cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9275939
title: Nematofauna of red piranha Pygocentrus nattereri (Kner, 1958) (Characiformes: Serrasalmidae) from Amazonia, Brazil

description: Abstract Between March and October 2008, 355 specimens of Pygocentrus nattereri were collected from the lowland lakes of Central Amazonia, Brazil, to study their nematode fauna. A total of 1.116 specimens of Nematoda were collected, belonging to six species. Procamallanus (Spirocamallanus) inopinatus was the species with the highest parasite indices. Larvae of Anisakis sp. have zoonotic potential and were found parasitizing the intestine and liver of Pygocentrus nattereri. Some of these nematode species were new records for the host P. nattereri. The diversity of nematodes that use P. nattereri as a host indicates the important role of this fish species in the maintenance of these six nematode species in the lowland lakes of Central Amazonia.
DOI: 10.6084/m9.figshare.9275942.v1
title: Phylogeography of msp4 genotypes of Anaplasma marginale in beef cattle from the Brazilian Pantanal

description: Abstract The msp4 gene of A. marginale is unicodon, stable and mostly homogeneous, being considered as a useful marker for phylogeographic characterization of this bacterium. The objective of this work was to analyze the phylogeography of A. marginale based on the msp4 gene in beef cattle from the Brazilian Pantanal, compared to those found in other regions worldwide. The blood samples investigated were collected from 400 animals (200 cows and 200 calves) reared in five extensive breeding farms in this region. The results indicated that of the evaluated samples, 56.75% (227/400) were positive for A. marginale based on the msp1β gene by quantitatitve PCR (qPCR), while 8.37% (19/227) were positive for the msp4 gene in the conventional PCR. In the Network distance analysis, 14 sequences from the Brazilian Pantanal were grouped into a single group with those from Thailand, India, Spain, Colombia, Parana (Brazil), Mexico, Portugal, Argentina, China, Venezuela, Australia, Italy and Minas Gerais (Brazil). Among 68 sequences from Brazil and the world, 15 genotypes were present while genotype number one (#1) was the most distributed worldwide. Both Splitstree and network analyses showed that the A. marginale msp4 sequences detected in beef cattle from the Brazilian Pantanal showed low polymorphism, with the formation of one genogroup phylogenetically related to those found in ruminants from South and Central America, Europe, and Asia.
DOI: 10.6084/m9.figshare.9275936
title: Florid cemento-osseous dysplasia: a contraindication to orthodontic treatment in compromised areas

description: ABSTRACT Florid cemento-osseous dysplasia is a sclerosing disease that affects the mandible, especially the alveolar process, and that is, in most cases, bilateral; however, in some cases it affects up to three or even four quadrants. During the disease, normal bone is replaced with a thinly formed, irregularly distributed tissue peppered with radiolucent areas of soft tissue. Newly formed bone does not seem to invade periodontal space, but, in several images, it is confused with the roots, without, however, compromising pulp vitality or tooth position in the dental arch. There is no replacement resorption, not even when the images suggest dentoalveolar ankylosis. Orthodontists should make an accurate diagnosis when planning treatments, as this disease, when fully established, is one of the extremely rare situations in which orthodontic treatment is contraindicated. This contraindication is due to: (a) procedures such as the installment of mini-implants and mini-plaques, surgical maneuvers to apply traction to unerupted teeth and extractions should be avoided to prevent contamination of the affected bone with bacteria from the oral microbiota; and (b) tooth movement in the areas affected is practically impossible because of bone disorganization in the alveolar process, characterized by high bone density and the resulting cotton-wool appearance. Densely mineralized and disorganized bone is unable to remodel or develop in an organized way in the periodontal ligaments and the alveolar process. Organized bone remodeling is a fundamental phenomenon for tooth movement.
DOI: 10.6084/m9.figshare.9275939.v1
title: Nematofauna of red piranha Pygocentrus nattereri (Kner, 1958) (Characiformes: Serrasalmidae) from Amazonia, Brazil

description: Abstract Between March and October 2008, 355 specimens of Pygocentrus nattereri were collected from the lowland lakes of Central Amazonia, Brazil, to study their nematode fauna. A total of 1.116 specimens of Nematoda were collected, belonging to six species. Procamallanus (Spirocamallanus) inopinatus was the species with the highest parasite indices. Larvae of Anisakis sp. have zoonotic potential and were found parasitizing the intestine and liver of Pygocentrus nattereri. Some of these nematode species were new records for the host P. nattereri. The diversity of nematodes that use P. nattereri as a host indicates the important role of this fish species in the maintenance of these six nematode species in the lowland lakes of Central Amazonia.
DOI: 10.6084/m9.figshare.9275945.v1
title: IPCC Coupled Models (CMIP3-CMIP5) and the Southern Ocean Surface Temperature Anomaly Gradient (SST) in the Tropical Atlantic Ocean

description: Abstract This study investigated the sensitivity models coupled ocean-atmosphere of CMIP3 and CMIP5 for the period of 1979-1999 to simulate the magnitude of the meridional gradient of sea surface temperature anomalies (SST) in Atlantic Tropical. In the results are presented to comparative analyses for this meridional gradient of SST anomalies of two seasonal seasons (summer and autumn autrais). The results showed the evolution of the models in simulating the variations of SST anomalies of this gradient from CMIP3 to CMIP5. For CMIP3 the models did not good perform in both seasons. For the CMIP5 the summer presented the highest number of models with Willmott performance index (equal to or above the median ID ≥ 0.6).
DOI: 10.6084/m9.figshare.9275924
title: Dataset for: Computationally efficient inference for center effects based on restricted mean survival time

description: Restricted mean survival time (RMST) has gained increased attention in biostatistical and clinical studies. Directly modeling RMST (as opposed to modeling then transforming the hazard function) is appealing computationally and in terms of interpreting covariate effects. We propose computationally convenient methods for evaluating center effects based on RMST. A multiplicative model for the RMST is assumed. Estimation proceeds through an algorithm analogous to stratification, which permits the evaluation of thousands of centers. We derive the asymptotic properties of the proposed estimators, and evaluate finite sample performance through simulation. We demonstrate that considerable decreases in computational burden are achievable through the proposed methods, in terms of both storage requirements and run time. The methods are applied to evaluate more than 5,000 U.S. dialysis facilities using data from a national end-stage renal disease registry.
DOI: 10.6084/m9.figshare.9275927
title: MDR-TB data

description: This is the dataset for my MDR-TB study.
DOI: 10.6084/m9.figshare.9275936.v1
title: Florid cemento-osseous dysplasia: a contraindication to orthodontic treatment in compromised areas

description: ABSTRACT Florid cemento-osseous dysplasia is a sclerosing disease that affects the mandible, especially the alveolar process, and that is, in most cases, bilateral; however, in some cases it affects up to three or even four quadrants. During the disease, normal bone is replaced with a thinly formed, irregularly distributed tissue peppered with radiolucent areas of soft tissue. Newly formed bone does not seem to invade periodontal space, but, in several images, it is confused with the roots, without, however, compromising pulp vitality or tooth position in the dental arch. There is no replacement resorption, not even when the images suggest dentoalveolar ankylosis. Orthodontists should make an accurate diagnosis when planning treatments, as this disease, when fully established, is one of the extremely rare situations in which orthodontic treatment is contraindicated. This contraindication is due to: (a) procedures such as the installment of mini-implants and mini-plaques, surgical maneuvers to apply traction to unerupted teeth and extractions should be avoided to prevent contamination of the affected bone with bacteria from the oral microbiota; and (b) tooth movement in the areas affected is practically impossible because of bone disorganization in the alveolar process, characterized by high bone density and the resulting cotton-wool appearance. Densely mineralized and disorganized bone is unable to remodel or develop in an organized way in the periodontal ligaments and the alveolar process. Organized bone remodeling is a fundamental phenomenon for tooth movement.
DOI: 10.6084/m9.figshare.9275924.v1
title: Dataset for: Computationally efficient inference for center effects based on restricted mean survival time

description: Restricted mean survival time (RMST) has gained increased attention in biostatistical and clinical studies. Directly modeling RMST (as opposed to modeling then transforming the hazard function) is appealing computationally and in terms of interpreting covariate effects. We propose computationally convenient methods for evaluating center effects based on RMST. A multiplicative model for the RMST is assumed. Estimation proceeds through an algorithm analogous to stratification, which permits the evaluation of thousands of centers. We derive the asymptotic properties of the proposed estimators, and evaluate finite sample performance through simulation. We demonstrate that considerable decreases in computational burden are achievable through the proposed methods, in terms of both storage requirements and run time. The methods are applied to evaluate more than 5,000 U.S. dialysis facilities using data from a national end-stage renal disease registry.
DOI: 10.6084/m9.figshare.9275813
title: Supplementary materials for “GnRH3 regulates PGC proliferation and sex differentiation in developing zebrafish”

description: SDS-PAGE analysis of recombinant zebrafish GnRH3 protein. Time-lapse confocal observation of PGCs in the <i>TG1 </i>and <i>TG3 </i>embryo from shield stage to 24 hpf. Primers used in the present study.
DOI: 10.6084/m9.figshare.9275807
title: Data Set_Li JGR.xlsx

description: Four datasets are presented. The first is for Figure 2 of the manuscript. Data sets 2-4 are for Table 1 to Table 3 of the manuscript.
DOI: 10.6084/m9.figshare.9275807.v1
title: Data Set_Li JGR.xlsx

description: Four datasets are presented. The first is for Figure 2 of the manuscript. Data sets 2-4 are for Table 1 to Table 3 of the manuscript.
DOI: 10.6084/m9.figshare.9275813.v1
title: Supplementary materials for “GnRH3 regulates PGC proliferation and sex differentiation in developing zebrafish”

description: SDS-PAGE analysis of recombinant zebrafish GnRH3 protein. Time-lapse confocal observation of PGCs in the <i>TG1 </i>and <i>TG3 </i>embryo from shield stage to 24 hpf. Primers used in the present study.
DOI: 10.6084/m9.figshare.9275582
title: SREP-19-04226A Data.xlsx

description: Complete data sets for personality profiling, judgment bias testing and startle reflex testing as described in Ross et al., 2019, Welfare-improving enrichments greatly reduce hens’ startle responses, despite little change in judgment bias
DOI: 10.6084/m9.figshare.9275216
title: Diaz et al 2019 Supporting Mat R1.pdf

description: Supplemental material AJP L-00007-2019
DOI: 10.6084/m9.figshare.9275210
title: Data for Assessing Graph-based Deep Learning Models for Predicting Flash Point

description: Supporting information for the following paper: Assessing Graph-based Deep Learning Models for Predicting Flash Point, Xiaoyu Sun, Nathaniel J. Krakauer, Alexander Politowicz, Wei-Ting Chen, Qiying Li, Zuoyi Li, Xianjia Shao, Alfred Sunaryo, Mingren Shen, James Wang, D. Morgan, Submitted to Molecular Informatics (2019).<br><br>Please see paper and README file here for more information.<br>
DOI: 10.6084/m9.figshare.9275216.v1
title: Diaz et al 2019 Supporting Mat R1.pdf

description: Supplemental material AJP L-00007-2019
DOI: 10.6084/m9.figshare.9275156
title: Quantitation of stereocilia dimensions during C57BL/6 development

description: For analyzing length and width of apical IHC stereocilia during development, z-stack images of phalloidin-stained IHC stereocilia from cochleas of C57BL/6J mice were obtained using identical image acquisition parameters. Images were acquired on a ZEISS Elyra PS.1/LSM 710 Airyscan combination setup, using a 63x 1.4 NA Plan-Apochromat or a 100x 1.46 NA alpha Plan-Apochromat lens, integrated under ZEN 2.1 software. Raw data processing for Airyscan-acquired images was performed using manufacturer-implemented automated settings. At least 2-4 cochleas were used for developmental ages E18.5 (embryonic), P0.5, P4.5, P7.5, P10.5, P12.5, P15.5, P19.5 (post-natal). For each developmental age, images containing hair bundles that were upright were selected for generating x-z reslices (Fig. S1C) of stereocilia with the ‘Reslice’ function in Fiji. Reslices were chosen with views of stereocilia rows 1 and 2; we chose central stereocilia in most bundles. Stereocilia lengths were measured individually in Fiji by manually drawing a vertical line from the top of a stereocilium to the point of insertion in the cuticular plate. For measuring stereocilia widths, horizontal lines were manually drawn at 50% of the bundle height for both rows 1 and 2.
DOI: 10.6084/m9.figshare.9275168
title: Quantitation of stereocilia dimensions in transduction and Myo15a mutants

description: Transduction mutant length and width data.xlsx contains data for <i>Tmie</i> KO and <i>Tmc</i> DKO mice at P7.5 and P21.5.<br><br>sh2 length and width data.xlsx contains data for <i>Myo15a^sh2</i> mice at P8.5.<br><br><br>For analyzing length and width of apical IHC stereocilia of <i>Tmie</i>, <i>Tmc1;Tmc2 </i>and <i>Myo15a^sh2</i> mutant mice at P7.5 and P21.5, z-stack images of phalloidin-stained IHC stereocilia from cochleas of mutant mice were obtained using identical image acquisition parameters. Images were acquired on a ZEISS Elyra PS.1/LSM 710 Airyscan combination setup, using a 63x 1.4 NA Plan-Apochromat or a 100x 1.46 NA alpha Plan-Apochromat lens, integrated under ZEN 2.1 software. Raw data processing for Airyscan-acquired images was performed using manufacturer-implemented automated settings. At least 2-4 cochleas were used for each genotype. Images containing hair bundles that were upright were selected for generating x-z reslices of stereocilia with the ‘Reslice’ function in Fiji. Reslices were chosen with views of stereocilia rows 1 and 2; we chose central stereocilia in most bundles. Stereocilia lengths were measured individually in Fiji by manually drawing a vertical line from the top of a stereocilium to the point of insertion in the cuticular plate. For measuring stereocilia widths, horizontal lines were manually drawn at 50% of the bundle height for both rows 1 and 2.<br>
DOI: 10.6084/m9.figshare.9275144
title: U-net weights for CT lung segmentation (don't use these---we've updated)

description: U-net weights for human CT lung segmentation
DOI: 10.6084/m9.figshare.9275153
title: EC2_B105.nwb

description: The enclosed data is collected using a high-density 256-channel electrocorticography array implanted in a human patient during treatment for epilepsy. The subjects are reading aloud consonant-vowel syllables from a list. The data was collected by Dr. Edward Chang at the University of California, San Francisco, and curated by Ben Dichter.<br>Data is organized by subject ID, and each file is a continuous recording session in Neurodata Without Borders: Neurophysiology (NWB:N) 2.0 format. Voltage traces are included for each of the recorded 256 channels. Microphone signal was recorded at the time but is removed for HIPAA compliance. Detailed hand-marked annotations are provided which mark what syllable was said, and the times of the start, consonant-vowel transition, and end of each syllable. A rest-period time is also included when the subject was silent, which can be used as a baseline. Hand-marked anatomical labels are included for electrodes in the relevant brain regions. All dates have been removed for HIPAA compliance and replaced with Jan 1, 1900.
DOI: 10.6084/m9.figshare.9275132
title: EC2_B8.nwb

description: The enclosed data is collected using a high-density 256-channel electrocorticography array implanted in a human patient during treatment for epilepsy. The subjects are reading aloud consonant-vowel syllables from a list. The data was collected by Dr. Edward Chang at the University of California, San Francisco, and curated by Ben Dichter.<br>Data is organized by subject ID, and each file is a continuous recording session in Neurodata Without Borders: Neurophysiology (NWB:N) 2.0 format. Voltage traces are included for each of the recorded 256 channels. Microphone signal was recorded at the time but is removed for HIPAA compliance. Detailed hand-marked annotations are provided which mark what syllable was said, and the times of the start, consonant-vowel transition, and end of each syllable. A rest-period time is also included when the subject was silent, which can be used as a baseline. Hand-marked anatomical labels are included for electrodes in the relevant brain regions. All dates have been removed for HIPAA compliance and replaced with Jan 1, 1900.
DOI: 10.6084/m9.figshare.9275141
title: Quantitation of row 1 and 2 proteins during C57BL/6 development

description: Row 1 proteins.zip includes data for EPS8, MYO15A-S, GNAI3, and WHRN.<br>Row 2 proteins.zip includes data for CAPZB, TWF2, EPS8L2, and MYO15A-L.<br>We estimated the total immunofluorescence signal in the top 1-2 µm of each tip. Airyscan z-stacks were imported into Fiji, which was used for all analysis steps. For analysis of P0.5 and P7.5 C57BL/6J mice, average Z-projections of Airyscan stacks were made that included row 1 and row 2 tips in the same projection. For analysis of P15.5 and P21.5 C57BL/6J mice, separate Z-projections were made for row 1 and row 2 tips, using the same number of projected x-y slices per row. Regions of interest (ROIs) used circles that encompassed most of each tip. Area and average intensity measurements were made from ten or more row 1 tips and ten or more row 2 tips, and blank measurements were taken from volumes outside the stereocilia and above the epithelium. The total signal (area times average intensity) in each stereocilia tip volume was calculated after subtracting the background. For each hair bundle, the average signal in rows 1 and 2 was calculated, which was used to normalize the individual row 1 and row 2 stereocilia tip signals within each bundle. The average signal row 1 and 2 signal for each bundle was also used for comparison of expression levels at different developmental times. For developmental comparisons, the average signal in rows 1 and 2 for each bundle was normalized to the highest average value for the protein’s developmental series.<br>
DOI: 10.6084/m9.figshare.9275153.v1
title: EC2_B105.nwb

description: The enclosed data is collected using a high-density 256-channel electrocorticography array implanted in a human patient during treatment for epilepsy. The subjects are reading aloud consonant-vowel syllables from a list. The data was collected by Dr. Edward Chang at the University of California, San Francisco, and curated by Ben Dichter.<br>Data is organized by subject ID, and each file is a continuous recording session in Neurodata Without Borders: Neurophysiology (NWB:N) 2.0 format. Voltage traces are included for each of the recorded 256 channels. Microphone signal was recorded at the time but is removed for HIPAA compliance. Detailed hand-marked annotations are provided which mark what syllable was said, and the times of the start, consonant-vowel transition, and end of each syllable. A rest-period time is also included when the subject was silent, which can be used as a baseline. Hand-marked anatomical labels are included for electrodes in the relevant brain regions. All dates have been removed for HIPAA compliance and replaced with Jan 1, 1900.
DOI: 10.6084/m9.figshare.9275141.v1
title: Quantitation of row 1 and 2 proteins during C57BL/6 development

description: Row 1 proteins.zip includes data for EPS8, MYO15A-S, GNAI3, and WHRN.<br>Row 2 proteins.zip includes data for CAPZB, TWF2, EPS8L2, and MYO15A-L.<br>We estimated the total immunofluorescence signal in the top 1-2 µm of each tip. Airyscan z-stacks were imported into Fiji, which was used for all analysis steps. For analysis of P0.5 and P7.5 C57BL/6J mice, average Z-projections of Airyscan stacks were made that included row 1 and row 2 tips in the same projection. For analysis of P15.5 and P21.5 C57BL/6J mice, separate Z-projections were made for row 1 and row 2 tips, using the same number of projected x-y slices per row. Regions of interest (ROIs) used circles that encompassed most of each tip. Area and average intensity measurements were made from ten or more row 1 tips and ten or more row 2 tips, and blank measurements were taken from volumes outside the stereocilia and above the epithelium. The total signal (area times average intensity) in each stereocilia tip volume was calculated after subtracting the background. For each hair bundle, the average signal in rows 1 and 2 was calculated, which was used to normalize the individual row 1 and row 2 stereocilia tip signals within each bundle. The average signal row 1 and 2 signal for each bundle was also used for comparison of expression levels at different developmental times. For developmental comparisons, the average signal in rows 1 and 2 for each bundle was normalized to the highest average value for the protein’s developmental series.<br>
DOI: 10.6084/m9.figshare.9275132.v1
title: EC2_B8.nwb

description: The enclosed data is collected using a high-density 256-channel electrocorticography array implanted in a human patient during treatment for epilepsy. The subjects are reading aloud consonant-vowel syllables from a list. The data was collected by Dr. Edward Chang at the University of California, San Francisco, and curated by Ben Dichter.<br>Data is organized by subject ID, and each file is a continuous recording session in Neurodata Without Borders: Neurophysiology (NWB:N) 2.0 format. Voltage traces are included for each of the recorded 256 channels. Microphone signal was recorded at the time but is removed for HIPAA compliance. Detailed hand-marked annotations are provided which mark what syllable was said, and the times of the start, consonant-vowel transition, and end of each syllable. A rest-period time is also included when the subject was silent, which can be used as a baseline. Hand-marked anatomical labels are included for electrodes in the relevant brain regions. All dates have been removed for HIPAA compliance and replaced with Jan 1, 1900.
DOI: 10.6084/m9.figshare.9275144.v2
title: U-net weights for CT lung segmentation (don't use these---we've updated)

description: U-net weights for human CT lung segmentation
DOI: 10.6084/m9.figshare.9275048
title: Flat periwinkles SNPs before filtering (reference Lobt4ind)

description: Raw vcf file (zipped) containing SNPs for flat periwinkles after mapping the reads against the transcriptome reference assembled with data from four L. obtusata individuals (Lobt4ind)
DOI: 10.6084/m9.figshare.9275054
title: Flat periwinkles SNPs before filtering (pseudoreference)

description: Raw VCF file (zipped) containing SNPs for flat periwinkles after mapping the reads against the pseudoreference transcriptome
DOI: 10.6084/m9.figshare.9275144.v1
title: U-net weights for CT lung segmentation

description: U-net weights for human CT lung segmentation