning with second chemotherapy cycle, among patients who received PP in that cycle and all previous cycles versus those who received PP in all previous cycles only, using recent real-world data. <b>Methods:</b> A matched-cohort design and data from two US healthcare claims repositories (2010-2015) were employed. Source population comprised cancer patients who received intermediate/high-risk chemotherapy and first-cycle PP. From source population, beginning with second cycle, all patients who received PP in all previous cycles were identified. From this subset, patients who did not receive PP in the cycle of interest (“comparison patients”) were matched to those who received PP in that cycle (“PP patients”); same process was repeated for subsequent cycles. Odds ratios (OR) for FN (broad and narrow definitions) were estimated using generalized estimating equations. <b>Results:</b> Among 47,254 patients in source population, 9% did not receive second-cycle PP and were matched to those who did. FN odds in cycle 2 were significantly higher among comparison patients versus PP patients (OR [broad definition]: 1.7, p <b>Conclusions:</b> In this real-world evaluation of cancer chemotherapy patients who received first-cycle PP, FN risk was substantially higher among patients who did not receive PP in subsequent cycles versus those who continued PP.
DOI: 10.6084/m9.figshare.5454553
title: Output (log and trees) files from BEAST analysis

description: This set contains all log and trees files for the 4 independent MCMC runs that were undertaken for Bayesian inference.
DOI: 10.6084/m9.figshare.5454541
title: Time-to-death approach to reveal chronic and cumulative toxicity of a fungicide for honeybees not revealed with the standard ten-day test.

description: Full analysis and raw data of the following paper :<br><br> Simon-Delso, N., San Martin, G., Bruneau, E., Hautier, L., 2018. Time-to-death approach to reveal chronic and cumulative toxicity of a fungicide for honeybees not revealed with the standard ten-day test. Scientific Reports 8, 7241. https://doi.org/10.1038/s41598-018-24746-9 <br>Summary of the paper : <br><br>Synthetic fungicides are pesticides widely used in agriculture to control phytopathogenic fungi. The systemicity, persistency and intense application of some of these fungicides, such as boscalid, leads to long periods of exposure for honeybees via contaminated water, pollen and nectar. We exposed adult honeybees in the lab to food contaminated with boscalid for 33 days instead of the standard 10-day test. Most of the toxic effects were observed after 10 days. The median time to death (LT<sub>50</sub>) ranged from 24.9 days (lowest concentration) to 7.1 days (highest concentration) and was significantly shorter in all cases than with the control (32.0 days). The concentration and dietary doses of boscalid inducing 50% mortality (LC<sub>50</sub> and LDD<sub>50</sub>, respectively) decreased strongly with the time of exposure: LC<sub>50</sub> = 14,729 and 1,174 mg/l and LDD<sub>50</sub> = 0.318 and 0.0301 mg bee<sup>−1</sup> day<sup>−1</sup> at days 8 and 25, respectively. We found evidence of reinforced toxicity when exposure is prolonged, but with an unusual pattern: no cumulative toxicity is observed until 17–18 days, when a point of inflexion appears that suggests a reduced capacity of bees to deal with the toxicant. Our results show the importance of time-to-death experiments rather than fixed-duration studies for evaluating chronic toxicity.<br><sup></sup>
DOI: 10.6084/m9.figshare.5454547
title: Haelewaters-Camacho_phyllostomidae_beast.xml

description: The XML file created for Bayesian inference for Camacho et al.
DOI: 10.6084/m9.figshare.5454538
title: 2015.iii.26_phyllostomidae-nine-gene-dataset.nex

description: The aligned nine-gene dataset used for phylogenetic analyses in Camacho et al.
DOI: 10.6084/m9.figshare.5454547.v1
title: Haelewaters-Camacho_phyllostomidae_beast.xml

description: The XML file created for Bayesian inference for Camacho et al.
DOI: 10.6084/m9.figshare.5454553.v1
title: Output (log and trees) files from BEAST analysis

description: This set contains all log and trees files for the 4 independent MCMC runs that were undertaken for Bayesian inference.
DOI: 10.6084/m9.figshare.5454526
title: Dataset for: Bayesian monotonic errors-in-variables models with applications to pathogen susceptibility testing

description: Drug dilution (MIC) and disk diffusion (DIA) are the two most common antimicrobial susceptibility assays used by hospitals and clinics to determine an unknown pathogen's susceptibility to various antibiotics. Since only one assay is commonly used, it is important that the two assays give similar results. Calibration of the DIA assay to the MIC assay is typically done using the error-rate bounded method, which selects DIA breakpoints that minimize the observed discrepancies between the two assays. In 2000, Craig proposed a model-based approach that specifically models the measurement error and rounding processes of each assay, the underlying pathogen distribution, and the true monotonic relationship between the two assays. The two assays are then calibrated by focusing on matching the probabilities of correct classification (susceptible, indeterminant, and resistant). This approach results in greater precision and accuracy for estimating DIA breakpoints. In this paper, we expand the flexibility of the model-based method by introducing a Bayesian four-parameter logistic model (extending Craig's original three-parameter model) as well as a Bayesian nonparametric spline model to describe the relationship between the two assays. We propose two ways to handle spline knot selection, considering many equally-spaced knots but restricting overfitting via a random walk prior and treating the number and location of knots as additional unknown parameters. We demonstrate the two approaches via a series of simulation studies and apply the methods to two real data sets.
DOI: 10.6084/m9.figshare.5454514
title: Dataset for: Sustained cell body reactivity and loss of NeuN in a subset of axotomized bulbospinal neurons after a chronic high cervical spinal cord injury.

description: Following central nervous system lesion, the ability of injured axons to regrowth may depend on the level and duration of the injured cell body response (CBR). Therefore, in order to investigate whether axotomized brainstem neurons maintain a durable growth-competent state after spinal cord injury, we studied the effect of a chronic C2 hemisection in rats on the expression of various CBR markers involved in axon regeneration, such as c-Jun, ATF-3, HSP27, NO synthase (NOS), and also of the neural mature phenotype marker NeuN, in the bulbospinal respiratory neurons as compared to the Gigantocellularis nucleus. Both at 7 and 30 days post-lesion (DPL), c-Jun and HSP27 were present in respectively ~60% and ~20% of the axotomized respiratory neurons, whereas the apoptotic factor caspase 3 was not detected in these cells. NOS appeared belatedly and it was detected in ~20% of the axotomized respiratory neurons at 30DPL. At 30DPL, these different CBR markers were strongly colocalized in a sub-population of axotomized respiratory neurons and also in a sub-population of injured neurons within the gigantocellularis nucleus. Such CBR was also accompanied by a sustained alteration of the neural mature phenotype, as indicated by a loss of NeuN immunoreactivity selectively in HSP27+ bulbospinal neurons at 7DPL and 30DPL. Altogether, this study shows that a subset of axotomized medullary respiratory neurons remains in a growth-competent state after a chronic injury, suggesting that they may play a preferential role in long-lasting respiratory neuroplasticity processes.
DOI: 10.6084/m9.figshare.5454541.v2
title: Time-to-death approach to reveal chronic and cumulative toxicity of a fungicide for honeybees not revealed with the standard ten-day test.

description: Full analysis and raw data of the following paper :<br><br> Simon-Delso, N., San Martin, G., Bruneau, E., Hautier, L., 2018. Time-to-death approach to reveal chronic and cumulative toxicity of a fungicide for honeybees not revealed with the standard ten-day test. Scientific Reports 8, 7241. https://doi.org/10.1038/s41598-018-24746-9 <br>Summary of the paper : <br><br>Synthetic fungicides are pesticides widely used in agriculture to control phytopathogenic fungi. The systemicity, persistency and intense application of some of these fungicides, such as boscalid, leads to long periods of exposure for honeybees via contaminated water, pollen and nectar. We exposed adult honeybees in the lab to food contaminated with boscalid for 33 days instead of the standard 10-day test. Most of the toxic effects were observed after 10 days. The median time to death (LT<sub>50</sub>) ranged from 24.9 days (lowest concentration) to 7.1 days (highest concentration) and was significantly shorter in all cases than with the control (32.0 days). The concentration and dietary doses of boscalid inducing 50% mortality (LC<sub>50</sub> and LDD<sub>50</sub>, respectively) decreased strongly with the time of exposure: LC<sub>50</sub> = 14,729 and 1,174 mg/l and LDD<sub>50</sub> = 0.318 and 0.0301 mg bee<sup>−1</sup> day<sup>−1</sup> at days 8 and 25, respectively. We found evidence of reinforced toxicity when exposure is prolonged, but with an unusual pattern: no cumulative toxicity is observed until 17–18 days, when a point of inflexion appears that suggests a reduced capacity of bees to deal with the toxicant. Our results show the importance of time-to-death experiments rather than fixed-duration studies for evaluating chronic toxicity.<br><sup></sup>
DOI: 10.6084/m9.figshare.5454514.v1
title: Dataset for: Sustained cell body reactivity and loss of NeuN in a subset of axotomized bulbospinal neurons after a chronic high cervical spinal cord injury.

description: Following central nervous system lesion, the ability of injured axons to regrowth may depend on the level and duration of the injured cell body response (CBR). Therefore, in order to investigate whether axotomized brainstem neurons maintain a durable growth-competent state after spinal cord injury, we studied the effect of a chronic C2 hemisection in rats on the expression of various CBR markers involved in axon regeneration, such as c-Jun, ATF-3, HSP27, NO synthase (NOS), and also of the neural mature phenotype marker NeuN, in the bulbospinal respiratory neurons as compared to the Gigantocellularis nucleus. Both at 7 and 30 days post-lesion (DPL), c-Jun and HSP27 were present in respectively ~60% and ~20% of the axotomized respiratory neurons, whereas the apoptotic factor caspase 3 was not detected in these cells. NOS appeared belatedly and it was detected in ~20% of the axotomized respiratory neurons at 30DPL. At 30DPL, these different CBR markers were strongly colocalized in a sub-population of axotomized respiratory neurons and also in a sub-population of injured neurons within the gigantocellularis nucleus. Such CBR was also accompanied by a sustained alteration of the neural mature phenotype, as indicated by a loss of NeuN immunoreactivity selectively in HSP27+ bulbospinal neurons at 7DPL and 30DPL. Altogether, this study shows that a subset of axotomized medullary respiratory neurons remains in a growth-competent state after a chronic injury, suggesting that they may play a preferential role in long-lasting respiratory neuroplasticity processes.
DOI: 10.6084/m9.figshare.5454526.v1
title: Dataset for: Bayesian monotonic errors-in-variables models with applications to pathogen susceptibility testing

description: Drug dilution (MIC) and disk diffusion (DIA) are the two most common antimicrobial susceptibility assays used by hospitals and clinics to determine an unknown pathogen's susceptibility to various antibiotics. Since only one assay is commonly used, it is important that the two assays give similar results. Calibration of the DIA assay to the MIC assay is typically done using the error-rate bounded method, which selects DIA breakpoints that minimize the observed discrepancies between the two assays. In 2000, Craig proposed a model-based approach that specifically models the measurement error and rounding processes of each assay, the underlying pathogen distribution, and the true monotonic relationship between the two assays. The two assays are then calibrated by focusing on matching the probabilities of correct classification (susceptible, indeterminant, and resistant). This approach results in greater precision and accuracy for estimating DIA breakpoints. In this paper, we expand the flexibility of the model-based method by introducing a Bayesian four-parameter logistic model (extending Craig's original three-parameter model) as well as a Bayesian nonparametric spline model to describe the relationship between the two assays. We propose two ways to handle spline knot selection, considering many equally-spaced knots but restricting overfitting via a random walk prior and treating the number and location of knots as additional unknown parameters. We demonstrate the two approaches via a series of simulation studies and apply the methods to two real data sets.
DOI: 10.6084/m9.figshare.5454538.v1
title: 2015.iii.26_phyllostomidae-nine-gene-dataset.nex

description: The aligned nine-gene dataset used for phylogenetic analyses in Camacho et al.
DOI: 10.6084/m9.figshare.5454541.v1
title: Chronic toxicity of the fungicide boscalid on honey bees

description: Full analysis and raw data of the following paper :<br><br> Simon-Delso, N., San Martin, G., Bruneau, E., Hautier, L., 2018. Time-to-death approach to reveal chronic and cumulative toxicity of a fungicide for honeybees not revealed with the standard ten-day test. Scientific Reports 8, 7241. https://doi.org/10.1038/s41598-018-24746-9 <br>Summary of the paper : <br><br>Synthetic fungicides are pesticides widely used in agriculture to control phytopathogenic fungi. The systemicity, persistency and intense application of some of these fungicides, such as boscalid, leads to long periods of exposure for honeybees via contaminated water, pollen and nectar. We exposed adult honeybees in the lab to food contaminated with boscalid for 33 days instead of the standard 10-day test. Most of the toxic effects were observed after 10 days. The median time to death (LT<sub>50</sub>) ranged from 24.9 days (lowest concentration) to 7.1 days (highest concentration) and was significantly shorter in all cases than with the control (32.0 days). The concentration and dietary doses of boscalid inducing 50% mortality (LC<sub>50</sub> and LDD<sub>50</sub>, respectively) decreased strongly with the time of exposure: LC<sub>50</sub> = 14,729 and 1,174 mg/l and LDD<sub>50</sub> = 0.318 and 0.0301 mg bee<sup>−1</sup> day<sup>−1</sup> at days 8 and 25, respectively. We found evidence of reinforced toxicity when exposure is prolonged, but with an unusual pattern: no cumulative toxicity is observed until 17–18 days, when a point of inflexion appears that suggests a reduced capacity of bees to deal with the toxicant. Our results show the importance of time-to-death experiments rather than fixed-duration studies for evaluating chronic toxicity.<br><sup></sup>
DOI: 10.6084/m9.figshare.5454388
title: Risk-factors for nodular hyperplasia of parathyroid glands in sHPT patients (PlosOne Paper)

description: minimal data set<br>
DOI: 10.6084/m9.figshare.5454289
title: Craig2017rawDataAndCode

description: raw data & code for Craig 2017 (PNAS). All code is written in matlab. <br>Raw data events are indexed according to event number. Within each event is the raw data and a list of the experimental conditions. Also included is a readMe describing the data. <br>Analysis is run from the central script hel308stepScript2.mat.
DOI: 10.6084/m9.figshare.5454388.v1
title: Risk-factors for nodular hyperplasia of parathyroid glands in sHPT patients (PlosOne Paper)

description: minimal data set<br>
DOI: 10.6084/m9.figshare.5451124
title: Genomic selection

description: Genomic selection for resistance against <i>Piscirickettsia salmonis</i><i> </i>in rainbow trout
DOI: 10.6084/m9.figshare.5451094
title: Untitled Item

description: Presentation slidedeck for SAGE Libraries talk on Tips for Student Success with Data.<br>
DOI: 10.6084/m9.figshare.5451124.v1
title: Genomic selection

description: Genomic selection for resistance against <i>Piscirickettsia salmonis</i><i> </i>in rainbow trout
DOI: 10.6084/m9.figshare.5451058
title: BHATIA FIGURE CORRIGENDUM

description: data for corrigendum
DOI: 10.6084/m9.figshare.5451058.v1
title: BHATIA FIGURE CORRIGENDUM

description: data for corrigendum
DOI: 10.6084/m9.figshare.5451379
title: Statistical supplement to: Biomechanics of the peafowl’s crest reveals frequencies tuned to social displays

description: Data and figures on peafowl crest feather vibration and mechanical properties. This fileset includes the data, R scripts, Matlab scripts, and figure files necessary to reproduce the figures and analysis.
DOI: 10.6084/m9.figshare.5451034
title: OpenCitations Corpus dataset of all the resource embodiments, archived on 2017-09-25

description: This archive contains the dump of the OpenCitations Corpus (OCC, http://opencitations.net) dataset about resource embodiments, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.
DOI: 10.6084/m9.figshare.5451016
title: OpenCitations Corpus dataset of all the agent roles, archived on 2017-09-25

description: This archive contains the dump of the OpenCitations Corpus (OCC, http://opencitations.net) dataset about author roles, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.
DOI: 10.6084/m9.figshare.5451019
title: OpenCitations Corpus provenance data of all the identifiers, archived on 2017-09-25

description: This archive contains the dump of the OpenCitations Corpus (OCC, http://opencitations.net) provenance data about identifiers, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.
DOI: 10.6084/m9.figshare.5451034.v1
title: OpenCitations Corpus dataset of all the resource embodiments, archived on 2017-09-25

description: This archive contains the dump of the OpenCitations Corpus (OCC, http://opencitations.net) dataset about resource embodiments, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.
DOI: 10.6084/m9.figshare.5451019.v1
title: OpenCitations Corpus provenance data of all the identifiers, archived on 2017-09-25

description: This archive contains the dump of the OpenCitations Corpus (OCC, http://opencitations.net) provenance data about identifiers, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.