cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3102451.v2
title: Characterisation of caecum and crop microbiota of Indian indigenous chicken targeting multiple hypervariable regions within 16S rRNA gene

description: A comparative analysis of caecum and crop microbiota of chick, grower and adult stages of Indian indigenous chickens was conducted to investigate the role of the microbiota of the gastrointestinal tract, which play an important role in host performance, health and immunity.High-throughput Illumina sequencing was performed for V3, V4 and V4-V6 hypervariable regions of the 16S rRNA gene. M5RNA and M5NR databases under MG-RAST were used for metagenomic datasets annotation.In the crop, <i>Firmicutes</i> (~78%) and <i>Proteobacteria</i> (~16%) were the predominant phyla whereas in the caecum, <i>Firmicutes</i> (~50%), <i>Bacteroidetes</i> (~29%) and <i>Actinobacteria</i> (~10%) were predominant. The Shannon-Wiener diversity index suggested that sample richness and diversity increased as the chicken aged.For the first time, the presence of <i>Lactobacillus</i> species such as <i>L. frumenti, L. antri, L. mucosae</i> in the chicken crop along with <i>Kineococcus radiotolerans, Desulfohalobium retbaense</i> and <i>L. jensenii</i> in the caecum are reported. Many of these bacterial species have been found to be involved in immune response modulation and disease prevention in pigs and humans. The gut microbiome of the indigenous chicken was enriched with microbes having probiotic potential which might be essential for their adaptability. A comparative analysis of caecum and crop microbiota of chick, grower and adult stages of Indian indigenous chickens was conducted to investigate the role of the microbiota of the gastrointestinal tract, which play an important role in host performance, health and immunity. High-throughput Illumina sequencing was performed for V3, V4 and V4-V6 hypervariable regions of the 16S rRNA gene. M5RNA and M5NR databases under MG-RAST were used for metagenomic datasets annotation. In the crop, <i>Firmicutes</i> (~78%) and <i>Proteobacteria</i> (~16%) were the predominant phyla whereas in the caecum, <i>Firmicutes</i> (~50%), <i>Bacteroidetes</i> (~29%) and <i>Actinobacteria</i> (~10%) were predominant. The Shannon-Wiener diversity index suggested that sample richness and diversity increased as the chicken aged. For the first time, the presence of <i>Lactobacillus</i> species such as <i>L. frumenti, L. antri, L. mucosae</i> in the chicken crop along with <i>Kineococcus radiotolerans, Desulfohalobium retbaense</i> and <i>L. jensenii</i> in the caecum are reported. Many of these bacterial species have been found to be involved in immune response modulation and disease prevention in pigs and humans. The gut microbiome of the indigenous chicken was enriched with microbes having probiotic potential which might be essential for their adaptability.
DOI: 10.6084/m9.figshare.3102451.v1
title: Characterization of caecum and crop microbiota of Indian indigenous chicken targeting multiple hypervariable regions within 16s rRNA gene

description: 1. A comparative analysis of caecum and crop microbiota of chick, grower and adult stages of Indian indigenous chickens was conducted to investigate the role of the microbiota of the gastrointestinal tract play an important role in host performance, health and immunity. 2. High-throughput Illumina sequencing was performed for V3, V4, and V4-V6 hypervariable regions of the 16S rRNA gene. M5RNA and M5NR databases under MG-RAST were used for metagenomic datasets annotation. 3. In the crop, <i>Firmicutes</i> (~78 %) and <i>Proteobacteria</i> (~16 %) were the predominant phyla whereas in the caecum, <i>Firmicutes</i> (~50 %), <i>Bacteroidetes</i> (~29 %) and <i>Actinobacteria</i> (~10 %) were predominant. The Shannon-Wiener diversity index suggested that sample richness and diversity increased as the chicken aged. 4. For the first time, the presence of <i>Lactobacillus</i> species such as <i>L. frumenti, L. antri, L. mucosae</i> in the chicken crop along with <i>Kineococcus radiotolerans, Desulfohalobium retbaense</i> and <i>L. jensenii</i> in the caecum are reported. Many of these bacterial species have been found to be involved in immune response modulation and disease prevention in pigs and humans. The gut microbiome of the indigenous chicken was enriched with microbes having probiotic potential which might be essential for their adaptability.
DOI: 10.6084/m9.figshare.3102400.v1
title: Processes governing the stable isotope composition of water in the St. Lawrence river system, Canada

description: Linkages between δ<sup>18</sup>O–δ<sup>2</sup>H and hydrological processes have been investigated from isotopic time series recorded in the St. Lawrence River basin. Three stations were monitored from 1997 to 2008. They include the Ottawa River, the St. Lawrence River main channel at Montreal and the fluvial estuary. All sites depict seasonal isotopic cycles characterized by heavy isotope depletions during the snowmelt period and heavy isotope enrichments throughout the ice-free period. The data define δ<sup>2</sup>H–δ<sup>18</sup>O regression lines falling below the meteoric water line. In the Ottawa River, calculations suggest that approximately 8 % of the total inflow to the basin is lost through evaporation. In the St. Lawrence River main channel, seasonal isotopic fluctuations most likely reflect hydrological processes occurring within the Great Lakes and mixing with tributaries located downstream. In the St. Lawrence River fluvial estuary, isotopic data allow partitioning streamflow components and suggest that the recorded seasonal variations mainly respond to mixing processes.
DOI: 10.6084/m9.figshare.3102244
title: The Scent of a Smell: A Comparison Between Structural and Textual Code Smells

description: Code smells are symptoms of poor design and implementation choices. Several studies demonstrate their negative effects on maintenance cost. Despite this, developers tend to not refactor code smells. Almost all the current code smell detectors and refactoring tools are based on structural information. In this paper, we conjecture that textual information, as opposed to structural information, is better aligned with developers’ perception of code smells. In this paper, we systematically investigate how textually or structurally detected code smells are treated and perceived by developers. To this aim, we first conduct a mining study to obtain a quantitative perspective. Secondly, we conduct an industrial user study with 5 quality experts in order to qualitatively analyze how developers perceive code smells identified using different sources of information and whether textually or structurally detected code smells are easier to refactor. Results clearly indicate that textually detected smells are easier to perceive and subject to more refactoring operations.
DOI: 10.6084/m9.figshare.3102247
title: Flow rates in liquid chromatography, gas chromatography and supercritical fluid chromatography: A tool for optimization

description: Flow rates in liquid chromatography, gas chromatography and supercritical fluid chromatography: A tool for optimization
DOI: 10.6084/m9.figshare.3102208
title: Migration data, Russia, 2003-2013

description: This Excel file contains annual net migration records for Russian regions by 1-year age groups, from 0 to 80, for the periods 2003-2010 and 2011-2013. The first period is defined by the two Russian Censuses (end of 2002 and end of 2010). The second period is limited by the availability of data. Moreover, there was a significant change in the current migration record in 2011; so, the data for the two periods are barely comparable. <br>There are 78 regions , as the data for Moscow and Leningrad regions are merged with the data for the federal cities of Moscow and St.Petersburg, correspondingly. <br><br>List of data files:<br>IR_0310.csv - inter-regional migration in 2003-2010<br>IN_0310.csv - international migration in 2003-2010<br>IR_1113.csv - inter-regional migration in 2011-2013<br>IN_1113.csv - international migration in 2011-2013 <br>
DOI: 10.6084/m9.figshare.3102244.v1
title: The Scent of a Smell: A Comparison Between Structural and Textual Code Smells

description: Code smells are symptoms of poor design and implementation choices. Several studies demonstrate their negative effects on maintenance cost. Despite this, developers tend to not refactor code smells. Almost all the current code smell detectors and refactoring tools are based on structural information. In this paper, we conjecture that textual information, as opposed to structural information, is better aligned with developers’ perception of code smells. In this paper, we systematically investigate how textually or structurally detected code smells are treated and perceived by developers. To this aim, we first conduct a mining study to obtain a quantitative perspective. Secondly, we conduct an industrial user study with 5 quality experts in order to qualitatively analyze how developers perceive code smells identified using different sources of information and whether textually or structurally detected code smells are easier to refactor. Results clearly indicate that textually detected smells are easier to perceive and subject to more refactoring operations.
DOI: 10.6084/m9.figshare.3102247.v1
title: Flow rates in liquid chromatography, gas chromatography and supercritical fluid chromatography: A tool for optimization

description: Flow rates in liquid chromatography, gas chromatography and supercritical fluid chromatography: A tool for optimization
DOI: 10.6084/m9.figshare.3102133
title: Designating a segregation parameter for contamination detection in behavioral assays using zebrafish larvae; supporting information

description: 96 hpf zebrafish larvae behavior upon acute exposure to cadmium chloride (3 replicates) and permethrine (2 replicates) <br>
DOI: 10.6084/m9.figshare.3102244.v2
title: The Scent of a Smell: A Comparison Between Structural and Textual Code Smells

description: Code smells are symptoms of poor design and implementation choices. Several studies demonstrate their negative effects on maintenance cost. Despite this, developers tend to not refactor code smells. Almost all the current code smell detectors and refactoring tools are based on structural information. In this paper, we conjecture that textual information, as opposed to structural information, is better aligned with developers’ perception of code smells. In this paper, we systematically investigate how textually or structurally detected code smells are treated and perceived by developers. To this aim, we first conduct a mining study to obtain a quantitative perspective. Secondly, we conduct an industrial user study with 5 quality experts in order to qualitatively analyze how developers perceive code smells identified using different sources of information and whether textually or structurally detected code smells are easier to refactor. Results clearly indicate that textually detected smells are easier to perceive and subject to more refactoring operations.
DOI: 10.6084/m9.figshare.3102127
title: cadmium chloride replicate 3

description: 96 hpf zebrafish larvae behavior upon acute exposure to cadmium chloride replicate 3<br>
DOI: 10.6084/m9.figshare.3102244.v4
title: The Scent of a Smell: A Comparison Between Structural and Textual Code Smells

description: Code smells are symptoms of poor design and implementation choices. Several studies demonstrate their negative effects on maintenance cost. Despite this, developers tend to not refactor code smells. Almost all the current code smell detectors and refactoring tools are based on structural information. In this paper, we conjecture that textual information, as opposed to structural information, is better aligned with developers’ perception of code smells. In this paper, we systematically investigate how textually or structurally detected code smells are treated and perceived by developers. To this aim, we first conduct a mining study to obtain a quantitative perspective. Secondly, we conduct an industrial user study with 5 quality experts in order to qualitatively analyze how developers perceive code smells identified using different sources of information and whether textually or structurally detected code smells are easier to refactor. Results clearly indicate that textually detected smells are easier to perceive and subject to more refactoring operations.
DOI: 10.6084/m9.figshare.3102133.v1
title: Zebrafish larvae behavioral data

description: 96 hpf zebrafish larvae behavior upon acute exposure to cadmium chloride (3 replicates) and permethrine (2 replicates) <br>
DOI: 10.6084/m9.figshare.3102121
title: cadmium chloride replicate 2

description: 96 hpf zebrafish larvae behavior upon acute exposure to cadmium chloride replicate 2<br>
DOI: 10.6084/m9.figshare.3102244.v3
title: The Scent of a Smell: A Comparison Between Structural and Textual Code Smells

description: Code smells are symptoms of poor design and implementation choices. Several studies demonstrate their negative effects on maintenance cost. Despite this, developers tend to not refactor code smells. Almost all the current code smell detectors and refactoring tools are based on structural information. In this paper, we conjecture that textual information, as opposed to structural information, is better aligned with developers’ perception of code smells. In this paper, we systematically investigate how textually or structurally detected code smells are treated and perceived by developers. To this aim, we first conduct a mining study to obtain a quantitative perspective. Secondly, we conduct an industrial user study with 5 quality experts in order to qualitatively analyze how developers perceive code smells identified using different sources of information and whether textually or structurally detected code smells are easier to refactor. Results clearly indicate that textually detected smells are easier to perceive and subject to more refactoring operations.
DOI: 10.6084/m9.figshare.3102133.v2
title: Designating a segregation parameter for contamination detection in behavioral assays using zebrafish larvae; supporting information

description: 96 hpf zebrafish larvae behavior upon acute exposure to cadmium chloride (3 replicates) and permethrine (2 replicates) <br>
DOI: 10.6084/m9.figshare.3102121.v1
title: cadmium chloride replicate 2

description: 96 hpf zebrafish larvae behavior upon acute exposure to cadmium chloride replicate 2<br>
DOI: 10.17632/x2dc473b5v.1
title: Data for: The exponential Pareto model with hidden income processes: evidence from Chile

description: Replication files for The exponential Pareto model with hidden income processes: evidence from Chile
DOI: 10.6084/m9.figshare.3102109
title: cadmium chloride replicate 1

description: 96 hpf zebrafish larvae behavior upon acute exposure to cadmium chloride replicate 1
DOI: 10.6084/m9.figshare.3102109.v1
title: cadmium chloride replicate 1

description: 96 hpf zebrafish larvae behavior upon acute exposure to cadmium chloride replicate 1
DOI: 10.6084/m9.figshare.3102133.v4
title: Designating a segregation parameter for contamination detection in behavioral assays using zebrafish larvae; supporting information

description: 96 hpf zebrafish larvae behavior upon acute exposure to cadmium chloride (3 replicates) and permethrine (2 replicates) <br>
DOI: 10.6084/m9.figshare.3102076
title: April Hall Behaviour and Growth Data for PLoS ONE.xlsx

description: These data are in direct reference to an article published in PLoS ONE entitled "Predators exacerbate competitive interactions and dominance hierarchies between two coral reef fishes". Authors are April Hall and Michael Kingsford. <br><b><i></i></b>
DOI: 10.6084/m9.figshare.3102133.v3
title: Zebrafish larvae behavioral data

description: 96 hpf zebrafish larvae behavior upon acute exposure to cadmium chloride (3 replicates) and permethrine (2 replicates) <br>
DOI: 10.6084/m9.figshare.3102049
title: An engineered endomorphin-2 gene for morphine withdrawal syndrome

description: S1 file is the data of fig2, S2 file is the data of fig4, S3 file is the data of fig5
DOI: 10.6084/m9.figshare.3102040
title: An engineered endomorphin-2 gene for morphine withdrawal syndrome

description: S1 is the data of fig2, S2 is the data of fig4, S3 is the data of fig5
DOI: 10.6084/m9.figshare.3102076.v1
title: April Hall Behaviour and Growth Data for PLoS ONE.xlsx

description: These data are in direct reference to an article published in PLoS ONE entitled "Predators exacerbate competitive interactions and dominance hierarchies between two coral reef fishes". Authors are April Hall and Michael Kingsford. <br><b><i></i></b>
DOI: 10.6084/m9.figshare.3102040.v2
title: An engineered endomorphin-2 gene for morphine withdrawal syndrome

description: S1 is the data of fig2, S2 is the data of fig4, S3 is the data of fig5
DOI: 10.6084/m9.figshare.3102040.v1
title: An engineered endomorphin-2 gene for morphine withdrawal syndrome

description: S1 is the data of fig2, S2 is the data of fig4, S3 is the data of fig5
DOI: 10.6084/m9.figshare.3102010
title: Assessing the Calibration of High-Dimensional Ensemble Forecasts Using Rank Histograms

description: Any decision-making process that relies on a probabilistic forecast of future events necessarily requires a calibrated forecast. This article proposes new methods for empirically assessing forecast calibration in a multivariate setting where the probabilistic forecast is given by an ensemble of equally probable forecast scenarios. Multivariate properties are mapped to a single dimension through a prerank function and the calibration is subsequently assessed visually through a histogram of the ranks of the observation’s preranks. Average ranking assigns a prerank based on the average univariate rank while band depth ranking employs the concept of functional band depth where the centrality of the observation within the forecast ensemble is assessed. Several simulation examples and a case study of temperature forecast trajectories at Berlin Tegel Airport in Germany demonstrate that both multivariate ranking methods can successfully detect various sources of miscalibration and scale efficiently to high-dimensional settings. Supplemental material in form of computer code is available online.
DOI: 10.6084/m9.figshare.3102010.v1
title: Assessing the Calibration of High-Dimensional Ensemble Forecasts Using Rank Histograms

description: Any decision-making process that relies on a probabilistic forecast of future events necessarily requires a calibrated forecast. This article proposes new methods for empirically assessing forecast calibration in a multivariate setting where the probabilistic forecast is given by an ensemble of equally probable forecast scenarios. Multivariate properties are mapped to a single dimension through a prerank function and the calibration is subsequently assessed visually through a histogram of the ranks of the observation’s preranks. Average ranking assigns a prerank based on the average univariate rank while band depth ranking employs the concept of functional band depth where the centrality of the observation within the forecast ensemble is assessed. Several simulation examples and a case study of temperature forecast trajectories at Berlin Tegel Airport in Germany demonstrate that both multivariate ranking methods can successfully detect various sources of miscalibration and scale efficiently to high-dimensional settings. Supplemental material in form of computer code is available online.
DOI: 10.6084/m9.figshare.3101989
title: DMOZ -open directory project data

description: DMOZ data as file hierarchy. Every folder named with the corresponding category in Open Directory Project (ODP) hierarchy. Every folder contains sub-folders which are children of that category in ODP hierarchy and text files which are leaves of that folder category.<br>
DOI: 10.6084/m9.figshare.3101992
title: Multi-Loci Gene Sequencing and Identification of Bifidobacteria Strains Isolated from Dairy and Pharmaceutical Sources in South Africa

description: The 16S rRNA gene sequence analysis of <i>Bifidobacterium</i> species reveals high interspecies sequence similarity in the range of 87.7–99.5%. This study illustrated the extent of superiority of a multigenic approach, involving protein-coding genes, in comparison to the 16S rRNA gene, to precisely delineate presumptive <i>Bifidobacterium</i> isolates obtained from probiotic milk beverages, culture collections and pharmaceutical probiotic preparations. Oligonucleotide pairs PurF-rev/PurF-uni; RpoC-uni/RpoC-rev; DnaB-uni/DnaB-rev; DnaG-uni/DnaG-rev; and ClpC-uni/ClpC-rev amplified housekeeping genes while 27F/1492R amplified the 16S rRNA gene of the presumptive bifidobacteria in a polymerase chain reaction. Sequences of 16S rRNA gene and some protein-coding genes effectively identified the isolates. Phylogenetic analysis together with concatenation showed that <i>clpC, purF</i> and <i>dnaG</i> genes had over 8-fold better discriminatory power than the 16S rRNA gene in discriminating between <i>Bifidobacterium</i> isolates. However, phylogenetic analysis involving <i>dnaB and rpoC</i> gene sequences or their concatenated trees showed discrepancies in clustering isolates with designated type strains.
DOI: 10.6084/m9.figshare.3101992.v1
title: Multi-Loci Gene Sequencing and Identification of Bifidobacteria Strains Isolated from Dairy and Pharmaceutical Sources in South Africa

description: The 16S rRNA gene sequence analysis of <i>Bifidobacterium</i> species reveals high interspecies sequence similarity in the range of 87.7–99.5%. This study illustrated the extent of superiority of a multigenic approach, involving protein-coding genes, in comparison to the 16S rRNA gene, to precisely delineate presumptive <i>Bifidobacterium</i> isolates obtained from probiotic milk beverages, culture collections and pharmaceutical probiotic preparations. Oligonucleotide pairs PurF-rev/PurF-uni; RpoC-uni/RpoC-rev; DnaB-uni/DnaB-rev; DnaG-uni/DnaG-rev; and ClpC-uni/ClpC-rev amplified housekeeping genes while 27F/1492R amplified the 16S rRNA gene of the presumptive bifidobacteria in a polymerase chain reaction. Sequences of 16S rRNA gene and some protein-coding genes effectively identified the isolates. Phylogenetic analysis together with concatenation showed that <i>clpC, purF</i> and <i>dnaG</i> genes had over 8-fold better discriminatory power than the 16S rRNA gene in discriminating between <i>Bifidobacterium</i> isolates. However, phylogenetic analysis involving <i>dnaB and rpoC</i> gene sequences or their concatenated trees showed discrepancies in clustering isolates with designated type strains.
DOI: 10.6084/m9.figshare.3101953
title: S1_Data.xlsx

description: Excel sheet with behavioural data from a finger tapping task.
DOI: 10.6084/m9.figshare.3101947
title: synergy and redundancy

description: Regions which form synergetic and redundant duplets with representative regions, separately selected among cerebrum and cerebellar regions as those maximizing the overall informational contributions. Regions are indicated by spheres centered in the MNI coordinates. The size of the spheres is proportional to the value of the duplet formed by the region and the representative one, depicted in black. The same scale as Figure 6 applies.
DOI: 10.6084/m9.figshare.3101953.v1
title: S1_Data.xlsx

description: Excel sheet with behavioural data from a finger tapping task.
DOI: 10.6084/m9.figshare.3101863
title: Anexo Productos.docx

description: Neuromarketing; Sustainability; Consumer Neurosciencie; Advertising; Green Advertising; fMRI; EEG<br>