cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11692665.v1
title: MOESM6 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 6. WGS-SNP-based phylogenetic analysis of local M. bovis mastitis-associated isolates (n = 89) performed in comparison to a reference genome M. bovis PG45 as described in Materials and Methods. The phylogenetic tree was constructed by using the Maximum-Likelihood method, and bootstrapped 500 times to assess support for the different branches using MEGA-X [25]. The designation of the isolates includes serial number or sequencing identifier (for isolates sequenced in this study), name of the isolate, type of mastitis (clinical (CM) or subclinical (SM)) and year isolation. For additional information about particular strain, see Additional file 1: Table S1. Total SNP count resulted in 16,910 SNPs. Comparison between phylogenetic trees obtained by total-genome-based SNP analysis with (Additional file 6) and without (Fig. 3a) comparison to the reference genome revealed almost the same intergroup clustering of the isolates. However, the clade distribution of isolates was slightly different between these two comparisons. This file can be opened using MEGA software [25] or via public available servers, e.g. the NCBI Tree Viewer (https://www.ncbi.nlm.nih.gov/tools/treeviewer/), ETE Toolkit (http://etetoolkit.org/treeview/) etc.
DOI: 10.6084/m9.figshare.11692656
title: MOESM5 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 5. WGS-SNP-based phylogenetic tree presented in Fig. 3b allows to see the scale bar and branches of support. This file can be opened using MEGA software [25] or via public available servers, e.g. the NCBI Tree Viewer (https://www.ncbi.nlm.nih.gov/tools/treeviewer/), ETE Toolkit (http://etetoolkit.org/treeview/) etc.
DOI: 10.6084/m9.figshare.11692653
title: MOESM4 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 4. WGS-SNP-based phylogenetic tree presented in Fig. 3a allows to see the scale bar and branches of support. This file can be opened using MEGA software [25] or via public available servers, e.g. the NCBI Tree Viewer (https://www.ncbi.nlm.nih.gov/tools/treeviewer/), ETE Toolkit (http://etetoolkit.org/treeview/) etc.
DOI: 10.6084/m9.figshare.11692653.v1
title: MOESM4 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 4. WGS-SNP-based phylogenetic tree presented in Fig. 3a allows to see the scale bar and branches of support. This file can be opened using MEGA software [25] or via public available servers, e.g. the NCBI Tree Viewer (https://www.ncbi.nlm.nih.gov/tools/treeviewer/), ETE Toolkit (http://etetoolkit.org/treeview/) etc.
DOI: 10.6084/m9.figshare.11692647
title: MOESM3 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 3: Table S3. Nucleotide substitution model selection.
DOI: 10.6084/m9.figshare.11692647.v1
title: MOESM3 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 3: Table S3. Nucleotide substitution model selection.
DOI: 10.6084/m9.figshare.11692644
title: MOESM2 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 2: Table S2. Assembly results. Assembly results of 175 M. bovis isolates sequenced in this study (N1–175) and 31 Israeli isolates (N176–206) previously sequenced by Wellcome Trust Sanger Institute (UK) and deposited in NCBI (Bio project PRJEB3408).
DOI: 10.6084/m9.figshare.11692641
title: MOESM1 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 1: Table S1. List of M. bovis strains used in this study. # Alternative IDs for isolates sequenced by Wellcome Trust Sanger Institute (UK) and used in our study. 1–14 The same superscript numbers indicate that M. bovis isolates were isolated on the different farms, located in the same settlement. A-I The same superscript characters indicate that M. bovis isolates were isolated on the same farm or from the same shipment. * There is an epidemiological link among the isolates. NR – not relevant; NA – not available.
DOI: 10.6084/m9.figshare.11692641.v1
title: MOESM1 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 1: Table S1. List of M. bovis strains used in this study. # Alternative IDs for isolates sequenced by Wellcome Trust Sanger Institute (UK) and used in our study. 1–14 The same superscript numbers indicate that M. bovis isolates were isolated on the different farms, located in the same settlement. A-I The same superscript characters indicate that M. bovis isolates were isolated on the same farm or from the same shipment. * There is an epidemiological link among the isolates. NR – not relevant; NA – not available.
DOI: 10.6084/m9.figshare.11692524
title: MOESM9 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 9. External validation results of the binary classification task I.
DOI: 10.6084/m9.figshare.11692524.v1
title: MOESM9 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 9. External validation results of the binary classification task I.
DOI: 10.6084/m9.figshare.11692518
title: MOESM7 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 7. 16 classes of representative compounds in DNP.
DOI: 10.6084/m9.figshare.11692521
title: MOESM8 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 8. Optimized scaffold libraries produced with DNP by using the BM method in pipeline pilot 2017.
DOI: 10.6084/m9.figshare.11692515
title: MOESM6 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 6. Binary classification task II model of RapidMiner Studio 9.2 and molecular fingerprint data set to test model.
DOI: 10.6084/m9.figshare.11692512
title: MOESM5 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 5. Chemical compounds of the binary classification task II.
DOI: 10.6084/m9.figshare.11692509
title: MOESM4 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 4. Binary classification task I model of RapidMiner Studio 9.2 and molecular fingerprint data set to test model.
DOI: 10.6084/m9.figshare.11692503
title: MOESM3 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 3. Chemical compounds of the binary classification task I.
DOI: 10.6084/m9.figshare.11692500
title: MOESM2 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 2. Python code to generate NC-MFP algorithm and select optimized scaffolds.
DOI: 10.6084/m9.figshare.11692503.v1
title: MOESM3 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 3. Chemical compounds of the binary classification task I.
DOI: 10.6084/m9.figshare.11692494
title: MOESM1 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 1. Chemical compounds of the Natural Compound Databases (NCDBs).
DOI: 10.6084/m9.figshare.11692491
title: MOESM1 of A de novo variant in OTX2 in a lamb with otocephaly

description: Additional file 1. List of private protein-changing sequence variants.
DOI: 10.6084/m9.figshare.11692494.v1
title: MOESM1 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 1. Chemical compounds of the Natural Compound Databases (NCDBs).
DOI: 10.6084/m9.figshare.11692491.v1
title: MOESM1 of A de novo variant in OTX2 in a lamb with otocephaly

description: Additional file 1. List of private protein-changing sequence variants.
DOI: 10.6084/m9.figshare.11692485
title: MOESM12 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 12. Y-randomization results of the binary classification task II.
DOI: 10.6084/m9.figshare.11692476
title: MOESM11 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 11. External validation results of the binary classification task II.
DOI: 10.6084/m9.figshare.11692476.v1
title: MOESM11 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 11. External validation results of the binary classification task II.
DOI: 10.6084/m9.figshare.11692467
title: MOESM10 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 10. Y-randomization results of the binary classification task I.
DOI: 10.6084/m9.figshare.11692467.v1
title: MOESM10 of Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

description: Additional file 10. Y-randomization results of the binary classification task I.
DOI: 10.6084/m9.figshare.11692452
title: MOESM6 of A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

description: Additional file 6: Table S5. AUPRs for cross-cell type trained supervised methods.
DOI: 10.6084/m9.figshare.11692452.v1
title: MOESM6 of A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

description: Additional file 6: Table S5. AUPRs for cross-cell type trained supervised methods.
DOI: 10.6084/m9.figshare.11692446
title: MOESM5 of A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

description: Additional file 5: Table S4. AUPRs for supervised methods.
DOI: 10.6084/m9.figshare.11692446.v1
title: MOESM5 of A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

description: Additional file 5: Table S4. AUPRs for supervised methods.
DOI: 10.6084/m9.figshare.11692440
title: MOESM4 of A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

description: Additional file 4: Table S3. AUPRs for unsupervised methods.
DOI: 10.6084/m9.figshare.11692440.v1
title: MOESM4 of A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

description: Additional file 4: Table S3. AUPRs for unsupervised methods.
DOI: 10.6084/m9.figshare.11692434
title: MOESM2 of A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

description: Additional file 2: Table S2. Characteristics of BENGI datasets.
DOI: 10.6084/m9.figshare.11692434.v1
title: MOESM2 of A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

description: Additional file 2: Table S2. Characteristics of BENGI datasets.
DOI: 10.6084/m9.figshare.11692431
title: MOESM1 of A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

description: Additional file 1: Table S1. Accessions for relevant ENCODE cCREs and RNA-seq experiments.
DOI: 10.6084/m9.figshare.11692431.v1
title: MOESM1 of A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

description: Additional file 1: Table S1. Accessions for relevant ENCODE cCREs and RNA-seq experiments.
DOI: 10.6084/m9.figshare.11692416
title: MOESM8 of Exploring molecular evolution of Rubisco in C3 and CAM Orchidaceae and Bromeliaceae

description: Additional file 8: Excel S2. Rubisco L-subunit variable sites among bromeliads. Dots: the same amino acid as the first species in the list. Dash: not available.
DOI: 10.6084/m9.figshare.11692416.v1
title: MOESM8 of Exploring molecular evolution of Rubisco in C3 and CAM Orchidaceae and Bromeliaceae

description: Additional file 8: Excel S2. Rubisco L-subunit variable sites among bromeliads. Dots: the same amino acid as the first species in the list. Dash: not available.
DOI: 10.6084/m9.figshare.11692410
title: MOESM7 of Exploring molecular evolution of Rubisco in C3 and CAM Orchidaceae and Bromeliaceae

description: Additional file 7: Excel S1. Rubisco L-subunit variable sites among orchids. Dots: the same amino acid as the first species in the list. Dash: not available.
DOI: 10.6084/m9.figshare.11692410.v1
title: MOESM7 of Exploring molecular evolution of Rubisco in C3 and CAM Orchidaceae and Bromeliaceae

description: Additional file 7: Excel S1. Rubisco L-subunit variable sites among orchids. Dots: the same amino acid as the first species in the list. Dash: not available.
DOI: 10.6084/m9.figshare.11692233
title: Publications 1980 - 2018 By Country.xlsx

description: Publications 1980 - 2018 By Country Based on Scopus
DOI: 10.6084/m9.figshare.11691957
title: Raw data

description: V3-V4 region of 16S ribosomal RNA gene
DOI: 10.6084/m9.figshare.11691828
title: genotype data.pdf

description: SNP genotyping analysis was carried out using the SoySNP660K BeadChip at Beijing Boao Biotechnology Co., Ltd. using the DNA samples of the soybean leaves.
DOI: 10.6084/m9.figshare.11691798
title: AA breakpoint graphs

description: AA-generated breakpoint graphs and in-silico digested Bionano CMAPs for each graph.
DOI: 10.6084/m9.figshare.11691798.v1
title: AA breakpoint graphs

description: AA-generated breakpoint graphs and in-silico digested Bionano CMAPs for each graph.
DOI: 10.6084/m9.figshare.11691786
title: Drosophilidae and other families (Insecta: Diptera) surveyed in 1991–1993 in regions of Australia recently impacted by bush fires and drought

description: Between 1991 and 1993 the New South Wales National Parks and Wildlife Service (NSW NPWS) supported wide-ranging surveys of fauna and flora as part of the North East Forests Biodiversity Study (NEFBS). One of the main invertebrate groups surveyed was the Drosophilidae (McEvey, 1994, 2020). Sampling was carried out at 42 localities (Table 1) using a range of methods and on a range of dates (Table 2); 825 records (Table 3) of 36 dipteran families and 51 drosophilid species were reported; the frequency abundance of drosophilid species and dipteran families at the 42 localities is presented (Table 4). This dataset together with McEvey’s (1994, 2020) 64-page submission, provides baseline information for ecologists and biogeographers interested in exploring faunal change following serious fire damage and drought.
DOI: 10.6084/m9.figshare.11691786.v1
title: Drosophilidae and other families (Insecta: Diptera) surveyed in 1991–1993 in regions of Australia recently impacted by bush fires and drought

description: Between 1991 and 1993 the New South Wales National Parks and Wildlife Service (NSW NPWS) supported wide-ranging surveys of fauna and flora as part of the North East Forests Biodiversity Study (NEFBS). One of the main invertebrate groups surveyed was the Drosophilidae (McEvey, 1994, 2020). Sampling was carried out at 42 localities (Table 1) using a range of methods and on a range of dates (Table 2); 825 records (Table 3) of 36 dipteran families and 51 drosophilid species were reported; the frequency abundance of drosophilid species and dipteran families at the 42 localities is presented (Table 4). This dataset together with McEvey’s (1994, 2020) 64-page submission, provides baseline information for ecologists and biogeographers interested in exploring faunal change following serious fire damage and drought.
DOI: 10.6084/m9.figshare.11691774
title: FISH

description: FISH images for cell lines in the AmpliconReconstructor paper.
DOI: 10.6084/m9.figshare.11691717
title: Example stimulus files for virtual auditory space stimuli

description: Example stimuli that we used for our virtual auditory space stimulation. These files are not intended to work in the replicated system because these files contain information of physical setup such as our specific speakers and horns.<br>These will be useful for testing the LabVIEW software that is published together with this dataset (https://github.com/shixnya/SoundLocalizationResearch/tree/master/LabVIEWCodes).
DOI: 10.6084/m9.figshare.11691678
title: JCEM_CHROMOGRANIN_A_EBERT-KAHALY_SUPPLEMENTARY_TABLE

description: The glycoprotein Chromogranin A (CgA) is expressed by endocrine and neuroendocrine cells. High levels of serum CgA serve as marker of neuroendocrine tumors (NET), but its role in autoimmunity has not been assessed. CgA serum levels were evaluated in 807 subjects in a cross-sectional study, of whom 385 had endocrine and 197 non-endocrine autoimmunity, and 32 NET, to investigate its utility as a marker of autoimmunity. Serum CgA concentrations were increased in 65.6%, 39.3%, 38.4%, and 23.5% of patients with NET, type 1 diabetes (T1D), autoimmune gastritis (AG) and autoimmune polyendocrinopathy (AP), respectively. Compared to 49 healthy controls (C) and 82 euthyroid subjects with thyroid nodules (TN), odds ratios for positive CgA levels were 27.4, 15.9, 7.82 (all p &lt; 0.0001) and 4.29 (p = 0.0034) in patients with NET, T1D, AG and AP, respectively. In AG, CgA and serum gastrin correlated positively (r = 0.55, p &lt; 0.0001). The area under receiver operating characteristic curve to predict AG was higher for parietal cell antibody (PCA) positivity than for CgA (0.84 versus 0.67, p &lt; 0.0001). However, in combination with PCA and intrinsic factor autoantibodies (IFA), CgA independently improves prediction of AG (odds ratio 6.5, p = 0.031). Further, for the first time, we describe that smoking significantly increases CgA serum levels by 21%. CgA qualifies as a novel biomarker for T1D, AP, and especially AG.<br><br>
DOI: 10.6084/m9.figshare.11691717.v1
title: Example stimulus files for virtual auditory stimuli

description: Example stimuli that we used for our virtual auditory space stimulation. These files are not intended to work in the replicated system because these files contain information of physical setup such as our specific speakers and horns.<br>These will be useful for testing the LabVIEW software that is published together with this dataset (https://github.com/shixnya/SoundLocalizationResearch/tree/master/LabVIEWCodes).
DOI: 10.6084/m9.figshare.11691717.v3
title: Example stimulus files for virtual auditory space stimuli

description: Example stimuli that we used for our virtual auditory space stimulation. These files are not intended to work in the replicated system because these files contain information of physical setup such as our specific speakers and horns.<br>These will be useful for testing the LabVIEW software that is published together with this dataset (https://github.com/shixnya/SoundLocalizationResearch/tree/master/LabVIEWCodes).
DOI: 10.6084/m9.figshare.11691615
title: Mouse Head Related Transfer Function processed data

description: Analyzed head related transfer function (HRTF) of 3 female CBA/CaJ mice. Please refer to an article for how the data are collected.<br><br>These data may not work for physiology experiment unless the playback speaker setup exactly matches with our setup (including the horns for EC1 speakers). Therefore, the purpose of publishing these data is mainly for exploratory browsing the mouse HRTFs.<br><br>These files contain HRTFs of 3 mice with a variety of modification of the sound localization cues.<br>allimps variable contains raw HRIR (impulse response) information derived from the raw recordings.Variables with _noitd is ITD-removed version of the impulse responses.Variables with _nospec is spectral-flatted version of the impulse responses.Variables with _ILDequal is ILD-equalized version of the impulse response.Variables with _percep is how the mouse should perceive the sound. This applies a setup-specific filter to mimic the sound structure near the ear drums.Variables with _present is what should be used for stimulation. When this sound is played through speaker, the speaker's own filter makes it closer to _percep version.Variables with _ILDcorrected adjust minor recording condition differences between the left and right ears. This variable should be used to generate the stimuli.<br><br>To browse the impulse responses. Please go to this github page to obtain a sample code.https://github.com/shixnya/SoundLocalizationResearch/tree/master/HRTFExample<br><br>
DOI: 10.6084/m9.figshare.11691717.v2
title: Example stimulus files for virtual auditory stimuli

description: Example stimuli that we used for our virtual auditory space stimulation. These files are not intended to work in the replicated system because these files contain information of physical setup such as our specific speakers and horns.<br>These will be useful for testing the LabVIEW software that is published together with this dataset (https://github.com/shixnya/SoundLocalizationResearch/tree/master/LabVIEWCodes).
DOI: 10.6084/m9.figshare.11691489
title: Domestic Pig Post-Inject Image Stack

description: 6 Month Old Pig post-injection (barium sulfate/latex) DICOM image stack from: O'Brien and Williams, 2014 PLoS One https://doi.org/10.1371/journal.pone.0097940<br>Scanned at the Holzer Clinic in Athens, Ohio, on a Philips Brilliance 64 slice CT scanner, at 0.67 mm slice thickness, 150 kV, 80 mA, and yielding a voxel size of 0.693359×0.693359×0.5 mm