cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14328643
title: Field and laboratory assessments of sugarcane mutants selected in vitro for resistance to imazapyr herbicide

description: Abstract Seven imazapyr-tolerant mutant sugarcane plants, previously generated by in vitro mutagenesis, were studied. The imazapyr concentrations required to inhibit their acetolactate synthase (ALS basal activity) (IC50 as μmoles acetoin h-1 mg-1 protein) were 0.77 - 5.36 times greater than that of the N12 ‘parent’. The basal ALS activities of Mut1 and Mut6 were 1.4-fold higher than that of N12. When the mutants were sprayed with Arsenal® GEN 2 (312 and 624 g a.i. imazapyr ha-1), 2 months after field planting, and evaluated 9 months later, live stalk height and number were significantly lowest in Mut2, Mut3 and the control N12. No differences in sucrose, fibre and estimated yield were observed amongst lines in untreated plots. Mutant plants germinated and grew in soil treated with the herbicide (at the lethal dose of 1248 g a.i. ha-1). The Mut lines tested in this study offer improved options for weed control.
DOI: 10.6084/m9.figshare.14328643.v1
title: Field and laboratory assessments of sugarcane mutants selected in vitro for resistance to imazapyr herbicide

description: Abstract Seven imazapyr-tolerant mutant sugarcane plants, previously generated by in vitro mutagenesis, were studied. The imazapyr concentrations required to inhibit their acetolactate synthase (ALS basal activity) (IC50 as μmoles acetoin h-1 mg-1 protein) were 0.77 - 5.36 times greater than that of the N12 ‘parent’. The basal ALS activities of Mut1 and Mut6 were 1.4-fold higher than that of N12. When the mutants were sprayed with Arsenal® GEN 2 (312 and 624 g a.i. imazapyr ha-1), 2 months after field planting, and evaluated 9 months later, live stalk height and number were significantly lowest in Mut2, Mut3 and the control N12. No differences in sucrose, fibre and estimated yield were observed amongst lines in untreated plots. Mutant plants germinated and grew in soil treated with the herbicide (at the lethal dose of 1248 g a.i. ha-1). The Mut lines tested in this study offer improved options for weed control.
DOI: 10.6084/m9.figshare.14328645
title: Overcoming crossing barriers between jatropha (Jatropha curcas L.) and castor bean (Ricinus communisL.)

description: Abstract A limitation in improvement of jatropha (Jatropha curcas) has been the low genetic variation among the available germplasm. An alternative to create genetic variability and incorporate desirable traits is through wide crossing. Due to reproductive barriers, wide crossing in jatropha has had limited success. In this experiment, intergeneric hybridization between jatropha and castor bean (Ricinus communis) was performed. In both direct and reciprocal crosses, a few stigma-compatible pollen grains were found. The pollen tube grew normally and reached the style base within an hour after pollination, but the embryo aborted a few days later. This indicated that the hybridization barrier was post-fertilization and thus the ovules were excised, cultured in MS medium supplemented with 1 mg L-1 IAA, and subcultured every four weeks. Finally we obtained one intergeneric hybrid plant, which was vegetatively propagated for further study.
DOI: 10.6084/m9.figshare.14328645.v1
title: Overcoming crossing barriers between jatropha (Jatropha curcas L.) and castor bean (Ricinus communisL.)

description: Abstract A limitation in improvement of jatropha (Jatropha curcas) has been the low genetic variation among the available germplasm. An alternative to create genetic variability and incorporate desirable traits is through wide crossing. Due to reproductive barriers, wide crossing in jatropha has had limited success. In this experiment, intergeneric hybridization between jatropha and castor bean (Ricinus communis) was performed. In both direct and reciprocal crosses, a few stigma-compatible pollen grains were found. The pollen tube grew normally and reached the style base within an hour after pollination, but the embryo aborted a few days later. This indicated that the hybridization barrier was post-fertilization and thus the ovules were excised, cultured in MS medium supplemented with 1 mg L-1 IAA, and subcultured every four weeks. Finally we obtained one intergeneric hybrid plant, which was vegetatively propagated for further study.
DOI: 10.6084/m9.figshare.5634991
title: Phenotypic stability in cassava estimated by the AMMI analysis with supplementary genotypes

description: Abstract Adaptability is the yield response of cassava genotypes to environmental improvement, and stability is the predictability of this response to variations. The objective of this study was to evaluate the yield stability and adaptability of cassava varieties and clones using the AMMI (Additive Main Effects and Multiplicative Interaction) methodology and auxiliary tools as supplementary genotype and environment. The responses of 24 cassava genotypes were evaluated in three environments located in the state of Alagoas, Brazil, in randomized blocks design, with 24 treatments and three replications. The effects of genotype and genotype x environment interactions significantly influenced yield. Genotypes differed regarding the adaptability and stability of yield response, and the varieties Cria Menino and Preta do Araripe were considered ideal genotypes due to high adaptability and yield stability. Among the three tested environments, Limoeiro de Anadia was the best since it presented high yield, phenotypically stable genotypes for cassava breeding programs.
DOI: 10.6084/m9.figshare.5634991.v1
title: Phenotypic stability in cassava estimated by the AMMI analysis with supplementary genotypes

description: Abstract Adaptability is the yield response of cassava genotypes to environmental improvement, and stability is the predictability of this response to variations. The objective of this study was to evaluate the yield stability and adaptability of cassava varieties and clones using the AMMI (Additive Main Effects and Multiplicative Interaction) methodology and auxiliary tools as supplementary genotype and environment. The responses of 24 cassava genotypes were evaluated in three environments located in the state of Alagoas, Brazil, in randomized blocks design, with 24 treatments and three replications. The effects of genotype and genotype x environment interactions significantly influenced yield. Genotypes differed regarding the adaptability and stability of yield response, and the varieties Cria Menino and Preta do Araripe were considered ideal genotypes due to high adaptability and yield stability. Among the three tested environments, Limoeiro de Anadia was the best since it presented high yield, phenotypically stable genotypes for cassava breeding programs.
DOI: 10.6084/m9.figshare.5634658
title: Artificial neural networks and linear discriminant analysis in early selection among sugarcane families

description: Abstract One of the major challenges in sugarcane breeding programs is an efficient selection of genotypes in the initial phase. The purpose of this study was to compare modelling by artificial neural networks (ANN) and linear discriminant analysis (LDA) as alternatives for the selection of promising sugarcane families based on the indirect traits number of sugarcane stalks (NS), stalk diameter (SD) and stalk height (SH). The analysis focused on two models, a full one with all predictors, and a reduced one, from which the variable SH was excluded. To compare and assess the applied methods, the apparent error rate (AER) and true positive rate (TPR) were used, derived from the confusion matrix. Modeling with ANN and LDA can be used successfully for selection among sugarcane families. The reduced model may be preferable, for having a low AER, high TPR and being easier to obtain in operational terms.
DOI: 10.6084/m9.figshare.5634658.v1
title: Artificial neural networks and linear discriminant analysis in early selection among sugarcane families

description: Abstract One of the major challenges in sugarcane breeding programs is an efficient selection of genotypes in the initial phase. The purpose of this study was to compare modelling by artificial neural networks (ANN) and linear discriminant analysis (LDA) as alternatives for the selection of promising sugarcane families based on the indirect traits number of sugarcane stalks (NS), stalk diameter (SD) and stalk height (SH). The analysis focused on two models, a full one with all predictors, and a reduced one, from which the variable SH was excluded. To compare and assess the applied methods, the apparent error rate (AER) and true positive rate (TPR) were used, derived from the confusion matrix. Modeling with ANN and LDA can be used successfully for selection among sugarcane families. The reduced model may be preferable, for having a low AER, high TPR and being easier to obtain in operational terms.
DOI: 10.6084/m9.figshare.14328649
title: Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence

description: Abstract In this study, we quantify and document the distribution and organization of cpSSRs in the chloroplast genome of 31 Eucalyptus species. Our sample included all previously sequenced plastomes of Eucalyptus species available from the NCBI online database. We processed the complete cpDNA sequences and identified mono-, di-, tri-, tetra-, penta-, and hexanucleotide cpSSRs, with the majority of cpSSRs classified as mononucleotide. After genome microsatellite selection, we evaluated the microsatellites for coding and non-coding regions and cpSSRs were predominantly identified in non-coding regions of cpDNA for all nucleotide types. Penta- and hexanucleotide cpSSRs were the least frequent types of microsatellites. We also developed and virtually amplified 60 primers pairs that can be used in studies of Eucalyptus species. Thus, these cpSSR regions can be used in studies assessing the ecology, breeding, and conservation of the genus.
DOI: 10.6084/m9.figshare.14328649.v1
title: Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence

description: Abstract In this study, we quantify and document the distribution and organization of cpSSRs in the chloroplast genome of 31 Eucalyptus species. Our sample included all previously sequenced plastomes of Eucalyptus species available from the NCBI online database. We processed the complete cpDNA sequences and identified mono-, di-, tri-, tetra-, penta-, and hexanucleotide cpSSRs, with the majority of cpSSRs classified as mononucleotide. After genome microsatellite selection, we evaluated the microsatellites for coding and non-coding regions and cpSSRs were predominantly identified in non-coding regions of cpDNA for all nucleotide types. Penta- and hexanucleotide cpSSRs were the least frequent types of microsatellites. We also developed and virtually amplified 60 primers pairs that can be used in studies of Eucalyptus species. Thus, these cpSSR regions can be used in studies assessing the ecology, breeding, and conservation of the genus.
DOI: 10.6084/m9.figshare.14328651
title: Water deficit increases the frequency of hybrid citrus with polyembryonic female parents

description: Abstract The aim of this study was to develop a methodology that uses water deficit induction to increase the frequency of hybrids in Citrus varieties that have a high and an intermediate level of polyembryony, respectively. The experiment examined the ‘Sunki Tropical’ mandarin and ‘Rangpur Santa Cruz’ lime genotypes at three water stress intensities: 20, 40 and 100% of the pot capacity (PC). The generated fruits were harvested, and the seeds were counted. After germination, the number of nucellar and hybrid seedlings was determined. For ‘Rangpur Santa Cruz’ lime genotype, the highest hybrid frequency generated was 64.2%, which occurred at a PC of 40% and exceeded by 12% that occurring at a PC of 100%. For ‘Sunki Tropical’ mandarin, the highest observed hybrid frequency was 21.75%, which occurred at a PC of 20% and was more than double the hybrid frequency of 8.57% observed at 100% of the PC.
DOI: 10.6084/m9.figshare.14328651.v1
title: Water deficit increases the frequency of hybrid citrus with polyembryonic female parents

description: Abstract The aim of this study was to develop a methodology that uses water deficit induction to increase the frequency of hybrids in Citrus varieties that have a high and an intermediate level of polyembryony, respectively. The experiment examined the ‘Sunki Tropical’ mandarin and ‘Rangpur Santa Cruz’ lime genotypes at three water stress intensities: 20, 40 and 100% of the pot capacity (PC). The generated fruits were harvested, and the seeds were counted. After germination, the number of nucellar and hybrid seedlings was determined. For ‘Rangpur Santa Cruz’ lime genotype, the highest hybrid frequency generated was 64.2%, which occurred at a PC of 40% and exceeded by 12% that occurring at a PC of 100%. For ‘Sunki Tropical’ mandarin, the highest observed hybrid frequency was 21.75%, which occurred at a PC of 20% and was more than double the hybrid frequency of 8.57% observed at 100% of the PC.
DOI: 10.6084/m9.figshare.14328652
title: Resistance to bacterial halo blight in Arabica coffee lines derivative from the genotype C1195-5-6-2 under natural infection conditions

description: Abstract The aim of this study was to identify resistance to bacterial halo blight in Arabica coffee lines carrying Coffea racemosa genes. Eighteen Arabica coffee lines derivative from the genotype C1195-5-6-2, and the cultivars IAPAR 59 and IPR 99 were evaluated for resistance to bacterial halo blight in two trials carried out in field conditions, in Londrina, PR, Brazil. The cultivars Mundo Novo IAC 376-4 and Catuaí Vermelho IAC 81 were included as susceptible controls. Ten lines and the cultivar IAPAR 59 showed resistance to bacterial halo blight. The cultivar IPR 99 presented intermediate reaction, and the controls were very susceptible. This is the first study to show that lines derivative from the genotype C1195-5-6-2, which has C. racemosa genes, could be a source of resistance to bacterial halo blight in coffee breeding programs.
DOI: 10.6084/m9.figshare.14328652.v1
title: Resistance to bacterial halo blight in Arabica coffee lines derivative from the genotype C1195-5-6-2 under natural infection conditions

description: Abstract The aim of this study was to identify resistance to bacterial halo blight in Arabica coffee lines carrying Coffea racemosa genes. Eighteen Arabica coffee lines derivative from the genotype C1195-5-6-2, and the cultivars IAPAR 59 and IPR 99 were evaluated for resistance to bacterial halo blight in two trials carried out in field conditions, in Londrina, PR, Brazil. The cultivars Mundo Novo IAC 376-4 and Catuaí Vermelho IAC 81 were included as susceptible controls. Ten lines and the cultivar IAPAR 59 showed resistance to bacterial halo blight. The cultivar IPR 99 presented intermediate reaction, and the controls were very susceptible. This is the first study to show that lines derivative from the genotype C1195-5-6-2, which has C. racemosa genes, could be a source of resistance to bacterial halo blight in coffee breeding programs.
DOI: 10.25345/c5fj7q
title: MassIVE MSV000087116 - Comprehensive Proteomic Quantification of Bladder Stone Progression in a Cystinuric Mouse Model Using Data-Independent Acquisitions
title: Cystinuria is one of various disorders that cause biomineralization in the urinary system, including bladder stone formation in humans. It is most prevalent in children and adolescents and more aggressive in males. There is no cure, and only limited disease management techniques help to solubilize the stones. Recurrence, even after treatment, occurs frequently. Other than a buildup of cystine, little is known about factors involved in the formation, expansion, and recurrence of these stones. This study sought to define the growth of bladder stones, guided by micro-computed tomography imaging, and to profile dynamic stone proteome changes in a cystinuria mouse model. After bladder stones developed in vivo, they were harvested and separated into four developmental stages (sand, small, medium and large stone), based on their size. Data-dependent and data-independent acquisitions allowed deep profiling of stone proteomics. The proteomic signatures and pathways illustrated major changes as the stones grew. Stones initiate from a small nidus, grow outward, and show major enrichment in ribosomal proteins and factors related to coagulation and platelet degranulation, suggesting a major dysregulation in specific pathways that can be targeted for new therapeutic options.
DOI: 10.5281/zenodo.4614656
title: Test Sets for Jet Anomaly Detection at the LHC

description: A few datasets are updated in Version 2.1. These datasets are tagged with 'new' in the file names. - pT~1.2TeV top jets, the mother Z' mass is slightly adjusted to better match pT peaks around 1.2TeV - Especially there was a bug in the previous version for top jets with mass 80 GeV `*top_m80_100k*` (the top jet mass was not correctly set). So please be careful when you use those datasets. <strong>Data Description</strong> These datasets are generated as a series of test sets for anomalous jet tagging at the LHC. They include boosted W jets, Top jets, and Higgs jets. Jet transverse momentum is focused around 600 GeV and 1200 GeV (with prefix "pt1200_" in file names). Each file includes 100k original events from MadGraph, but might have slightly less events in the final h5 files due to fatjet pre-selection. Production processes include: pp -&gt; W' -&gt; W (jj) Z(\(\nu \nu\)); \(m_{W} = 59, 80, 120, 174 ~ \textrm{GeV}\) pp -&gt; Z' -&gt; t t~; \(m_t=80, 174 ~ \textrm{GeV}\). For m_t=80 GeV, the decay product W mass is set to 20 GeV. pp -&gt; HH -&gt; (hh) (hh), (h -&gt; jj); \(m_H=174 ~ \textrm{GeV}\), \(m_h = 20, 80 ~ \textrm{GeV}\) <strong>Data Generation</strong> Jet samples in this dataset are generated with MadGraph, Pythia8, and Delphes (no pile-up effects simulated). Particle flow objects are used to cluster jets. FastJet was used for jet clustering. Jets are clustered using the anti-kt algorithm with the cone size R=1.0. Leading jet: \(p_T&gt;450 ~ \textrm{GeV}\); sub-leading jet: \(p_T&gt;200 ~ \textrm{GeV}\) <strong>Data Structure</strong> To get jets: f['objects/jets'] For jets, there are two datasets: ['constituents', 'obs']. (jets information is stored with the higher-pt jet first) `obs[:, n_j - 1]`: jet four vectors and n-subjettiness for the \(n_j\)-th jet (pt, eta, phi, m, tau1, tau2, tau3, tau4, tau5) pt-sorted (highest first) jet constituents information are stored in variable length arrays for the \(n_j\)-th jet `constituents[:, n_j - 1]`: \(\{ E_i, P_{xi}, P_{yi}, P_{zi}, \textrm{PID}_i\}\) (PID: PDG for tracks; [22] for photons; [0] for neutral hadrons) <strong>Extra Notes</strong> Since the dataset is structured as events, for W jet samples, only leading jet is available; while for Top and Higgs jets, leading and sub-leading jets are both valid. One might need to restrict the jet \(p_T\) range at use. e.g. to get leading jet constituents: `f["objects/jets/constituents"][:, 0]` The file names are self-explanatory on the corresponding generation process. Each file was generated in 100K original Madgraph events. After the preselection, a small fraction of events is discarded. <strong>Contact</strong> we are welcoming any feedback, suggestions, or requests on new test samples. Please contact <em>chengtaoli.1990@gmail.com</em> for more information.
DOI: 10.5281/zenodo.3774559
title: Test Sets for Jet Anomaly Detection at the LHC

description: A few datasets are updated in Version 2.1. These datasets are tagged with 'new' in the file names. - pT~1.2TeV top jets, the mother Z' mass is slightly adjusted to better match pT peaks around 1.2TeV - Especially there was a bug in the previous version for top jets with mass 80 GeV `*top_m80_100k*` (the top jet mass was not correctly set). So please be careful when you use those datasets. <strong>Data Description</strong> These datasets are generated as a series of test sets for anomalous jet tagging at the LHC. They include boosted W jets, Top jets, and Higgs jets. Jet transverse momentum is focused around 600 GeV and 1200 GeV (with prefix "pt1200_" in file names). Each file includes 100k original events from MadGraph, but might have slightly less events in the final h5 files due to fatjet pre-selection. Production processes include: pp -&gt; W' -&gt; W (jj) Z(\(\nu \nu\)); \(m_{W} = 59, 80, 120, 174 ~ \textrm{GeV}\) pp -&gt; Z' -&gt; t t~; \(m_t=80, 174 ~ \textrm{GeV}\). For m_t=80 GeV, the decay product W mass is set to 20 GeV. pp -&gt; HH -&gt; (hh) (hh), (h -&gt; jj); \(m_H=174 ~ \textrm{GeV}\), \(m_h = 20, 80 ~ \textrm{GeV}\) <strong>Data Generation</strong> Jet samples in this dataset are generated with MadGraph, Pythia8, and Delphes (no pile-up effects simulated). Particle flow objects are used to cluster jets. FastJet was used for jet clustering. Jets are clustered using the anti-kt algorithm with the cone size R=1.0. Leading jet: \(p_T&gt;450 ~ \textrm{GeV}\); sub-leading jet: \(p_T&gt;200 ~ \textrm{GeV}\) <strong>Data Structure</strong> To get jets: f['objects/jets'] For jets, there are two datasets: ['constituents', 'obs']. (jets information is stored with the higher-pt jet first) `obs[:, n_j - 1]`: jet four vectors and n-subjettiness for the \(n_j\)-th jet (pt, eta, phi, m, tau1, tau2, tau3, tau4, tau5) pt-sorted (highest first) jet constituents information are stored in variable length arrays for the \(n_j\)-th jet `constituents[:, n_j - 1]`: \(\{ E_i, P_{xi}, P_{yi}, P_{zi}, \textrm{PID}_i\}\) (PID: PDG for tracks; [22] for photons; [0] for neutral hadrons) <strong>Extra Notes</strong> Since the dataset is structured as events, for W jet samples, only leading jet is available; while for Top and Higgs jets, leading and sub-leading jets are both valid. One might need to restrict the jet \(p_T\) range at use. e.g. to get leading jet constituents: `f["objects/jets/constituents"][:, 0]` The file names are self-explanatory on the corresponding generation process. Each file was generated in 100K original Madgraph events. After the preselection, a small fraction of events is discarded. <strong>Contact</strong> we are welcoming any feedback, suggestions, or requests on new test samples. Please contact <em>chengtaoli.1990@gmail.com</em> for more information.
DOI: 10.6084/m9.figshare.14328657
title: New microsatellite loci for annatto (Bixa orellana), a source of natural dyes from Brazilian Amazonia

description: Abstract Annatto (Bixa orellana) is a tropical crop native to the Americas with Amazonia as the likely center of origin of domestication. Annatto is important because it produces the dye bixin, which is widely used in the pharmaceutical, food, cosmetic and textile industries. A total of 32 microsatellite loci were isolated from a microsatellite-enriched genomic library, of which 12 polymorphic loci were used to characterize four populations of B. orellana and B. orellana var. urucurana, the wild relative. Higher genetic diversity estimates were detected for the wild populations when compared to the cultivated populations. Also, higher apparent outcrossing rates were found for the two wild than the cultivated populations. These results indicate a mixed mating system for the species. All markers described herein have potential to be used in further studies evaluating the genetic diversity, population dynamics, domestication, breeding, and conservation genetics of annatto.