cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5036162.v1
title: Looking for that perfect fit: Overcoming roadblocks to an optimal sequencing strategy with biocontrol agent Nesidiocoris tenuis as a case study

description: This is a presentation given at the Royal Entomological Society’s 2nd Meeting of the Insect Genomics Special Interest Group, 16th May 2017, held at Rothamsted Research (Harpenden, UK). With some adaptations and explanatory notes in the Notes section, it should be helpful for those looking for an optimal <i>de novo </i>sequencing strategy for non-model insect species. Here, I outline the process of my own project (past 1.5 years of process with it's own roadblocks and intricacies), and some things that need to be considered for insects, those that are small and/or difficult to rear in particular. I discuss three different sequencing approaches: PacBio/Illumina hybrid, mixed Illumina strategy using a single individual, and the 10xGenomics Chromium library prep and method. I use the biocontrol agent <i>Nesidiocoris tenuis</i> as an example. I've included the PowerPoint file with notes and animations, a plain PDF, and a PDF with the Notes printed.
DOI: 10.17632/j8tctwdmmp.1
title: Data for: A Changing Estuary: Understanding Historical Patterns in Salinity and Fecal Coliform Levels in the May River, SC

description: Here are the data we used for statistical analyses.
DOI: 10.6084/m9.figshare.13315583.v2
title: Comprehensive evolution analysis with genome-scale metabolic models reveals diverse mechanisms in metabolic innovations across 332 yeast species

description: EC number prediction using DeepECDomain annotation for 332 yeast speciesEssential gene prediction using machine learning
DOI: 10.6084/m9.figshare.14473650
title: Untitled Item

description: <b>Characterization of the complete chloroplast genome of </b><b><i>Rohdea wattii</i></b><b> (Asparagaceae)</b><b></b>
DOI: 10.6084/m9.figshare.14473650.v1
title: Untitled Item

description: <b>Characterization of the complete chloroplast genome of </b><b><i>Rohdea wattii</i></b><b> (Asparagaceae)</b><b></b>
DOI: 10.6084/m9.figshare.12506222
title: Model reduction for structural health monitoring accounting for soil-structure-interaction

description: This work addresses structural model reduction, a process necessary in structural health monitoring, where large quantities of data are recorded and must be evaluated. Therefore, numerical modelling of a structure is necessary for processing the recorded data and for estimating structural degradation over time. In order to avoid complex structural models and to economize computational resources, reduced order models have to be introduced. The goal is to develop a replacement single-degree-of-freedom oscillator that takes into account soil-structure-interaction effects. The dynamic characteristics of this oscillator are estimated by using the total displacement equality criterion. More specifically, the replacement process exhibits the following characteristics: (i) The complete time history of the “equality parameter” is considered and not just the resonance amplitudes; (ii) the problem is solved in the frequency domain using the complete set of the equations of motion; (iii) the outcome is independent of the excitation motion; (iv) the method can be applied for any mechanical parameter desired; and (v) the foundation impedance matrix is included. Following this development, parametric studies are conducted for assessing the dependency of the dynamic properties of the equivalent oscillator on the soil profile, the inertial characteristics of the foundation and its embedment depth.
DOI: 10.6084/m9.figshare.12506222.v1
title: Model reduction for structural health monitoring accounting for soil-structure-interaction

description: This work addresses structural model reduction, a process necessary in structural health monitoring, where large quantities of data are recorded and must be evaluated. Therefore, numerical modelling of a structure is necessary for processing the recorded data and for estimating structural degradation over time. In order to avoid complex structural models and to economize computational resources, reduced order models have to be introduced. The goal is to develop a replacement single-degree-of-freedom oscillator that takes into account soil-structure-interaction effects. The dynamic characteristics of this oscillator are estimated by using the total displacement equality criterion. More specifically, the replacement process exhibits the following characteristics: (i) The complete time history of the “equality parameter” is considered and not just the resonance amplitudes; (ii) the problem is solved in the frequency domain using the complete set of the equations of motion; (iii) the outcome is independent of the excitation motion; (iv) the method can be applied for any mechanical parameter desired; and (v) the foundation impedance matrix is included. Following this development, parametric studies are conducted for assessing the dependency of the dynamic properties of the equivalent oscillator on the soil profile, the inertial characteristics of the foundation and its embedment depth.
DOI: 10.15468/g5fxru
title: Morphological and genetic evidence supports the separation of two Tapinoma ants (Formicidae, Dolichoderinae) from the Atlantic Forest biome

description: This dataset contains the digitized treatments in Plazi based on the original journal article Escarraga, Mayron E., Lattke, John E., Pie, Marcio R., Guerrero, Roberto J. (2021): Morphological and genetic evidence supports the separation of two Tapinoma ants (Formicidae, Dolichoderinae) from the Atlantic Forest biome. ZooKeys 1033: 35-62, DOI: http://dx.doi.org/10.3897/zookeys.1033.59880, URL: http://dx.doi.org/10.3897/zookeys.1033.59880
DOI: 10.15468/nxrqfr
title: Revision of the Afrotropical genus Fainia Zumpt, 1958, with notes on the morphology of Rhiniidae subfamilies (Diptera, Oestroidea)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Thomas-Cabianca, Arianna, Martinez-Sanchez, Anabel, Villet, Martin H., Rojo, Santos (2021): Revision of the Afrotropical genus Fainia Zumpt, 1958, with notes on the morphology of Rhiniidae subfamilies (Diptera, Oestroidea). ZooKeys 1033: 127-157, DOI: http://dx.doi.org/10.3897/zookeys.1033.58539, URL: http://dx.doi.org/10.3897/zookeys.1033.58539
DOI: 10.15468/g4njth
title: Revision of Korean species of the genus Batriscenellus Jeannel (Staphylinidae, Pselaphinae, Batrisitae) with description of one new species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Kang, Jun-Young, Park, Sun-Jae, Kim, A-Young, Park, Jong-Seok (2021): Revision of Korean species of the genus Batriscenellus Jeannel (Staphylinidae, Pselaphinae, Batrisitae) with description of one new species. ZooKeys 1033: 159-171, DOI: http://dx.doi.org/10.3897/zookeys.1033.59558, URL: http://dx.doi.org/10.3897/zookeys.1033.59558
DOI: 10.17632/68f3fg56ff.1
title: Effects of phonological neighbourhood density and frequency in picture naming
DOI: 10.17632/x3kj5hmvdc.1
title: Loss of Fis1 impairs proteostasis during skeletal muscle aging in Drosophila

description: Increased dysfunctional mitochondria within skeletal muscle is correlated with many aged-related physiopathological conditions. Understanding the links between mitochondrial function and muscle proteohomeostasis is necessary to develop treatments, yet the underlying connections remain unclear. The mitochondrial outer membrane protein Fis1, a yeast fission factor, may also maintain mitochondrial morphology in metazoans. Here, we found Fis1 isoform expression increased with age. Moreover, Fis1MI10520 (MiMIC insertion mutant) showed the higher ratio of damaged mitochondria during aging. These damaged mitochondria possessed compromised inner membrane structures, generated reduced ATP concentration and showed elevated ROS levels. This caused increased oxidative stress resulting in large accumulations of ubiquitinated protein and an accelerated decline in muscle function. Our findings indicate that Fis1 is crucial for Drosophila mitochondrial homeostasis, and Fis1 mutations cause aged phenotypes in young mutant flies. Further investigation into the larger homeostatic network containing Fis1 is necessary to improve understanding of how mitochondrial function changes with age.
DOI: 10.17632/crzmm5ggzg.1
title: Tunicamycin induced ER stress in liver of C57Bl/6N mice

description: Once protein synthesis is excessive or misfolded protein become aggregated that eventually overwhelm the capacity of the endoplasmic reticulum (ER), a state named ER stress would be reached. ER stress could affect many tissues, especially liver, in which non-alcoholic fatty liver disease, liver steatosis, etc. have been reported relative. But there still lack systematic insight into ER stress in liver, which can be obtained by integrating metabolomics and transcriptomics of the tissue. Here, tunicamycin was utilized to induce ER stress in C57BL/6N mice. Microarray and untargeted metabolomics were performed to identify the genes and metabolites significantly altered. Surprisingly, apart from classical unfolded protein response, liver lipid, arginine and proline metabolism were affirmed to be related with ER stress. And ketone body metabolism changed most prominently in ER stress, with few studies backing. What’s more, succinate receptor 1(Sucnr1) may be a novel marker and therapeutical target of liver ER stress. In this study, combination of metabolome and transcriptome provided reliable information about liver pathological processes, markers and even potential targets involved in liver ER stress.
DOI: 10.17632/dwbfbzv939.1
title: Male FFA

description: Table 1: Demographics, associated disorders, daily medications and laboratory profile of 33 male patients with FFA. Table 2: Clinical features of 33 male patients with FFA.
DOI: 10.17632/d9vmn6pfhj.1
title: Urban Trees Inventory Data with Tape and iPad Pro 2020 Laser Scanner

description: Our objective was to test the possibility of using the laser scanner in iPad Pro 2020 to estimate trunk DBH (Diameter at the Breast Height) in an urban forest. We used 3D Scanner APP 1.9.1 (Laan Consulting Corp, 2021) installed in iPad Pro 2020, as an APP for scanning. We compared 3 different resolutions (10 mm, 15 mm, 20 mm), 2 different confidence (Low, High) as well as 2 different scanning modes (Multiple-tree mode, Single-tree mode), which combined into 12 methods for DBH estimation on urban trees (n = 101, area = 6423 m2) in Zvolen, Slovakia. The position of all trees was measured by Coordinates - GPS Formatter APP 7.1 (Mapnitude Company Limited, 2021) installed in iPad Pro 2020 at 1.3 m height. The reference data were collected by one person. It took 132 minutes with a tape. Only 3 trees were missed during the cross-section step.
DOI: 10.15468/u8k8nx
title: Neotropical Nilothauma Kieffer, 1921 (Diptera, Chironomidae): Key, eleven new species, re-descriptions, new combination and new records

description: This dataset contains the digitized treatments in Plazi based on the original journal article Pinho, Luiz Carlos, Andersen, Trond (2021): Neotropical Nilothauma Kieffer, 1921 (Diptera, Chironomidae): Key, eleven new species, re-descriptions, new combination and new records. ZooKeys 1033: 81-125, DOI: http://dx.doi.org/10.3897/zookeys.1033.60686, URL: http://dx.doi.org/10.3897/zookeys.1033.60686
DOI: 10.17632/s9rx4myvnn.1
title: Treatment of Pediatric Alopecia Areata: A Systematic Review

description: Background: Alopecia areata (AA) is an autoimmune, non-scarring hair loss disorder with slightly greater prevalence in children than adults. Various treatment modalities exist; however, their evidence in pediatric AA patients is lacking. Methods: We conducted a systematic review on the PubMed database in October 2019 for all published articles involving patients &lt;18 years old. Articles discussing AA treatment in pediatric patients, and both pediatric and adult patients, were included if individual data on pediatric patients was available. Results: 122 total reports discussing 1,032 patients met inclusion criteria. Reports consisted of two randomized controlled trials, four prospective comparative cohorts, 83 case series, two case-control studies, and 31 case reports. Included articles assessed the use of aloe, apremilast, anthralin, anti-IFN gamma antibodies, botulinum toxin, corticosteroids, contact immunotherapies, cryotherapy, hydroxychloroquine, hypnotherapy, imiquimod, JAK inhibitors, laser and light therapy, methotrexate, minoxidil, phototherapy, psychotherapy, prostaglandin analogs, sulfasalazine, topical calcineurin inhibitors, topical nitrogen mustard, and ustekinumab. Conclusion: Topical corticosteroids are the preferred first-line treatment for pediatric AA, as they hold the highest level of evidence, followed by contact immunotherapy. More clinical trials and comparative studies are needed to further guide management of pediatric AA, and to promote potential use of pre-existing, low-cost, and novel therapies, including JAK inhibitors.
DOI: 10.15468/gvkdd6
title: Genome sequencing reveals extraordinary cephalic horns in the Madagascan dung beetle genus Helictopleurus (Coleoptera, Scarabaeinae): insight from a revision of fungicola species group

description: This dataset contains the digitized treatments in Plazi based on the original journal article Rossini, Michele, Montreuil, Olivier, Grebennikov, Vasily, Tarasov, Sergei (2021): Genome sequencing reveals extraordinary cephalic horns in the Madagascan dung beetle genus Helictopleurus (Coleoptera, Scarabaeinae): insight from a revision of fungicola species group. ZooKeys 1033: 63-79, DOI: http://dx.doi.org/10.3897/zookeys.1033.63527, URL: http://dx.doi.org/10.3897/zookeys.1033.63527
DOI: 10.15468/mk9uaj
title: New species and material of Hagloidea (Insecta, Ensifera) from the Yanliao biota of China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Gu, Jun-Jie, Yang, Xin, Huang, Rong, Yang, Guijun, Yue, Yanli, Ren, Dong (2021): New species and material of Hagloidea (Insecta, Ensifera) from the Yanliao biota of China. ZooKeys 1033: 183-190, DOI: http://dx.doi.org/10.3897/zookeys.1033.63571, URL: http://dx.doi.org/10.3897/zookeys.1033.63571
DOI: 10.15468/8wyb8e
title: A new species of Hemiptarsenus Westwood (Hymenoptera, Eulophidae) from China, with a key to Chinese species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Tao, Shu-xia, Huang, Kun, Tian, Jing, Ruan, Chang-chun (2021): A new species of Hemiptarsenus Westwood (Hymenoptera, Eulophidae) from China, with a key to Chinese species. ZooKeys 1033: 173-181, DOI: http://dx.doi.org/10.3897/zookeys.1033.62129, URL: http://dx.doi.org/10.3897/zookeys.1033.62129
DOI: 10.17632/r5y668c92d.2
title: Arabic Letter Utterance

description: This dataset contains audio recordings taken from 13 men and 13 women. Each subject was asked to read ten different Arabic letters four times. The files are named in the format "XXYYY.wav." - XX is the ID of the read letter (please refer to Guide_Dataset.png) - YYY is the ID of the subject We can see ten letters along with their ID at Guide_Dataset.png. We selected the ten classes based on their similarities: - Class 0 and 1 have similar sounds and properties - Class 2 and 3 have similar sounds and properties - Class 4 and 5 have similar sounds and properties - Classes 6, 7, 8, and 9 have similar sounds and properties
DOI: 10.17632/zs8b8jdzxn.1
title: ADAR1 as a Key Regulatory Molecule between MiR-432 and Circ_0000418 in Antidepressant Action

description: In this study, all the data were analyzed by using GraphPad Prism 7.0 and IBM SPSS Statistics 23.0. All the data were expressed as the means±SD. The behavior data of C1 group and CUS1 group was analyzed by u test. In addition, t test was used to analyze the variance for the groups with and without chronic unpredictable stress, the groups with and without ADAR1 target intervention in the mice, as well as the groups with and without transfection in SH-SY5Y cell line. Two-way ANOVA was used to determine whether there is an interaction between chronic unpredictable stress and ADAR1 target intervention (two independent variables) on ADAR1 mRNA expression, BDNF mRNA expression, circ_0000418 expression, and miR-432 expression (dependent variable) respectively among the mice. One-way ANOVA was used for comparison of samples among multiple groups. Tukey’s test was used for significance analysis. p&lt; 0.05 was considered to be statistical significantly.
DOI: 10.21227/wa2w-yx63
title: Request execution times GraphQL vs. REST

description: This Data contains measurements on reading and writing data to OPC UA servers directly and via REST and GraphQL interfaces. Each measurement is conducted 50 times. Measurements include reading a single value and reading a value 50 times. Measurements are conducted with Wireshark and the csv files are exported from it.
DOI: 10.6084/m9.figshare.14473608
title: Integrated Seurat Object

description: QC filtered using EmptyDropsIndividually scaledMerged then Integrated with HarmonyClustered with SeuratSubclustered with SeuratManually Annotated
DOI: 10.25345/c5q22g
title: MassIVE MSV000087291 - A three-organelle complex formed by wrappER contacts with peroxisome and mitochondria responds to shifts in hepatic lipid flux
title: Hepatic lipid homeostasis depends on fatty acid (FA) content in the liver, which, in turn, depends on intracellular pathways that respire FA in mitochondria and peroxisomes, as well as on systemic pathways that secrete FA in the bloodstream, either free or condensed as very-low-density lipoprotein (VLDL) triglycerides. These two pathways are interdependent because they share the same FA pool, but whether and how they integrate into a single cellular circuit is unclear. In this study, we report that mouse liver wrappER, a type of endoplasmic reticulum with FA- and VLDL-secretion function, connects mitochondria and peroxisomes, the two FA-respiring organelles of the cell. Correlative light-electron microscopy, 3D-serial section electron tomography, and quantitative electron microscopy analysis show that the number of mitochondria-wrappER-peroxisome complex changes according to the nutritional status of the animal and nearly doubles when the systemic flux of FA is compromised by acute genetic ablation of Mttp in the liver, the most upstream regulator of VLDL synthesis. Proteomics analysis of mitochondria-wrappER-peroxisome complex isolated from control and Mttp -/- livers indicates that these organelles' structural reorganization is accompanied by upregulated mitochondrial and peroxisomal FA B-oxidation. Hepatic lipid homeostasis is therefore also maintained through the convergence of systemic and beta-oxidative FA-lowering pathways into a previously unreported dynamic mitochondria-wrappER-peroxisome tri-organelle complex.
DOI: 10.6084/m9.figshare.13315583.v3
title: Comprehensive evolution analysis for 332 yeast species

description: EC number prediction using DeepECDomain annotation for 332 yeast speciesEssential gene prediction using machine learning
DOI: 10.6084/m9.figshare.12901078
title: Palynology and organic petrography of the Tyler Formation (lower Pennsylvanian), Williston Basin, North Dakota, USA

description: The palynoflora and organic petrography of core samples from the Tyler Formation in the Williston Basin, North Dakota, USA were evaluated to determine their age and depositional environment. The palynofloras are assigned to seven plant groups used by previous authors who studied Carboniferous floras. Lycopsid trees, represented by <i>Lycospora</i> species and <i>Crassispora kosankei</i> are the most abundant and well-preserved miospores recorded. Palynomorphs representing small lycopsids, calamites, cordaites, and conifers, comprise a relatively minor part of the palynoflora. The petrographic component from seven coeval coal samples contain moderate to high mineral content and macerals which are dominated by vitrinite (woody components) and to a lesser extent inertinite and liptinite (lipid-rich plant material). Common vitrinite macerals include collotelinite and collodetrinite, and semifusinite and minor fusinite representing inertinite macerals. The palynofloras are of Early Pennsylvanian age, based on the presence of the age-significant fossils <i>Schulzospora rara</i> and <i>Cirratriradites saturnii</i> together with abundant <i>Lycospora</i> spp. The palynoflora and petrographic data suggest that the Tyler Formation in this location was deposited in a fluvially-dominated delta with some tidal influence. Wet, stagnant anoxic environments (coal swamps) were frequently flooded with clastic material from a fluvial source. Macerals, especially inertinite, imply periods of subaerial exposure, fire, or highly oxygenated waters, and liptinite (lipid-rich plant material), suggests periodic drowning of the coal swamp and formation of shallow lacustrine paleoenvironments.
DOI: 10.6084/m9.figshare.12901078.v2
title: Palynology and organic petrography of the Tyler Formation (lower Pennsylvanian), Williston Basin, North Dakota, USA

description: The palynoflora and organic petrography of core samples from the Tyler Formation in the Williston Basin, North Dakota, USA were evaluated to determine their age and depositional environment. The palynofloras are assigned to seven plant groups used by previous authors who studied Carboniferous floras. Lycopsid trees, represented by <i>Lycospora</i> species and <i>Crassispora kosankei</i> are the most abundant and well-preserved miospores recorded. Palynomorphs representing small lycopsids, calamites, cordaites, and conifers, comprise a relatively minor part of the palynoflora. The petrographic component from seven coeval coal samples contain moderate to high mineral content and macerals which are dominated by vitrinite (woody components) and to a lesser extent inertinite and liptinite (lipid-rich plant material). Common vitrinite macerals include collotelinite and collodetrinite, and semifusinite and minor fusinite representing inertinite macerals. The palynofloras are of Early Pennsylvanian age, based on the presence of the age-significant fossils <i>Schulzospora rara</i> and <i>Cirratriradites saturnii</i> together with abundant <i>Lycospora</i> spp. The palynoflora and petrographic data suggest that the Tyler Formation in this location was deposited in a fluvially-dominated delta with some tidal influence. Wet, stagnant anoxic environments (coal swamps) were frequently flooded with clastic material from a fluvial source. Macerals, especially inertinite, imply periods of subaerial exposure, fire, or highly oxygenated waters, and liptinite (lipid-rich plant material), suggests periodic drowning of the coal swamp and formation of shallow lacustrine paleoenvironments.