cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20003359
title: Additional file 1 of Evaluation of sustainable susceptibility to Plasmodium vivax infection among colonized Anopheles darlingi and Anopheles deaneorum

description: Additional file 1: Table S1. Data from each patient and mosquitoes number used to DMFA. Table S2. Oocyst and sporozoites number of each DMFA from paired feeding assay. Table S3. Oocyst and sporozoites number of each DMFA using only Anopheles darlingi. Table S4.Oocyst and sporozoites number of each DMFA using only Anopheles deaneorum.
DOI: 10.6084/m9.figshare.20003371
title: Additional file 3 of Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR

description: Additional file 3: Supplementary Table 1. Sampling details for the analysed metagenomes. Supplementary Table 2. Completeness of MAGs calculated based on 43 SCGs (Anantharaman, Brown, Hug, et al. 2016). Supplementary Table 3. Basic statistics and taxonomy (GTDB, NCBI) for the MAGs assembled in this study. Supplementary Table 4. List of final, dereplicated bins and the ones of lower quatily that were collapsed into them. Supplementary Table 5. Annotation results of CPRs at class level. KEGG modules were manually checked for completeness after annotationg the bins using different databases (Panda, TIGR, COG, Interproscan and Pfam). Supplementary Table 6. Recruitment results (coverage per Gbp) for all bins versus all samples analyzed in this study. Supplementary Table 7. Basic statistics for Refseq 81 database, representative CPR genomes from GTDB r89 and the MAGs assembled in this study. Supplementary Table 8. Basic statistics for the manually curated SPC database used in this study. Supplementary Table 9. Basic statistics for the manually curated free-living bacteria database used in this study. Supplementary Table 10. Basic statistics for the representative CPRs genomes in GTDB versions r89 database. Supplementary Table 11. List of CPR FISH probes (their sequence, specificity and target group) and cells measurements and statistics. Supplementary Table 12. Average nucleotide identity (ANI) values computed between all pairs of freshwater CPR MAGs obtained in this study. Supplementary Table 13. GRiD results for the dereplicated bins, estimating the rate of genome replication. Supplementary Table 14. Phage defense systems and their occurencess in CPRs, SPCs and free-living bacteria. Supplementary Table 15. Predicted rhodopsins in CPRs, including all GTDB representative genomes and the282 MAGs obtained in this study. Supplementary Table S16. CAZys and their occurence in freshwater CPR genomes.
DOI: 10.6084/m9.figshare.20003371.v1
title: Additional file 3 of Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR

description: Additional file 3: Supplementary Table 1. Sampling details for the analysed metagenomes. Supplementary Table 2. Completeness of MAGs calculated based on 43 SCGs (Anantharaman, Brown, Hug, et al. 2016). Supplementary Table 3. Basic statistics and taxonomy (GTDB, NCBI) for the MAGs assembled in this study. Supplementary Table 4. List of final, dereplicated bins and the ones of lower quatily that were collapsed into them. Supplementary Table 5. Annotation results of CPRs at class level. KEGG modules were manually checked for completeness after annotationg the bins using different databases (Panda, TIGR, COG, Interproscan and Pfam). Supplementary Table 6. Recruitment results (coverage per Gbp) for all bins versus all samples analyzed in this study. Supplementary Table 7. Basic statistics for Refseq 81 database, representative CPR genomes from GTDB r89 and the MAGs assembled in this study. Supplementary Table 8. Basic statistics for the manually curated SPC database used in this study. Supplementary Table 9. Basic statistics for the manually curated free-living bacteria database used in this study. Supplementary Table 10. Basic statistics for the representative CPRs genomes in GTDB versions r89 database. Supplementary Table 11. List of CPR FISH probes (their sequence, specificity and target group) and cells measurements and statistics. Supplementary Table 12. Average nucleotide identity (ANI) values computed between all pairs of freshwater CPR MAGs obtained in this study. Supplementary Table 13. GRiD results for the dereplicated bins, estimating the rate of genome replication. Supplementary Table 14. Phage defense systems and their occurencess in CPRs, SPCs and free-living bacteria. Supplementary Table 15. Predicted rhodopsins in CPRs, including all GTDB representative genomes and the282 MAGs obtained in this study. Supplementary Table S16. CAZys and their occurence in freshwater CPR genomes.
DOI: 10.6084/m9.figshare.20003376.v1
title: Additional file 1 of SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV

description: Additional file 1: Consensus sequences and PID results. Consensus sequences for each genotype (A–H) and the pan-genotype, and corresponding PID as calculated by MAFFT.
DOI: 10.6084/m9.figshare.20003376
title: Additional file 1 of SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV

description: Additional file 1: Consensus sequences and PID results. Consensus sequences for each genotype (A–H) and the pan-genotype, and corresponding PID as calculated by MAFFT.
DOI: 10.6084/m9.figshare.20003379
title: Additional file 2 of SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV

description: Additional file 2: Consensus sequence alignments results from various tools. We compared the alignment results of Kalign, MAFFT (8 consensus sequences) and Jalview/MAFFT (over 20,000 sequences). Aligning the 8 HBV genotypes before creating a consensus avoided bias towards the more common genotypes (C and B) and excluded the sequences with long insertions (highlighted in green).
DOI: 10.6084/m9.figshare.20003413
title: Adding guarana powder to medfly diets: an alternative for improving the Sterile Insect Technique

description: ABSTRACT Ceratitis capitata (medfly) is a globally important horticultural pest that can be controlled using the sterile insect technique (SIT), but the success of SIT depends on the sexual performance of mass-reared males when released into the field. We added “guarana” (Paullinia cupana) powder (derived from an Amazonian fruit that is considered to be a stimulant with aphrodisiac effects, capable of improving human physical stamina) to the diets of adult male medflies to determine whether it increased their sexual performance. The basic diet of a protein extract + sucrose (1:3) was enriched with guarana powder (3 % on a volume basis). Experiments examining sexual competitiveness were performed using lab-reared males fed with the enriched diet vs. lab-reared males fed on the basic diet (and lab-reared females fed on the basic diet), as well as lab-reared males fed with the enriched diet vs. wild males fed on the basic diet (and wild females fed on the basic diet). The results of both experiments indicated that males maintained on diets enriched with guarana powder showed higher copulation successes than males fed only with the basic diet. Guarana powder therefore contributed to the greater mating success of lab-reared males (probably because of its stimulant properties), and may represent a new and viable option for increasing SIT effectiveness.
DOI: 10.6084/m9.figshare.20003411
title: Water erosion in surface soil conditions: runoff velocity, concentration and D50 index of sediments in runoff

description: ABSTRACT Water erosion and contamination of water resources are influenced by concentration and diameter of sediments in runoff. This study aimed to quantify runoff velocity and concentration and the D50 index of sediments in runoff under different soil surface managements, in the following treatments: i) cropped systems: no-tilled soil covered by ryegrass (Lolium multiflorum Lam.) residue, with high soil cover and minimal roughness (HCR); no tilled soil covered by vetch (Vicia sativa L.) residue, with high soil cover and minimal roughness (HCV); chiseled soil after ryegrass crop removing the above-ground residues and keeping only the root system, with high roughness (HRR); chiseled soil after vetch crop removing the above-ground residues and keeping only the root system, with high roughness (HRV); ii) bare and chiseled soil, with high roughness (BHR). The research was conducted on a Humic Dystrupept under simulated rainfall. The design was completely randomized and each treatment was replicated twice. Eight rainfall events of controlled intensity (65 mm h−1) were applied to each treatment for 90 minutes. The D50 index, runoff velocity and sediment concentration were influenced by crop and soil management. Runoff velocity was more intensely reduced by cover crop residues than by surface roughness. Regardless of surface condition, the D50 index and concentration of sediment in runoff were lower under ryegrass than vetch crop. Runoff velocity and the D50 index were exponentially and inversely correlated with soil cover by residues and with surface roughness, while the D50 index was positively and exponentially correlated with runoff velocity.
DOI: 10.6084/m9.figshare.20003414.v1
title: Bacterial strains from floodplain soils perform different plant-growth promoting processes and enhance cowpea growth

description: ABSTRACT Certain nodulating nitrogen-fixing bacteria in legumes and other nodule endophytes perform different plant-growth promoting processes. The objective of this study was to evaluate 26 bacterial strains isolated from cowpea nodules grown in floodplain soils in the Brazilian savannas, regarding performance of plant-growth promoting processes and ability to enhance cowpea growth. We also identified these strains by 16S rRNA sequencing. The following processes were evaluated: free-living biological nitrogen fixation (BNF), solubilization of calcium, aluminum and iron phosphates and production of indole-3-acetic acid (IAA). The abilities to nodulate and promote cowpea growth were evaluated in Leonard jars. Partial sequencing of the 16S rRNA gene identified 60 % of the strains as belonging to genus Paenibacillus. The following four genera were also identified: Bacillus, Bradyrhizobium, Enterobacter and Pseudomonas. None of the strains fixed N2 free-living. Among the strains, 80 % solubilized Ca phosphate and one solubilized Al phosphate and none solubilized Fe phosphate. The highest IAA concentrations (52.37, 51.52 and 51.00 μg mL−1) were obtained in the 79 medium with tryptophan by Enterobacter strains UFPI B5-7A, UFPI B5-4 and UFPI B5-6, respectively. Only eight strains nodulated cowpea, however, all increased production of total dry matter. The fact that the strains evaluated perform different biological processes to promote plant growth indicates that these strains have potential use in agricultural crops to increase production and environmental sustainability.
DOI: 10.6084/m9.figshare.20003411.v1
title: Water erosion in surface soil conditions: runoff velocity, concentration and D50 index of sediments in runoff

description: ABSTRACT Water erosion and contamination of water resources are influenced by concentration and diameter of sediments in runoff. This study aimed to quantify runoff velocity and concentration and the D50 index of sediments in runoff under different soil surface managements, in the following treatments: i) cropped systems: no-tilled soil covered by ryegrass (Lolium multiflorum Lam.) residue, with high soil cover and minimal roughness (HCR); no tilled soil covered by vetch (Vicia sativa L.) residue, with high soil cover and minimal roughness (HCV); chiseled soil after ryegrass crop removing the above-ground residues and keeping only the root system, with high roughness (HRR); chiseled soil after vetch crop removing the above-ground residues and keeping only the root system, with high roughness (HRV); ii) bare and chiseled soil, with high roughness (BHR). The research was conducted on a Humic Dystrupept under simulated rainfall. The design was completely randomized and each treatment was replicated twice. Eight rainfall events of controlled intensity (65 mm h−1) were applied to each treatment for 90 minutes. The D50 index, runoff velocity and sediment concentration were influenced by crop and soil management. Runoff velocity was more intensely reduced by cover crop residues than by surface roughness. Regardless of surface condition, the D50 index and concentration of sediment in runoff were lower under ryegrass than vetch crop. Runoff velocity and the D50 index were exponentially and inversely correlated with soil cover by residues and with surface roughness, while the D50 index was positively and exponentially correlated with runoff velocity.
DOI: 10.6084/m9.figshare.20003413.v1
title: Adding guarana powder to medfly diets: an alternative for improving the Sterile Insect Technique

description: ABSTRACT Ceratitis capitata (medfly) is a globally important horticultural pest that can be controlled using the sterile insect technique (SIT), but the success of SIT depends on the sexual performance of mass-reared males when released into the field. We added “guarana” (Paullinia cupana) powder (derived from an Amazonian fruit that is considered to be a stimulant with aphrodisiac effects, capable of improving human physical stamina) to the diets of adult male medflies to determine whether it increased their sexual performance. The basic diet of a protein extract + sucrose (1:3) was enriched with guarana powder (3 % on a volume basis). Experiments examining sexual competitiveness were performed using lab-reared males fed with the enriched diet vs. lab-reared males fed on the basic diet (and lab-reared females fed on the basic diet), as well as lab-reared males fed with the enriched diet vs. wild males fed on the basic diet (and wild females fed on the basic diet). The results of both experiments indicated that males maintained on diets enriched with guarana powder showed higher copulation successes than males fed only with the basic diet. Guarana powder therefore contributed to the greater mating success of lab-reared males (probably because of its stimulant properties), and may represent a new and viable option for increasing SIT effectiveness.
DOI: 10.6084/m9.figshare.20003414
title: Bacterial strains from floodplain soils perform different plant-growth promoting processes and enhance cowpea growth

description: ABSTRACT Certain nodulating nitrogen-fixing bacteria in legumes and other nodule endophytes perform different plant-growth promoting processes. The objective of this study was to evaluate 26 bacterial strains isolated from cowpea nodules grown in floodplain soils in the Brazilian savannas, regarding performance of plant-growth promoting processes and ability to enhance cowpea growth. We also identified these strains by 16S rRNA sequencing. The following processes were evaluated: free-living biological nitrogen fixation (BNF), solubilization of calcium, aluminum and iron phosphates and production of indole-3-acetic acid (IAA). The abilities to nodulate and promote cowpea growth were evaluated in Leonard jars. Partial sequencing of the 16S rRNA gene identified 60 % of the strains as belonging to genus Paenibacillus. The following four genera were also identified: Bacillus, Bradyrhizobium, Enterobacter and Pseudomonas. None of the strains fixed N2 free-living. Among the strains, 80 % solubilized Ca phosphate and one solubilized Al phosphate and none solubilized Fe phosphate. The highest IAA concentrations (52.37, 51.52 and 51.00 μg mL−1) were obtained in the 79 medium with tryptophan by Enterobacter strains UFPI B5-7A, UFPI B5-4 and UFPI B5-6, respectively. Only eight strains nodulated cowpea, however, all increased production of total dry matter. The fact that the strains evaluated perform different biological processes to promote plant growth indicates that these strains have potential use in agricultural crops to increase production and environmental sustainability.
DOI: 10.6084/m9.figshare.20003421
title: Additional file 2 of Modeling binding specificities of transcription factor pairs with random forests

description: Additional file 2. Excel sheet of TF pair AUROC values with studied CAP-SELEX libraries (N = 362).
DOI: 10.6084/m9.figshare.20003421.v1
title: Additional file 2 of Modeling binding specificities of transcription factor pairs with random forests

description: Additional file 2. Excel sheet of TF pair AUROC values with studied CAP-SELEX libraries (N = 362).
DOI: 10.6084/m9.figshare.20003424
title: Additional file 1 of WeCoNET: a host–pathogen interactome database for deciphering crucial molecular networks of wheat-common bunt cross-talk mechanisms

description: Additional file 1. Potential protein-protein interaction pairs for experimental validation.
DOI: 10.6084/m9.figshare.20003424.v1
title: Additional file 1 of WeCoNET: a host–pathogen interactome database for deciphering crucial molecular networks of wheat-common bunt cross-talk mechanisms

description: Additional file 1. Potential protein-protein interaction pairs for experimental validation.
DOI: 10.6084/m9.figshare.20003426
title: Effects of glutamine on performance and intestinal mucosa morphometry of broiler chickens vaccinated against coccidiosis

description: ABSTRACT This study aimed to assess the effects of glutamine as feed additive on performance and intestinal mucosa morphometry of broiler chickens vaccinated against coccidiosis. A total of 400 day-old male chicks were randomly assigned to four treatments (NVNG – no vaccination, no glutamine supplementation; NVG – no vaccination, glutamine supplementation (10 g kg−1); VNG – vaccination, no glutamine supplementation; VG – vaccination, glutamine supplementation) replicated four times with 25 birds per replicate. A commercial sprayed-on vaccine against coccidiosis containing Eimeria acervulina, E. maxima, E. mivati, and E. tenella was administered at the hatchery. Broiler performance was evaluated from 1-28 days, and morphometric parameters were analyzed at 14, 21, and 28 days of age. Body weight gain and feed intake were negatively affected by vaccination, but not by glutamine. Vaccination increased crypt depth in the duodenum and jejunum at 21 and 28 days. In conclusion, this study showed that glutamine was not able to increase weight gain of broiler chickens, irrespective of whether the animals were vaccinated or not against coccidiosis. Glutamine supplementation was able to improve feed conversion in vaccinated birds suggesting trophic effect on intestinal epithelium improving.
DOI: 10.6084/m9.figshare.20003426.v1
title: Effects of glutamine on performance and intestinal mucosa morphometry of broiler chickens vaccinated against coccidiosis

description: ABSTRACT This study aimed to assess the effects of glutamine as feed additive on performance and intestinal mucosa morphometry of broiler chickens vaccinated against coccidiosis. A total of 400 day-old male chicks were randomly assigned to four treatments (NVNG – no vaccination, no glutamine supplementation; NVG – no vaccination, glutamine supplementation (10 g kg−1); VNG – vaccination, no glutamine supplementation; VG – vaccination, glutamine supplementation) replicated four times with 25 birds per replicate. A commercial sprayed-on vaccine against coccidiosis containing Eimeria acervulina, E. maxima, E. mivati, and E. tenella was administered at the hatchery. Broiler performance was evaluated from 1-28 days, and morphometric parameters were analyzed at 14, 21, and 28 days of age. Body weight gain and feed intake were negatively affected by vaccination, but not by glutamine. Vaccination increased crypt depth in the duodenum and jejunum at 21 and 28 days. In conclusion, this study showed that glutamine was not able to increase weight gain of broiler chickens, irrespective of whether the animals were vaccinated or not against coccidiosis. Glutamine supplementation was able to improve feed conversion in vaccinated birds suggesting trophic effect on intestinal epithelium improving.
DOI: 10.6084/m9.figshare.20003434
title: Agriculture and food security challenge of climate change: a dynamic analysis for policy selection

description: ABSTRACT This study presents an empirical examination of climate change related to vulnerability impacts on food security and remedial adaptation options as a suitable strategy by prioritizing needs over a 50-year period. An Empirical Dynamic Commutable General Equilibrium Model for Climate and the Economy (EDCGECE) is applied using future strategies for Malaysia against a baseline scenario of existing conditions, following the top-down options. The model takes into account various climatic variables, including climatic damage, carbon cycle, temperature and rainfall fluctuation, carbon emissions, vulnerability and carbon concentrations, which were adapted from national observational predictions of climatic changes caused by global warming from 2015 to 2065. The results prioritize climate change mitigation for the future. Specifically, this study estimates Malaysia’s food sustainability prospects without adaptation actions and with 5 % to 20 % adaptation actions overtime in different adaptation scenarios, as contrasted with the baseline. The results indicate that food sustainability cost in the baseline in 2015 is 859.3 million US Dollar (USD), which is about a 30-35 % shortage compared with the national targets, and that the shortage will rise over time to USD 987.3 million in 2065. However, the cost of applying different levels of adaptation for food sustainability over time is rising considerably. However, the residual damage also decreases with all adaptation actions in the different scenarios. Thus, adaptation shows a positive sign for Malaysia’s agricultural sectors. As growth values are positive and show rising trends, therefore the projected adaptation policy can be effective for food sustainability for sustainable future strategies in Malaysia.
DOI: 10.6084/m9.figshare.20003434.v1
title: Agriculture and food security challenge of climate change: a dynamic analysis for policy selection

description: ABSTRACT This study presents an empirical examination of climate change related to vulnerability impacts on food security and remedial adaptation options as a suitable strategy by prioritizing needs over a 50-year period. An Empirical Dynamic Commutable General Equilibrium Model for Climate and the Economy (EDCGECE) is applied using future strategies for Malaysia against a baseline scenario of existing conditions, following the top-down options. The model takes into account various climatic variables, including climatic damage, carbon cycle, temperature and rainfall fluctuation, carbon emissions, vulnerability and carbon concentrations, which were adapted from national observational predictions of climatic changes caused by global warming from 2015 to 2065. The results prioritize climate change mitigation for the future. Specifically, this study estimates Malaysia’s food sustainability prospects without adaptation actions and with 5 % to 20 % adaptation actions overtime in different adaptation scenarios, as contrasted with the baseline. The results indicate that food sustainability cost in the baseline in 2015 is 859.3 million US Dollar (USD), which is about a 30-35 % shortage compared with the national targets, and that the shortage will rise over time to USD 987.3 million in 2065. However, the cost of applying different levels of adaptation for food sustainability over time is rising considerably. However, the residual damage also decreases with all adaptation actions in the different scenarios. Thus, adaptation shows a positive sign for Malaysia’s agricultural sectors. As growth values are positive and show rising trends, therefore the projected adaptation policy can be effective for food sustainability for sustainable future strategies in Malaysia.