cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12906086.v2
title: Molecular cloning, tissue expression and polymorphism analysis of the Caveolin-3 gene in ducks

description: 1. Duck meat is considered a delicacy, but choosing the best meat is problematic. Caveolin-3 (<i>CAV-3</i>) is a muscle-specific protein marker in animals. The goal of the current study was to detect the characteristics of <i>CAV-3</i> gene in ducks. 2. Full-length <i>CAV-3</i> was acquired from ducks (<i>Anas platyrhynchos)</i> using reverse transcriptase PCR and rapid amplification of cDNA ends. DNAMAN software was used for homology comparisons. Quantitative reverse transcription-PCR, PCR-single-strand conformation polymorphism, and sequencing were used to determine <i>CAV-3</i> expression and polymorphism of a single nucleotide, respectively. The study examined four types of ducks, including Jinding, Chaohu, Cherry Valley, and Gaoyou ducks. 3. The study acquired 1066 bp of <i>CAV-3</i> cDNA sequences, including a 456 bp complete open reading frame encoding 151 amino acids. Both coding sequences (CDSs) and translated amino acids exhibited highest homology with <i>Gallus gallus</i> (CDS homology 91.67%, amino acids 94.04%), followed by mammalian species (CDS homology 79.0%, amino acids 78.0%). Single nucleotide polymorphism analysis revealed five mutations in exons (A489G, G501A, A557G, T563A, and A602G), and a C805T mutation in an intron. Among amplified polymorphic loci detected using primer 2, allele frequency was higher for A (489A501G507A563T602A) than B (489G501G507G563T602C) or C (489G501A507G563A602C). The highest occurred in Cherry Valley ducks (0.7587). Using primer 4, the M allele frequency was higher than that of the N allele. <i>CAV-3</i> was most highly expressed in the heart, followed by skeletal muscles. Additionally, <i>CAV-3</i> had higher expression in heart and breast muscle of overfed Muscovy ducks than control ducks, but no difference was seen in thigh muscle. 4. <i>CAV-3</i> in ducks had the highest homology with Gallus gallus <i>CAV-3</i>, and it could be used as a marker for muscle quality in ducks.
DOI: 10.6084/m9.figshare.12906116
title: Effects of the <i>FABP4</i> gene on steroid hormone secretion in goose ovarian granulosa cells

description: 1. To investigate the physiological role of <i>FABP4</i> in the goose ovary, this study determined the effects of overexpressing and siRNA interfering FABP4 on progesterone (P<sub>4</sub>) and oestradiol (E<sub>2</sub>) production in granulosa cells. Measurements were made by ELISA, real-time qRT-PCR and western blotting. 2. The concentrations of P<sub>4</sub> and E<sub>2</sub> in the <i>FABP4</i> overexpression granulosa cells were increased compared to the control group (P &gt; 0.05 for P<sub>4</sub>; P 2). Likewise, the mRNA and protein expression levels of <i>CYP11A1</i> and <i>CYP19A1</i> were significantly higher than in the control group (P 4 and E<sub>2</sub> in the FABP4 silencing granulosa cells were significantly decreased compared with the control group (P CYP11A1 and <i>CYP19A1</i> were significantly lower than in the control group (P 3. The study indicated that the <i>FABP4</i> gene may regulate steroid hormone secretion and the expression of the steroidogenic genes in geese ovarian granulosa cells. These results support the possibility that the <i>FABP4</i> gene mediates ovarian steroid hormone biosynthesis function and reproduction in geese.
DOI: 10.6084/m9.figshare.12906116.v2
title: Effects of the <i>FABP4</i> gene on steroid hormone secretion in goose ovarian granulosa cells

description: 1. To investigate the physiological role of <i>FABP4</i> in the goose ovary, this study determined the effects of overexpressing and siRNA interfering FABP4 on progesterone (P<sub>4</sub>) and oestradiol (E<sub>2</sub>) production in granulosa cells. Measurements were made by ELISA, real-time qRT-PCR and western blotting. 2. The concentrations of P<sub>4</sub> and E<sub>2</sub> in the <i>FABP4</i> overexpression granulosa cells were increased compared to the control group (P &gt; 0.05 for P<sub>4</sub>; P 2). Likewise, the mRNA and protein expression levels of <i>CYP11A1</i> and <i>CYP19A1</i> were significantly higher than in the control group (P 4 and E<sub>2</sub> in the FABP4 silencing granulosa cells were significantly decreased compared with the control group (P CYP11A1 and <i>CYP19A1</i> were significantly lower than in the control group (P 3. The study indicated that the <i>FABP4</i> gene may regulate steroid hormone secretion and the expression of the steroidogenic genes in geese ovarian granulosa cells. These results support the possibility that the <i>FABP4</i> gene mediates ovarian steroid hormone biosynthesis function and reproduction in geese.
DOI: 10.6084/m9.figshare.12848044.v2
title: Molecular identification and characterisation of a novel chicken leukocyte immunoglobulin-like receptor A5

description: 1. Leukocyte immunoglobulin-like receptor A5 (LILRA5) is a key molecule that regulates the immune system. However, the <i>LILRA5</i> gene has not been characterised in avian species, including chickens. The present study aimed to identify and functionally characterise <i>LILRA5</i> identified from two genetically disparate chicken lines, <i>viz</i>., Marek’s disease (MD)-resistant (R) line 6.3 and MD-susceptible (S) line 7.2. 2. Multiple sequence alignment and phylogenetic analyses confirmed that the identity and similarity homologies of amino acids of LILRA5 in chicken lines 6.3 and 7.2 ranged between 93% and 93.7%, whereas those between chicken and mammals ranged between 20.9% and 43.7% and 21.1% to 43.9%, respectively. The newly cloned <i>LILRA5</i> from chicken lines 6.3 and 7.2 revealed high conservation and a close relationship with other known mammalian LILRA5 proteins. 3. The results indicated that LILRA5 from chicken lines 6.3 and 7.2 was associated with phosphorylation of Src kinases and protein tyrosine phosphatase non-receptor type 11 (SHP2), which play a regulatory role in immune functions. Moreover, the results demonstrated that <i>LILRA5</i> in these lines was associated with the activation of major histocompatibility complex (MHC) class I and β2-microglobulin and induced the expression of the transporter associated with antigen processing. In addition, <i>LILRA5</i> in both chicken lines activated and induced Janus kinase (JAK)–signal transducer and the activator of transcription (STAT), nuclear factor kappa B (NF-κB), phosphoinositide-3-kinase (PI3K)/protein kinase B (AKT) and the extracellular signal-regulated kinase (ERK)1/2 signalling pathways; toll-like receptors; and Th1-, Th2-, and Th17- cytokines. 4. The data suggested that LILRA5 has innate immune receptors essential for macrophage immune response and provide novel insights into the regulation of immunity and immunopathology.
DOI: 10.6084/m9.figshare.12848044
title: Molecular identification and characterisation of a novel chicken leukocyte immunoglobulin-like receptor A5

description: 1. Leukocyte immunoglobulin-like receptor A5 (LILRA5) is a key molecule that regulates the immune system. However, the <i>LILRA5</i> gene has not been characterised in avian species, including chickens. The present study aimed to identify and functionally characterise <i>LILRA5</i> identified from two genetically disparate chicken lines, <i>viz</i>., Marek’s disease (MD)-resistant (R) line 6.3 and MD-susceptible (S) line 7.2. 2. Multiple sequence alignment and phylogenetic analyses confirmed that the identity and similarity homologies of amino acids of LILRA5 in chicken lines 6.3 and 7.2 ranged between 93% and 93.7%, whereas those between chicken and mammals ranged between 20.9% and 43.7% and 21.1% to 43.9%, respectively. The newly cloned <i>LILRA5</i> from chicken lines 6.3 and 7.2 revealed high conservation and a close relationship with other known mammalian LILRA5 proteins. 3. The results indicated that LILRA5 from chicken lines 6.3 and 7.2 was associated with phosphorylation of Src kinases and protein tyrosine phosphatase non-receptor type 11 (SHP2), which play a regulatory role in immune functions. Moreover, the results demonstrated that <i>LILRA5</i> in these lines was associated with the activation of major histocompatibility complex (MHC) class I and β2-microglobulin and induced the expression of the transporter associated with antigen processing. In addition, <i>LILRA5</i> in both chicken lines activated and induced Janus kinase (JAK)–signal transducer and the activator of transcription (STAT), nuclear factor kappa B (NF-κB), phosphoinositide-3-kinase (PI3K)/protein kinase B (AKT) and the extracellular signal-regulated kinase (ERK)1/2 signalling pathways; toll-like receptors; and Th1-, Th2-, and Th17- cytokines. 4. The data suggested that LILRA5 has innate immune receptors essential for macrophage immune response and provide novel insights into the regulation of immunity and immunopathology.
DOI: 10.5281/zenodo.4003429
title: Experimental data on elastic modulus, thermal expansion, and pyrolysis shrinkage of Norway spruce under high temperature

description: Raw DMTA data on samples presented in the manuscript and MATLAB code of the Finite Difference simulation.
description: This work was supported by the Academy of Finland (Grant Number 297030).
DOI: 10.5281/zenodo.4003428
title: Experimental data on elastic modulus, thermal expansion, and pyrolysis shrinkage of Norway spruce under high temperature

description: Raw DMTA data on samples presented in the manuscript and MATLAB code of the Finite Difference simulation.
description: This work was supported by the Academy of Finland (Grant Number 297030).
DOI: 10.23641/asha.14403026
title: Standardized assessment for Jamaican DLLs (Wright Karem & Washington, 2021)

description: <b>Purpose:</b> The aim of this study was to investigate the appropriateness of standardized assessments of expressive grammar and vocabulary in a sample of preschool-age dual language learners (DLLs) who use Jamaican Creole (JC) and English. Adult models from the same linguistic community as these children were used to inform culturally and linguistically appropriate interpretation of children’s responses to a standardized assessment.<b>Method: </b>JC-English–speaking preschoolers (<i>n</i> = 176) and adults (<i>n</i> = 33) completed the Word Structure and Expressive Vocabulary subtests of the Clinical Evaluation of Language Fundamentals Preschool–Second Edition. Adults’ responses were used to develop an adapted scoring procedure that considered the influence of JC linguistic features on responses. DLLs’ responses scored using the standard English and adapted JC procedures were compared.<b>Results: </b>JC–English DLLs and adults used similar linguistic structures in response to subtest questions. DLLs’ scores differed significantly from the standardized sample on both subtests. Children received higher raw and corresponding standard scores with adapted scoring compared to standard scoring. Adapted scoring that made use of adult models yielded high classification accuracy at a rate of 93.8% for Word Structure and 92.1% for Expressive Vocabulary.<b>Conclusions: </b>Adapting standardized assessment scoring procedures using adult models may offer an ecologically valid approach to working with DLL preschoolers that can support a more accurate assessment of language functioning. These findings suggest that the use of standardized assessments for bilingual JC–English speakers requires a culturally responsive approach.<br><b>Supplemental Material S1.</b> Word Structure subtest alternate responses for Jamaican Creole-English speaking adults and children.<br><b>Supplemental Material S2. </b>Expressive Vocabulary Structure subtest alternate responses for Jamaican Creole-English speaking adults and children.<br>Wright Karem, R., & Washington, K. N. (2021). The cultural and diagnostic appropriateness of standardized assessments for dual language learners: A focus on Jamaican preschoolers. <i>Language, Speech, and Hearing Services in Schools.</i> Advance online publication. https://doi.org/10.1044/2021_LSHSS-20-00106
DOI: 10.23641/asha.14403026.v1
title: Standardized assessment for Jamaican DLLs (Wright Karem & Washington, 2021)

description: <b>Purpose:</b> The aim of this study was to investigate the appropriateness of standardized assessments of expressive grammar and vocabulary in a sample of preschool-age dual language learners (DLLs) who use Jamaican Creole (JC) and English. Adult models from the same linguistic community as these children were used to inform culturally and linguistically appropriate interpretation of children’s responses to a standardized assessment.<b>Method: </b>JC-English–speaking preschoolers (<i>n</i> = 176) and adults (<i>n</i> = 33) completed the Word Structure and Expressive Vocabulary subtests of the Clinical Evaluation of Language Fundamentals Preschool–Second Edition. Adults’ responses were used to develop an adapted scoring procedure that considered the influence of JC linguistic features on responses. DLLs’ responses scored using the standard English and adapted JC procedures were compared.<b>Results: </b>JC–English DLLs and adults used similar linguistic structures in response to subtest questions. DLLs’ scores differed significantly from the standardized sample on both subtests. Children received higher raw and corresponding standard scores with adapted scoring compared to standard scoring. Adapted scoring that made use of adult models yielded high classification accuracy at a rate of 93.8% for Word Structure and 92.1% for Expressive Vocabulary.<b>Conclusions: </b>Adapting standardized assessment scoring procedures using adult models may offer an ecologically valid approach to working with DLL preschoolers that can support a more accurate assessment of language functioning. These findings suggest that the use of standardized assessments for bilingual JC–English speakers requires a culturally responsive approach.<br><b>Supplemental Material S1.</b> Word Structure subtest alternate responses for Jamaican Creole-English speaking adults and children.<br><b>Supplemental Material S2. </b>Expressive Vocabulary Structure subtest alternate responses for Jamaican Creole-English speaking adults and children.<br>Wright Karem, R., & Washington, K. N. (2021). The cultural and diagnostic appropriateness of standardized assessments for dual language learners: A focus on Jamaican preschoolers. <i>Language, Speech, and Hearing Services in Schools.</i> Advance online publication. https://doi.org/10.1044/2021_LSHSS-20-00106
DOI: 10.5281/zenodo.4734997
title: Pragmatic prediction in the processing of referring expressions containing scalar quantifiers

description: Data and analysis scripts pertaining to a study by Macuch Silva & Franke (submitted).
DOI: 10.5281/zenodo.4735540
title: Brienomyrus longianalis SPAdes assembly

description: .
DOI: 10.5281/zenodo.4735539
title: Brienomyrus longianalis SPAdes assembly

description: .
DOI: 10.6073/pasta/89e8189093392325ee139eccc6b2ff85
title: Time-lapse camera (phenocam) imagery of Sensor Network plots from 2017 to ongoing

description: Images from time-lapse cameras were analyzed to track the greenness curves of 16 plots in the Sensor Network at Niwot Ridge. Images were taken every 30 minutes during daylight hours throughout the growing season. Cameras were angled to view 1m^2 vegetation plots located at each sensor node. Pixels in the portion of the image capturing the vegetation plot were used to calculate the green chromatic coordinate (GCC). The change in GCC over the growing season represents the growth and phenology of the plant communities captured.
DOI: 10.5281/zenodo.4735549
title: Callirhytis valhalla SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735548
title: Callirhytis valhalla SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735557
title: Campylomormyrus numenius SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735556
title: Campylomormyrus numenius SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735561
title: Carybdea marsupialis auct. non (Linnaeus, 1758) SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735560
title: Carybdea marsupialis auct. non (Linnaeus, 1758) SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735566
title: Dependency Smells in JavaScript Projects

description: This is the replication package for our paper on dependency smells. Here is a short description of what is contained in this package: <strong>Code</strong> This folder contains the code used for extracting, parsing, and analyzing the smells in the dataset, along with statistical analyses. The "parser.py" parses the project information (such as package.json) and prepares them in the databases. The "analyzer.py" file is responsible for the majority of the empirical analyses. <strong>Datasets</strong> This folder contains the intermediate datasets created and used in our analyses. The "smelldataset.db" file contains all smelly and clean dependencies for the latest snapshot. The "smell_counts.csv" file contains smells statistics for the projects in our dataset. The "changehistory.db" file contains the historical smell statistics for a period of 5 years. The code also requires the GhTorrent Dataset available at: https://ghtorrent.org/downloads.html. <strong>Survey Questionnaires and Responses</strong> These two folders contain the full set of questions that we asked the developers in our surveys along with the responses for survey 2. <strong>Tool</strong> This is the published tool which is also available at: https://github.com/abbasjavan/DependencySniffer <strong>Visualization Scripts</strong> This folder contains the scripts used to create the figures for the paper.
DOI: 10.5281/zenodo.4701497
title: Dependency Smells in JavaScript Projects

description: This is the replication package for our paper on dependency smells. Here is a short description of what is contained in this package: <strong>Code</strong> This folder contains the code used for extracting, parsing, and analyzing the smells in the dataset, along with statistical analyses. The "parser.py" parses the project information (such as package.json) and prepares them in the databases. The "analyzer.py" file is responsible for the majority of the empirical analyses. <strong>Datasets</strong> This folder contains the intermediate datasets created and used in our analyses. The "smelldataset.db" file contains all smelly and clean dependencies for the latest snapshot. The "smell_counts.csv" file contains smells statistics for the projects in our dataset. The "changehistory.db" file contains the historical smell statistics for a period of 5 years. The code also requires the GhTorrent Dataset available at: https://ghtorrent.org/downloads.html. <strong>Survey Questionnaires and Responses</strong> These two folders contain the full set of questions that we asked the developers in our surveys along with the responses for survey 2. <strong>Tool</strong> This is the published tool which is also available at: https://github.com/abbasjavan/DependencySniffer <strong>Visualization Scripts</strong> This folder contains the scripts used to create the figures for the paper.
DOI: 10.5281/zenodo.4735572
title: Chaetosphaerella phaeostroma SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735571
title: Chaetosphaerella phaeostroma SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735015
title: Output data for "Deep learned process parameterizations provide better representations of turbulent heat fluxes in hydrologic models"

description: This contains all of the processed/merged output from the simulations for the paper "Deep learned process parameterizations provide better representations of turbulent heat fluxes in hydrologic models", submitted to WRR.
DOI: 10.5281/zenodo.4735014
title: Output data for "Deep learned process parameterizations provide better representations of turbulent heat fluxes in hydrologic models"

description: This contains all of the processed/merged output from the simulations for the paper "Deep learned process parameterizations provide better representations of turbulent heat fluxes in hydrologic models", submitted to WRR.
DOI: 10.6084/m9.figshare.12827615
title: TMS gene data (final)

description: The data for the TMS gene analysis accompanying the paper "Mouse Aging Cell Atlas Analysis Reveals Global and Cell Type Specific Aging Signatures", eLife, 2021.
DOI: 10.5281/zenodo.4735579
title: Charaxes varanes SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735578
title: Charaxes varanes SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735581
title: Chitala chitala SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735580
title: Chitala chitala SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735584
title: Chrysaora achlyos SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735583
title: Chrysaora achlyos SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735588
title: Chrysaora chesapeakei SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735587
title: Chrysaora chesapeakei SPAdes preassembly

description: .
DOI: 10.6084/m9.figshare.11891430
title: Evaluation on microwave drying of waste paper towel with multi-magnetron and mode stirrer

description: The thin-layer drying performance for a typical solid waste (paper towel) was evaluated at hot air temperatures of 90–130 °C (0.5 m/s air velocity) and microwave powers of 200–800 W in a bench-scale microwave combined convective drying setup. Influences of hot air and radiation modes (multi-magnetron and mode stirrer) on the temperature distribution uniformity were examined. The effective moisture diffusivities of sample during pure hot air drying ranged from 6.07 × 10<sup>−9</sup> to 1.31 × 10<sup>−8</sup> m<sup>2</sup>/s, while those for pure microwave drying were from 3.54 × 10<sup>−8</sup> to 1.52 × 10<sup>−7</sup> m<sup>2</sup>/s. The apparent activation energy of sample in pure hot air drying was estimated as 23.17 kJ/mol, while that for pure microwave drying was 22.64 W/g. The effective moisture diffusivities of sample in combined drying ranged from 5.71 × 10<sup>−8</sup> to 2.05 × 10<sup>−7</sup> m<sup>2</sup>/s. The heating uniformity for microwave was improved effectively by the combined drying. The application of the mode stirrers and multi-magnetron radiation modes further improved the microwave heating uniformity. Midilli model can well describe moisture content of paper towel over time.
DOI: 10.6084/m9.figshare.11891430.v1
title: Evaluation on microwave drying of waste paper towel with multi-magnetron and mode stirrer

description: The thin-layer drying performance for a typical solid waste (paper towel) was evaluated at hot air temperatures of 90–130 °C (0.5 m/s air velocity) and microwave powers of 200–800 W in a bench-scale microwave combined convective drying setup. Influences of hot air and radiation modes (multi-magnetron and mode stirrer) on the temperature distribution uniformity were examined. The effective moisture diffusivities of sample during pure hot air drying ranged from 6.07 × 10<sup>−9</sup> to 1.31 × 10<sup>−8</sup> m<sup>2</sup>/s, while those for pure microwave drying were from 3.54 × 10<sup>−8</sup> to 1.52 × 10<sup>−7</sup> m<sup>2</sup>/s. The apparent activation energy of sample in pure hot air drying was estimated as 23.17 kJ/mol, while that for pure microwave drying was 22.64 W/g. The effective moisture diffusivities of sample in combined drying ranged from 5.71 × 10<sup>−8</sup> to 2.05 × 10<sup>−7</sup> m<sup>2</sup>/s. The heating uniformity for microwave was improved effectively by the combined drying. The application of the mode stirrers and multi-magnetron radiation modes further improved the microwave heating uniformity. Midilli model can well describe moisture content of paper towel over time.
DOI: 10.6084/m9.figshare.14403776
title: Dataset S1 for "Spotted lanternfly nymphs use multiple righting behaviors during landing"

description: R-code, Matlab scripts and data required to generate statistics and fits.<br>
DOI: 10.6084/m9.figshare.14403776.v1
title: Dataset S1 for "Spotted lanternfly nymphs use multiple righting behaviors during landing"

description: R-code, Matlab scripts and data required to generate statistics and fits.<br>