cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5882317
title: Low temperature exposure (20 °C) during the sealed brood stage induces abnormal venation of honey bee wings

description: All insects are influenced by low temperature. However, as a typical stenothermic insect, the honey bee is perhaps the most severely affected. Low temperature exposure during the capped brood stages leads to high mortality and shortened worker longevity. The impact of low temperature stress on vein development has not, however, been investigated. In this study, the eight different developmental stages of capped brood (<i>Apis mellifera</i>) were exposed to 20 °C for 12, 24, 36, 48, 60, 72, 84, and 96 h, and then incubated at 35 °C (the optimum temperature for brood development) until emergence. We found a total of 21 abnormal vein types, consisting of 16 types of supernumerary veins and five types of lost veins. The abnormal phenomena in the brood occurred mainly 1–4 days after capping, when the metamorphosis process from larvae to pupa occurs. Our results suggest that this metamorphosis process is critical for the development of veins, indicating it as the most sensitive period to low-temperature. In addition, we found a cross vein “rs-m” between Rs and M in the hind wing of the honey bee, which has previously been ignored due to its very short length. This study on the effects of temperature on wing venation in stenothermic insects adds to our understanding of the thermal requirements for shaping the wing vein pattern, and for predicting wing venation deformation. This also adds a new research route for the investigation of the evolutionary relationship between honey bees and other hymenopteran insects.
DOI: 10.6084/m9.figshare.5882317.v1
title: Low temperature exposure (20 °C) during the sealed brood stage induces abnormal venation of honey bee wings

description: All insects are influenced by low temperature. However, as a typical stenothermic insect, the honey bee is perhaps the most severely affected. Low temperature exposure during the capped brood stages leads to high mortality and shortened worker longevity. The impact of low temperature stress on vein development has not, however, been investigated. In this study, the eight different developmental stages of capped brood (<i>Apis mellifera</i>) were exposed to 20 °C for 12, 24, 36, 48, 60, 72, 84, and 96 h, and then incubated at 35 °C (the optimum temperature for brood development) until emergence. We found a total of 21 abnormal vein types, consisting of 16 types of supernumerary veins and five types of lost veins. The abnormal phenomena in the brood occurred mainly 1–4 days after capping, when the metamorphosis process from larvae to pupa occurs. Our results suggest that this metamorphosis process is critical for the development of veins, indicating it as the most sensitive period to low-temperature. In addition, we found a cross vein “rs-m” between Rs and M in the hind wing of the honey bee, which has previously been ignored due to its very short length. This study on the effects of temperature on wing venation in stenothermic insects adds to our understanding of the thermal requirements for shaping the wing vein pattern, and for predicting wing venation deformation. This also adds a new research route for the investigation of the evolutionary relationship between honey bees and other hymenopteran insects.
DOI: 10.6084/m9.figshare.5885731
title: Additional file 2: of Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes

description: Table S1. Information on sequencing depth of 16S rRNA genes. Table S2. Information on assembly, contigs, and ORFs. Table S3. Relative abundance of ARG types. Table S4. Relative abundance of ARG subtypes and their significance in different groups. Table S5. Changes in taxonomic phyla over time in different samples (%). Table S6. Changes in taxonomic genera over time in the therapeutic dose group and in the control group (%). Table S7. Average percentages of bacterial hosts carrying antibiotic resistance genes (%). Table S8. Variations of predominant ARGs carried by bacterial hosts over time in the therapeutic group. Table S9. Details of bacterial hosts and their harboring ARGs in the control group and in the therapeutic dose group on T5. Table S10. Changes in predominant bacterial hosts carrying ARGs in the therapeutic group. (XLSX 120Â kb)
DOI: 10.6084/m9.figshare.5885731.v1
title: Additional file 2: of Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes

description: Table S1. Information on sequencing depth of 16S rRNA genes. Table S2. Information on assembly, contigs, and ORFs. Table S3. Relative abundance of ARG types. Table S4. Relative abundance of ARG subtypes and their significance in different groups. Table S5. Changes in taxonomic phyla over time in different samples (%). Table S6. Changes in taxonomic genera over time in the therapeutic dose group and in the control group (%). Table S7. Average percentages of bacterial hosts carrying antibiotic resistance genes (%). Table S8. Variations of predominant ARGs carried by bacterial hosts over time in the therapeutic group. Table S9. Details of bacterial hosts and their harboring ARGs in the control group and in the therapeutic dose group on T5. Table S10. Changes in predominant bacterial hosts carrying ARGs in the therapeutic group. (XLSX 120Â kb)
DOI: 10.6084/m9.figshare.5885755
title: Additional file 2: Table S2. of Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments

description: Distribution of repetitive elements among species. (XLS 96 kb)
DOI: 10.6084/m9.figshare.5885755.v1
title: Additional file 2: Table S2. of Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments

description: Distribution of repetitive elements among species. (XLS 96 kb)
DOI: 10.6084/m9.figshare.5885827
title: Additional file 5 of MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies

description: Table of all details of the identified time intervals by MetaLonDA, LOWESS, and MetaSplines in the hygiene hypothesis study. (CSV 21 kb)
DOI: 10.6084/m9.figshare.5885827.v1
title: Additional file 5 of MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies

description: Table of all details of the identified time intervals by MetaLonDA, LOWESS, and MetaSplines in the hygiene hypothesis study. (CSV 21 kb)
DOI: 10.6084/m9.figshare.5885932
title: Additional file 1: Table S1a. of Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India

description: Sample information and clinical characteristics. Table S1b. Summary of clinical characteristics of MODY patient samples. Table S2a. Sequencing statistics of combined exome and WGS. Table S2b. Sequencing statistics of targeted exome samples. Table S3. Targeted gene panel. Table S4. Candidate variants identified in MODY samples. Table S5. Differentially expressed genes - NKX6â 1 (XLS 292Â kb)
DOI: 10.6084/m9.figshare.5885932.v1
title: Additional file 1: Table S1a. of Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India

description: Sample information and clinical characteristics. Table S1b. Summary of clinical characteristics of MODY patient samples. Table S2a. Sequencing statistics of combined exome and WGS. Table S2b. Sequencing statistics of targeted exome samples. Table S3. Targeted gene panel. Table S4. Candidate variants identified in MODY samples. Table S5. Differentially expressed genes - NKX6â 1 (XLS 292Â kb)
DOI: 10.6084/m9.figshare.5885956
title: Additional file 2: Figure S1. of Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India

description: Box plot showing (a) fasting plasma glucose, (b) fasting insulin, (c) C-peptide fasting, (d) C-peptide stimulated and (e) creatinine in MODY and control samples. The median value is shown as a line with the whiskers extending from the highest value within 1.5 * IQR of the third quartile to the lowest value within 1.5 * IQR of the first quartile where IQR is the inter-quartile range. Figure S2. Heatmap depicting the genotype based identity of the discovery and validation MODY cohort and control samples. Genomic regions for which we obtained data for the validation cohort samples and corresponding regions from the discovery set samples using GATK joint-variant caller. The sample identity was computed based on the high-confidence set of single nucleotide variants (SNVs) that passed GATK Hard-Filtering criteria. Figure S3. Expression level of mouse Nkx6–1 (top) or human NKX6–1 (bottom) following induction in cells stably expressing the indicated variant or wildtype. Figure S4. Western blot showing the expression of NKX6–1 48 h post dox induction. Hsp90 was used as a loading control. (ZIP 5136 kb)
DOI: 10.6084/m9.figshare.5885956.v1
title: Additional file 2: Figure S1. of Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India

description: Box plot showing (a) fasting plasma glucose, (b) fasting insulin, (c) C-peptide fasting, (d) C-peptide stimulated and (e) creatinine in MODY and control samples. The median value is shown as a line with the whiskers extending from the highest value within 1.5 * IQR of the third quartile to the lowest value within 1.5 * IQR of the first quartile where IQR is the inter-quartile range. Figure S2. Heatmap depicting the genotype based identity of the discovery and validation MODY cohort and control samples. Genomic regions for which we obtained data for the validation cohort samples and corresponding regions from the discovery set samples using GATK joint-variant caller. The sample identity was computed based on the high-confidence set of single nucleotide variants (SNVs) that passed GATK Hard-Filtering criteria. Figure S3. Expression level of mouse Nkx6–1 (top) or human NKX6–1 (bottom) following induction in cells stably expressing the indicated variant or wildtype. Figure S4. Western blot showing the expression of NKX6–1 48 h post dox induction. Hsp90 was used as a loading control. (ZIP 5136 kb)
DOI: 10.6084/m9.figshare.5886154
title: MOESM2 of RRS1 gene expression involved in the progression of papillary thyroid carcinoma

description: Additional file 2. Additional table.
DOI: 10.6084/m9.figshare.5886154.v1
title: MOESM2 of RRS1 gene expression involved in the progression of papillary thyroid carcinoma

description: Additional file 2. Additional table.
DOI: 10.6084/m9.figshare.5886400
title: A dataset for the relationship between breakdown voltage and electrode spacing under different conditions.

description: A dataset for the relationship between breakdown voltage and electrode spacing under different conditions.
DOI: 10.6084/m9.figshare.5886400.v1
title: A dataset for the relationship between breakdown voltage and electrode spacing under different conditions.

description: A dataset for the relationship between breakdown voltage and electrode spacing under different conditions.
DOI: 10.6084/m9.figshare.5890786
title: Aberration elimination for full FOV reconstruction

description: Comparison of full FOV reconstruction using FPM and mcFPM
DOI: 10.6084/m9.figshare.24320974
title: Data of Figures in “<b>Unveiling Value Patterns via Deep Reinforcement Learning in Heterogeneous Data Analytics</b>”

description: Data of Figures in Paper "<b><i>Unveiling value patterns via deep reinforcement </i></b><b><i>learning in heterogeneous data analytics</i></b>"<i>https://doi.org/10.1016/j.patter.2024.100965</i><br><br><b>Note:</b> The file named "Figure5b-e", "Figure6a" and "Figure6b" are corresponding to the Figure 6, Figure7a and Figure7b in the final version of the article.<br>
DOI: 10.23729/aec40643-48e6-4775-86fa-920c2cd1ae4b
title: SMEAR I Värriö forest meteorology, air quality and soil

description: This dataset contains long-term measurements of meteorology, ambient air trace gases, solar and terrestrial radiation, and soil performed at SMEAR I research station in Värriö, Salla, Finland during years 1992–2022.

The data were exported from SMEAR database on the dataset release date. Most recent version of the data are available at https://smear.avaa.csc.fi/.
DOI: 10.6084/m9.figshare.5891164
title: Additional file 3: of Transcriptome analysis of different growth stages of Aspergillus oryzae reveals dynamic changes of distinct classes of genes during growth

description: Table S2. The expression levels and functional annotation of DEGs between Ao_24 and Ao_48. (XLS 1701 kb)
DOI: 10.6084/m9.figshare.5891164.v1
title: Additional file 3: of Transcriptome analysis of different growth stages of Aspergillus oryzae reveals dynamic changes of distinct classes of genes during growth

description: Table S2. The expression levels and functional annotation of DEGs between Ao_24 and Ao_48. (XLS 1701 kb)
DOI: 10.6084/m9.figshare.5891182
title: Additional file 4: of Transcriptome analysis of different growth stages of Aspergillus oryzae reveals dynamic changes of distinct classes of genes during growth

description: Table S3. The expression levels and functional annotation of DEGs between Ao_24 and Ao_72. (XLS 1836 kb)
DOI: 10.6084/m9.figshare.5891182.v1
title: Additional file 4: of Transcriptome analysis of different growth stages of Aspergillus oryzae reveals dynamic changes of distinct classes of genes during growth

description: Table S3. The expression levels and functional annotation of DEGs between Ao_24 and Ao_72. (XLS 1836 kb)
DOI: 10.6084/m9.figshare.5891197
title: Additional file 5: of Transcriptome analysis of different growth stages of Aspergillus oryzae reveals dynamic changes of distinct classes of genes during growth

description: Table S4. The expression levels and functional annotation of DEGs between Ao_48 and Ao_72. (XLS 215 kb)
DOI: 10.6084/m9.figshare.5891197.v1
title: Additional file 5: of Transcriptome analysis of different growth stages of Aspergillus oryzae reveals dynamic changes of distinct classes of genes during growth

description: Table S4. The expression levels and functional annotation of DEGs between Ao_48 and Ao_72. (XLS 215 kb)
DOI: 10.6084/m9.figshare.5891218
title: Additional file 2: of Proteomic identification and characterization of hepatic glyoxalase 1 dysregulation in non-alcoholic fatty liver disease

description: Peptide Lists. (XLSX 1682 kb)
DOI: 10.6084/m9.figshare.5891218.v1
title: Additional file 2: of Proteomic identification and characterization of hepatic glyoxalase 1 dysregulation in non-alcoholic fatty liver disease

description: Peptide Lists. (XLSX 1682 kb)
DOI: 10.6084/m9.figshare.5891230
title: Additional file 3: of Proteomic identification and characterization of hepatic glyoxalase 1 dysregulation in non-alcoholic fatty liver disease

description: Protein Lists. (XLSX 309 kb)
DOI: 10.6084/m9.figshare.5891230.v1
title: Additional file 3: of Proteomic identification and characterization of hepatic glyoxalase 1 dysregulation in non-alcoholic fatty liver disease

description: Protein Lists. (XLSX 309 kb)
DOI: 10.6084/m9.figshare.5895562
title: The Variation of Microbial Communities in a Depth Profile of Peat in the Gahai Lake Wetland Natural Conservation Area

description: The Gahai Lake wetland natural conservation area in northwestern China includes peatland that has been accumulating over hundreds of years and is seldom disturbed by industry. Bacteria and archaea in peat soil, which is a reservoir for carbon and water, may influence its ecological function. The objective of this study was to obtain a clearer understanding of peat microbial ecology and its relationship to the environmental conditions of this area. Hence, the microbial community of the peatland ecosystem was investigated by sequencing bacterial and archaeal DNA extracted from samples collected at different peat depths. Results showed that in all samples the dominant bacterial phyla were <i>Proteobacteria</i> (relative abundance 0.39 ± 0.12) and <i>Chloroflexi</i> (0.16 ± 0.09), while the dominant archaeal phyla were Miscellaneous Crenarchaeotic Group (MCG) (0.62 ± 0.21) and <i>Euryarchaeota</i> (0.27 ± 0.16). The diversity and microbial community structure at deeper depths (90 and 120 cm below the peat surface) significantly differ from that at shallower depths (10, 30 and 50 cm deep). In contrast to the shallow layers, the deeper layers became more abundant in the bacterial phyla <i>Chloroflexi, Bacteroidetes</i>, Atribacteria, Aminicenantes, <i>Chlorobi</i>, TA06, Caldiserica and <i>Spirochaetae</i>; and in the archaeal phyla MCG and Miscellaneous Euryarchaeotic Group (MEG). This study revealed a significant shift in microbial community in peat between 50 cm and 90 cm deep, as probably influenced by the oxygen supply at different depths. Furthermore, new insights into the microbial taxa were obtained, thus providing a baseline for future studies of this peat ecosystem.
DOI: 10.6084/m9.figshare.5895562.v1
title: The Variation of Microbial Communities in a Depth Profile of Peat in the Gahai Lake Wetland Natural Conservation Area

description: The Gahai Lake wetland natural conservation area in northwestern China includes peatland that has been accumulating over hundreds of years and is seldom disturbed by industry. Bacteria and archaea in peat soil, which is a reservoir for carbon and water, may influence its ecological function. The objective of this study was to obtain a clearer understanding of peat microbial ecology and its relationship to the environmental conditions of this area. Hence, the microbial community of the peatland ecosystem was investigated by sequencing bacterial and archaeal DNA extracted from samples collected at different peat depths. Results showed that in all samples the dominant bacterial phyla were <i>Proteobacteria</i> (relative abundance 0.39 ± 0.12) and <i>Chloroflexi</i> (0.16 ± 0.09), while the dominant archaeal phyla were Miscellaneous Crenarchaeotic Group (MCG) (0.62 ± 0.21) and <i>Euryarchaeota</i> (0.27 ± 0.16). The diversity and microbial community structure at deeper depths (90 and 120 cm below the peat surface) significantly differ from that at shallower depths (10, 30 and 50 cm deep). In contrast to the shallow layers, the deeper layers became more abundant in the bacterial phyla <i>Chloroflexi, Bacteroidetes</i>, Atribacteria, Aminicenantes, <i>Chlorobi</i>, TA06, Caldiserica and <i>Spirochaetae</i>; and in the archaeal phyla MCG and Miscellaneous Euryarchaeotic Group (MEG). This study revealed a significant shift in microbial community in peat between 50 cm and 90 cm deep, as probably influenced by the oxygen supply at different depths. Furthermore, new insights into the microbial taxa were obtained, thus providing a baseline for future studies of this peat ecosystem.
DOI: 10.6084/m9.figshare.5896315
title: Additional file 2: of Comparative analysis of alfalfa (Medicago sativa L.) leaf transcriptomes reveals genotype-specific salt tolerance mechanisms

description: This excel file contains all of the additional Tables (Table S1-S9) associated with the manuscript. Each Table is in a different tab. Table numbers and titles are listed below: Table S1. Summary of clean reads and mapping ratio. Table S2. Number of annotated unigenes in alfalfa. Table S3. Annotations of DEGs in two cultivars of alfalfa. Table S4. The DEGs involved in ROS homeostasis in two cultivars. Table S5. The DEGs involved in Ca2+ signaling in two cultivars. Table S6. The DEGs involved in phytohormone biosynthesis in two cultivars. Table S7. The DEGs involved in ion transport in two cultivars. Table S8. The DEGs involved in transcription factor in two cultivars. Table S9. The photosynthesis-related DEGs in two cultivars. (XLSX 6789Â kb)
DOI: 10.6084/m9.figshare.5896315.v1
title: Additional file 2: of Comparative analysis of alfalfa (Medicago sativa L.) leaf transcriptomes reveals genotype-specific salt tolerance mechanisms

description: This excel file contains all of the additional Tables (Table S1-S9) associated with the manuscript. Each Table is in a different tab. Table numbers and titles are listed below: Table S1. Summary of clean reads and mapping ratio. Table S2. Number of annotated unigenes in alfalfa. Table S3. Annotations of DEGs in two cultivars of alfalfa. Table S4. The DEGs involved in ROS homeostasis in two cultivars. Table S5. The DEGs involved in Ca2+ signaling in two cultivars. Table S6. The DEGs involved in phytohormone biosynthesis in two cultivars. Table S7. The DEGs involved in ion transport in two cultivars. Table S8. The DEGs involved in transcription factor in two cultivars. Table S9. The photosynthesis-related DEGs in two cultivars. (XLSX 6789Â kb)
DOI: 10.6084/m9.figshare.5896336
title: MOESM4 of Identification and characterization of microRNA in the lung tissue of pigs with different susceptibilities to PCV2 infection

description: Additional file 4. Information of the novel miRNA in porcine lung tissues. This excel file contains all information of the 95 novel miRNA, including mature miRNA sequence, precursor sequence, precursor location, minimal free energy, normalized expression value, fold-change and P value. a If the normalized expression of a given miRNA was less than 1 in both samples of a sample pair, the normalized expression of both samples were not shown and the miRNA was removed from the differential expression analysis. b Sig-label: **: fold-change &gt; 1 or &lt; −1, and P value &lt; 0.01.
DOI: 10.6084/m9.figshare.5896336.v1
title: MOESM4 of Identification and characterization of microRNA in the lung tissue of pigs with different susceptibilities to PCV2 infection

description: Additional file 4. Information of the novel miRNA in porcine lung tissues. This excel file contains all information of the 95 novel miRNA, including mature miRNA sequence, precursor sequence, precursor location, minimal free energy, normalized expression value, fold-change and P value. a If the normalized expression of a given miRNA was less than 1 in both samples of a sample pair, the normalized expression of both samples were not shown and the miRNA was removed from the differential expression analysis. b Sig-label: **: fold-change &gt; 1 or &lt; −1, and P value &lt; 0.01.
DOI: 10.6084/m9.figshare.5896369
title: Additional file 2: of RNA secondary structure profiling in zebrafish reveals unique regulatory features

description: Load score and percentage coverage of 54,083 transcripts. (TXT 3635Â kb)
DOI: 10.6084/m9.figshare.5896369.v1
title: Additional file 2: of RNA secondary structure profiling in zebrafish reveals unique regulatory features

description: Load score and percentage coverage of 54,083 transcripts. (TXT 3635Â kb)
DOI: 10.6084/m9.figshare.5896375
title: Additional file 3: of RNA secondary structure profiling in zebrafish reveals unique regulatory features

description: Multi-conformation position counts in transcripts with overlapping peaks. (TXT 712Â kb)
DOI: 10.6084/m9.figshare.5896375.v1
title: Additional file 3: of RNA secondary structure profiling in zebrafish reveals unique regulatory features

description: Multi-conformation position counts in transcripts with overlapping peaks. (TXT 712Â kb)
DOI: 10.6084/m9.figshare.5896384
title: Additional file 4: of RNA secondary structure profiling in zebrafish reveals unique regulatory features

description: Number of read starts for every position covered in RNase V1 sample. (TXT 32051Â kb)
DOI: 10.6084/m9.figshare.5896384.v1
title: Additional file 4: of RNA secondary structure profiling in zebrafish reveals unique regulatory features

description: Number of read starts for every position covered in RNase V1 sample. (TXT 32051Â kb)