cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19092663
title: Additional file 2 of Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens

description: Additional file 2. Metadata associated with all samples.
DOI: 10.6084/m9.figshare.13323755
title: Additional file 8 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 8. Subcluster 3 GO enrichment. Gene ontology enrichment of subcluster 3 as determined by k-means clustering
DOI: 10.6084/m9.figshare.13323758
title: Additional file 9 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 9. Phytohormone genes expressed in NEC and EC cells in Jin668. A list of all phytohormone annotated genes in the v2.0 of Gossypium hirsutum reference assembly with logFC values in EC.
DOI: 10.6084/m9.figshare.19092672
title: Additional file 5 of Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens

description: Additional file 5: Table S1. Results of the Anova test on individual Salmonella carriage for line, sex and experiment. Table S2. Proportion of phylum and family types over the 228 caecal microbiota analysed. Table S3. Results of the Anova test on alpha diversity and beta diversity for line, sex, experiment and high- and low-carriers. Table S4. Results of the Permanova on Bray–Curtis distance for experiment, isolators, sex and line. Table S5. Differentially abundant operational taxonomic units (DA OTU) between the N and 6l lines over the two experiments, when adjusting for isolator effect. Table S6. Differentially abundant genera and families between the N and 6l lines over the two experiments, when adjusting for isolator effect. Table S7. Differentially abundant operational taxonomic units (DA OTU) between the high and low carriers (line 6l-Experiment 1), when adjusting for isolator effect. Table S8. Differentially abundant genera and families between high and low carriers (line 6l-Experiment 1) when adjusting for isolator effect. Table S9. Differentially abundant pathways in common for the comparisons between lines N and 61 and between high and low carriers from line 6l in Experiment 1.
DOI: 10.5517/ccdc.csd.cc2cj345
title: CCDC 2190216: Experimental Crystal Structure Determination

description: Related Article: Yao Ge, Weiheng Huang, Sebastian Ahrens, Anke Spannenberg, Ralf Jackstell, Matthias Beller |2023|Nat. Synth.|3|202|doi:10.1038/s44160-023-00411-6
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cj356
title: CCDC 2190217: Experimental Crystal Structure Determination

description: Related Article: Yao Ge, Weiheng Huang, Sebastian Ahrens, Anke Spannenberg, Ralf Jackstell, Matthias Beller |2023|Nat. Synth.|3|202|doi:10.1038/s44160-023-00411-6
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.19097051
title: Combining pangenome analysis to identify potential cross-protective antigens against avian pathogenic <i>Escherichia coli</i>

description: Avian pathogenic <i>Escherichia coli</i> (APEC) is the bacterial pathogen of poultry colibacillosis, which causes significant economic losses to the poultry industry. The lack of an effective vaccine against multiple serotypes and the emergence of multi-resistant isolates have made the control of avian colibacillosis troublesome. To identify conserved potential vaccine candidates, 58 genomes of APEC were obtained (54 sequenced by our laboratory and four downloaded from NCBI). A reverse vaccinology (RV) method based on the pangenome – called Pan-RV analysis – was performed in APEC-protective protein mining for the first time. Finally, four proteins were selected, and their immunoreactivity with anti-O1, O2, and O78 serum was verified by western blotting. Our <i>in silico</i> method of analysis will pave the way for rapid screening of vaccine candidates and will lay the foundation for the development of a highly effective subunit vaccine controlling APEC infection. RESEARCH HIGHLIGHTSPan-RV analysis was used for the first time in the discovery of APEC-protective proteins.A total of 53 potential protective proteins were screened out.Four proteins were verified as potential vaccine candidates using western blotting. Pan-RV analysis was used for the first time in the discovery of APEC-protective proteins. A total of 53 potential protective proteins were screened out. Four proteins were verified as potential vaccine candidates using western blotting.
DOI: 10.6084/m9.figshare.11757039
title: Linguistic and cultural adaptation to the Portuguese language of antimicrobial dose adjustment software

description: ABSTRACT Objective To adapt an antibiotic dose adjustment software initially developed in English, to Portuguese and to the Brazilian context. Methods This was an observational, descriptive study in which the Delphi method was used to establish consensus among specialists from different health areas, with questions addressing the visual and operational aspects of the software. In a second stage, a pilot experimental study was performed with the random comparison of patients for evaluation and adaptation of the software in the real environment of an intensive care unit, where it was compared between patients who used the standardized dose of piperacillin/tazobactam, and those who used an individualized dose adjusted through the software Individually Designed and Optimized Dosing Strategies. Results Twelve professionals participated in the first round, whose suggestions were forwarded to the software developer for adjustments, and subsequently submitted to the second round. Eight specialists participated in the second round. Indexes of 80% and 90% of concordance were obtained between the judges, characterizing uniformity in the suggestions. Thus, there was modification in the layout of the software for linguistic and cultural adequacy, minimizing errors of understanding and contradictions. In the second stage, 21 patients were included, and there were no differences between doses of piperacillin in the standard dose and adjusted dose Groups. Conclusion The adapted version of the software is safe and reliable for its use in Brazil.
DOI: 10.6084/m9.figshare.11757039.v1
title: Linguistic and cultural adaptation to the Portuguese language of antimicrobial dose adjustment software

description: ABSTRACT Objective To adapt an antibiotic dose adjustment software initially developed in English, to Portuguese and to the Brazilian context. Methods This was an observational, descriptive study in which the Delphi method was used to establish consensus among specialists from different health areas, with questions addressing the visual and operational aspects of the software. In a second stage, a pilot experimental study was performed with the random comparison of patients for evaluation and adaptation of the software in the real environment of an intensive care unit, where it was compared between patients who used the standardized dose of piperacillin/tazobactam, and those who used an individualized dose adjusted through the software Individually Designed and Optimized Dosing Strategies. Results Twelve professionals participated in the first round, whose suggestions were forwarded to the software developer for adjustments, and subsequently submitted to the second round. Eight specialists participated in the second round. Indexes of 80% and 90% of concordance were obtained between the judges, characterizing uniformity in the suggestions. Thus, there was modification in the layout of the software for linguistic and cultural adequacy, minimizing errors of understanding and contradictions. In the second stage, 21 patients were included, and there were no differences between doses of piperacillin in the standard dose and adjusted dose Groups. Conclusion The adapted version of the software is safe and reliable for its use in Brazil.
DOI: 10.6084/m9.figshare.11757042
title: Investigation of transmigrated mandibular canines

description: ABSTRACT Introduction: Canine transmigration is a rare orthodontic condition and it is relevant to perform the proper diagnose at an early age. Objective: The aim of the current study was to find out the frequency of transmigrated mandibular canines (TRC) in orthodontic patients obtained from South Asian population of Pakistan origin. Methods: Panoramic radiographs of 2,550 untreated orthodontic patients (1,248 males; 1,302 females) were included, to investigate the presence, site, and type of TRC. Any permanent mandibular canine that was found to be crossing the midline in panoramic radiographs was considered as TRC. Results: The frequency of TRC was found to be 0.98%. TRC were only found unilaterally. No significance regarding gender and side was found. Nineteen TRC displayed a type 1 transmigratory pattern, while type 2 and type 5 transmigratory patterns were encountered in three patients. Conclusion: Frequency of transmigrated mandibular canines in the studied sample was 0.98%.
DOI: 10.6084/m9.figshare.11757042.v1
title: Investigation of transmigrated mandibular canines

description: ABSTRACT Introduction: Canine transmigration is a rare orthodontic condition and it is relevant to perform the proper diagnose at an early age. Objective: The aim of the current study was to find out the frequency of transmigrated mandibular canines (TRC) in orthodontic patients obtained from South Asian population of Pakistan origin. Methods: Panoramic radiographs of 2,550 untreated orthodontic patients (1,248 males; 1,302 females) were included, to investigate the presence, site, and type of TRC. Any permanent mandibular canine that was found to be crossing the midline in panoramic radiographs was considered as TRC. Results: The frequency of TRC was found to be 0.98%. TRC were only found unilaterally. No significance regarding gender and side was found. Nineteen TRC displayed a type 1 transmigratory pattern, while type 2 and type 5 transmigratory patterns were encountered in three patients. Conclusion: Frequency of transmigrated mandibular canines in the studied sample was 0.98%.
DOI: 10.6084/m9.figshare.19092684.v1
title: Additional file 2 of Risk stratification of lung adenocarcinoma using a nomogram combined with ferroptosis-related LncRNAs and subgroup analysis with immune and N6-methyladenosine modification

description: Additional file 2. The data analysis.
DOI: 10.25387/g3.12277268
title: Supplemental Material for Zheng et al., 2020

description: Figure S1 contains sequence alignment of GRMZM2G021276 between
CHuangzaosi and A619. Table S1 contains fertility identification of F<sub>1</sub>
hybrids crossed between CMS-C lines and A619. Table S2 contains fertility
ratings of BC<sub>2</sub>F<sub>1</sub>, BC<sub>3</sub>F<sub>1</sub>, BC<sub>6</sub>F<sub>1</sub>
and F<sub>2:3</sub> progenies derived from the cross between CHuangzaosi and
A619. Table S3 contains the information of 11 markers for QTL mapping. Table S4
contains genotypes of each individual for QTL mapping. Table S5 contains
phenotype of each individual for QTL mapping. File S1 contains SNP information
for QTL-seq.
DOI: 10.6084/m9.figshare.19092828
title: Effect of stand age on the temporal dynamics of soil active carbon and nitrogen in Chinese cypress artificial forests

description: Stand age is a key factor for reforestation, and it has an important influence on the sustainable development of artificial forests. In order to reveal the temporal dynamics of soil active carbon (C) and nitrogen (N) in Chinese cypress artificial forests (CAFs) under different stand ages, soil samples were collected from five stands (25, 35, 45, 55, and 65 years old) in rocky mountainous of North China. The characterization of soil active C and N components, like soil microbial biomass C (MBC), microbial biomass N (MBN), dissolved organic C (DOC), dissolved organic N (DON), ammonium-N (NH<sub>4</sub><sup>+</sup>-N) and nitrate-N (NO<sub>3</sub><sup>−</sup>-N), as well as other soil properties were determined. The results showed that with the increase of stand age, the contents of soil MBC, MBN, DOC, DON, NH<sub>4</sub><sup>+</sup>-N and NO<sub>3</sub><sup>−</sup>-N tended to increase first and then decrease, and most of them reached the highest values in 45 years old. Soil active C and N components all reached peak values in June, and all of them showed the most significant variations in 0 ~ 10 cm soil layer (<i>P</i> &lt; 0.01). Correlation analysis revealed that soil active C and N components showed significantly positive correlations with soil total N, total C, the number of microorganism communities and soil water content, as well as litter biomass (<i>P</i> &lt; 0.01). Stepwise multiple regression analysis demonstrated that soil total N was the key controlling factor to soil active C and N components. In conclusion, with the increase of stand ages, soil active C and N components of CAFs did not accumulate all the time, indicating that stand age should be regarded as an important factor for the sustainable management of artificial forests.
DOI: 10.6084/m9.figshare.24340057
title: Genotyping data for <i>Quercus</i> <i>aliena</i> and <i>Q</i><i>uercus dent</i><i>ata</i>

description: "SSR_ALL.txt" is the genotyping data for all 538 samples of the <i>Quercus aliena </i>and<i> Quercus dentata</i> scored using Genemarker v. 2.2, then normalized the score by FlexiBinv2 in TXT format.
DOI: 10.6084/m9.figshare.19092828.v1
title: Effect of stand age on the temporal dynamics of soil active carbon and nitrogen in Chinese cypress artificial forests

description: Stand age is a key factor for reforestation, and it has an important influence on the sustainable development of artificial forests. In order to reveal the temporal dynamics of soil active carbon (C) and nitrogen (N) in Chinese cypress artificial forests (CAFs) under different stand ages, soil samples were collected from five stands (25, 35, 45, 55, and 65 years old) in rocky mountainous of North China. The characterization of soil active C and N components, like soil microbial biomass C (MBC), microbial biomass N (MBN), dissolved organic C (DOC), dissolved organic N (DON), ammonium-N (NH<sub>4</sub><sup>+</sup>-N) and nitrate-N (NO<sub>3</sub><sup>−</sup>-N), as well as other soil properties were determined. The results showed that with the increase of stand age, the contents of soil MBC, MBN, DOC, DON, NH<sub>4</sub><sup>+</sup>-N and NO<sub>3</sub><sup>−</sup>-N tended to increase first and then decrease, and most of them reached the highest values in 45 years old. Soil active C and N components all reached peak values in June, and all of them showed the most significant variations in 0 ~ 10 cm soil layer (<i>P</i> &lt; 0.01). Correlation analysis revealed that soil active C and N components showed significantly positive correlations with soil total N, total C, the number of microorganism communities and soil water content, as well as litter biomass (<i>P</i> &lt; 0.01). Stepwise multiple regression analysis demonstrated that soil total N was the key controlling factor to soil active C and N components. In conclusion, with the increase of stand ages, soil active C and N components of CAFs did not accumulate all the time, indicating that stand age should be regarded as an important factor for the sustainable management of artificial forests.
DOI: 10.25387/g3.12277268.v1
title: Supplemental Material for Zheng et al., 2020

description: Figure S1 contains sequence alignment of GRMZM2G021276 between
CHuangzaosi and A619. Table S1 contains fertility identification of F<sub>1</sub>
hybrids crossed between CMS-C lines and A619. Table S2 contains fertility
ratings of BC<sub>2</sub>F<sub>1</sub>, BC<sub>3</sub>F<sub>1</sub>, BC<sub>6</sub>F<sub>1</sub>
and F<sub>2:3</sub> progenies derived from the cross between CHuangzaosi and
A619. Table S3 contains the information of 11 markers for QTL mapping. Table S4
contains genotypes of each individual for QTL mapping. Table S5 contains
phenotype of each individual for QTL mapping. File S1 contains SNP information
for QTL-seq.
DOI: 10.6084/m9.figshare.19617166
title: Gold-based strip sensor for the rapid and sensitive detection of butralin in tomatoes and peppers

description: Butralin is a widely used dinitroaniline herbicide. Butralin residues in vegetables or fruits represent a threat to human health. In this study, we developed a rapid and sensitive gold-based lateral flow immunoassay (LFIA) for butralin detection in tomato and green pepper samples based on a screened monoclonal antibody (mAb) against butralin. The mAb possessed a half-maximal inhibitory concentration (IC<sub>50</sub>) of 12.7 ng/mL, with no cross-reactivity toward other dinitroaniline herbicides. The established LFIA strip had a visible limit of detection (LOD) of 50 ng/g and a cut-off value of 2000 ng/g in tomato and green pepper samples. According to the calibration curves for quantitative analysis, the calculated LODs of the LFIA strip were 4.7 ng/g and 4.3 ng/g in tomato and green pepper, respectively. The results were obtained within 10 min. The average recoveries ranged between 95.4% and 109.6% with a coefficient of variation (CV) of 4.3% to 7.1% in tomato samples and between 94.8% and 109.1% with a CV of 3.9% to 6.1% in green pepper samples. These data suggested that our proposed LFIA is a sensitive, specific, and reliable method for the rapid detection of butralin in real samples.
DOI: 10.6084/m9.figshare.7034279
title: Transcription factors Rv0081 and Rv3334 connect the early and the enduring hypoxic response of <i>Mycobacterium tuberculosis</i>

description: The ability of <i>Mycobacterium tuberculosis</i> (<i>M. tb</i>) to survive and persist in the host for decades in an asymptomatic state is an important aspect of tuberculosis pathogenesis. Although adaptation to hypoxia is thought to play a prominent role underlying <i>M. tb</i> persistence, how the bacteria achieve this goal is largely unknown. <i>Rv0081</i>, a member of the DosR regulon, is induced at the early stage of hypoxia while <i>Rv3334</i> is one of the enduring hypoxic response genes. In this study, we uncovered genetic interactions between these two transcription factors. RNA-seq analysis of Δ<i>Rv0081</i> and Δ<i>Rv3334</i> revealed that the gene expression profiles of these two mutants were highly similar. We also found that under hypoxia, Rv0081 positively regulated the expression of <i>Rv3334</i> while Rv3334 repressed transcription of <i>Rv0081</i>. In addition, we demonstrated that Rv0081 formed dimer and bound to the promoter region of <i>Rv3334</i>. Taken together, these data suggest that Rv0081 and Rv3334 work in the same regulatory pathway and that Rv3334 functions immediately downstream of Rv0081. We also found that Rv3334 is a bona fide regulator of the enduring hypoxic response genes. Our study has uncovered a regulatory pathway that connects the early and the enduring hypoxic response, revealing a transcriptional cascade that coordinates the temporal response of <i>M. tb</i> to hypoxia.
DOI: 10.6084/m9.figshare.7558916
title: Additional file 1: of A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication

description: Table S1. Summary of RNA-seq datasets used in this study. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.19617166.v1
title: Gold-based strip sensor for the rapid and sensitive detection of butralin in tomatoes and peppers

description: Butralin is a widely used dinitroaniline herbicide. Butralin residues in vegetables or fruits represent a threat to human health. In this study, we developed a rapid and sensitive gold-based lateral flow immunoassay (LFIA) for butralin detection in tomato and green pepper samples based on a screened monoclonal antibody (mAb) against butralin. The mAb possessed a half-maximal inhibitory concentration (IC<sub>50</sub>) of 12.7 ng/mL, with no cross-reactivity toward other dinitroaniline herbicides. The established LFIA strip had a visible limit of detection (LOD) of 50 ng/g and a cut-off value of 2000 ng/g in tomato and green pepper samples. According to the calibration curves for quantitative analysis, the calculated LODs of the LFIA strip were 4.7 ng/g and 4.3 ng/g in tomato and green pepper, respectively. The results were obtained within 10 min. The average recoveries ranged between 95.4% and 109.6% with a coefficient of variation (CV) of 4.3% to 7.1% in tomato samples and between 94.8% and 109.1% with a CV of 3.9% to 6.1% in green pepper samples. These data suggested that our proposed LFIA is a sensitive, specific, and reliable method for the rapid detection of butralin in real samples.
DOI: 10.6084/m9.figshare.7558895.v1
title: Identification of novel microRNAs in rice (<i>Oryza sativa)</i> based on the cleavage signals in precursors

description: MicroRNAs (miRNAs) are crucial regulators of gene expression in plants and a growing number of novel miRNA genes have been cloned in rice in recent years. However, there is no evidence that all miRNAs have been discovered, especially for those low expression ones which are difficult to be found by conventional methods. By taking advantage of the finding that DCL1-mediated cleavage signals for the processing of the miRNA precursors could be used as the clues for novel miRNAs’ discovery, a genome-wide search for rice miRNA candidates was carried out. As a result, 51 previously validated miRNAs and 24 novel miRNA candidates were discovered. After target prediction and degradome sequencing data-based validation, coupled with reverse approach retest, 10 miRNA candidate–mRNA target pairs were further identified, providing a basis for in-depth functional analysis of these miRNA candidates. Besides, some isomiRs found in this study showed more likely to be the real miRNAs. We also found an exceptional example which did not obey the rule that 22-nt miRNAs have the ability to trigger the phased siRNAs production from the cleaved targets.