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Effects of inoculation of restored and remnant prairie soils on growth, nodulation, and root colonization of three prairie legumes
In this dataset, we present legume biomass, nodule number, and % root colonization of three species of prairie legumes (Amorpha canescens, Lespedeza capitata, and Dalea purpurea) when inoculated with soil from one of 6 remnant or 10 restored prairies in southwest Michigan, USA. Plants were grown for 10 weeks in a growth chamber.
Prevalence and Characterization of Asymptomatic Thyroid Nodules in Assin North District, Ghana
<p><strong>Study design and sampling </strong></p> <p>The study was cross-sectional involving six (6) communities in the Assin North District of the Central Region of Ghana. Ethical approval was obtained from the Institutional Review Board of the University of Cape Coast, Ghana, with this reference number: UCCIRB/EXT/2017/18. All community entry protocols with local authorities were observed before the study commenced. Further, protocol involving informed consent was also duly observed during and after this study. Both verbal and written consent were obtained from each participant prior to participation. Participation in the study was strictly on voluntary basis.</p> <p>Each of these six (6) communities was considered a stratum in which all households were listed to constitute a sampling frame from which the respective number of households in each community were sampled using systematic random sampling technique. The sampling interval (<em>K</em><sup>th</sup>) in each community was determined by dividing the total number of listed households (N) by the number of households respectively require (n) (based on proportion-to-population size) as shown in Table 1. The simple random sampling technique was then employed to select the first household (<em>i</em><<em>K</em>) in each community, from which every <em>K</em><sup>th</sup> household was selected until the expected number of households in each community was met. One eligible consenting participant in each selected household was then randomly selected for the study. In a few instances where there were no consenting or eligible participant, the next household on the roll was considered.</p> <p>Exclusion criteria included participants with anterior neck swelling or clinical evidence of thyroid disease, smokers, persons on lithium, phenytoin, oral contraceptive drugs, and women during menstruation, pregnant women or women who had delivered within the last 12 months and persons with any systemic disorder</p> <p><strong>Data collection</strong></p> <p>Data collection was conducted in July, 2019 in two phases. The first phase consisted of face-to-face interviews with participants using a structured interview guide to elicit socio-demographic information such as age, sex, marital status, and highest level of education; history dietary salt intake (often intake- at least 5g or one teaspoon of iodized salt per day and not often intake- less than 5g or one teaspoon of iodized salt per day or not at all); and history of alcohol intake (yes- consumed alcohol regardless of quantity and no- had not consume alcohol before). Anthropometric measurements of body weight (kg) and height (cm) were measured using standard anthropometric techniques and further computed to generate measures of body surface area (BSA) and body mass index (BMI). Data collection in the phase was conducted by six (6) trained research assistants from UCCSMS and duly supervised by key investigators (listed authors) of the study.</p> <p>The second phase of the data collection mainly focused on diagnostic imaging of the thyroid gland by a specialist radiologist with over five (5) working experience in thyroid examination using various imaging technologies. A screening center was staged in each of the study communities on different days while ensuring that such days did not conflict with market days or other important community events. Participants who were interviewed at the household level were given an identification chit to present with to the screening stage for easy synchronization of their interview data with thyroid data. Given that ultrasound has been recognized as the initial imaging modality of choice for the early detection of thyroid nodules [2,9,22,23], a real-time ultrasound scanner (MEDISON SA8000SE-MAI, 1003 Dachi-Dong, Gangnam-Gu, Seoul Korea) with a 7.5 MHz, 50 mm linear transducer was used in examining the thyroid gland of study participants.</p> <p>Participants were examined while in a supine position with hyperextended cervical spine. Ultrasound gel was applied over the thyroid area with the transducer directly placed on the skin over the thyroid gland. Longitudinal and transverse scans were performed, to obtain length and width in centimeters, of each thyroid nodule. If there were multiple nodules in a single thyroid lobe only the dimensions of the largest were recorded. Documented characteristics of thyroid nodules included the location of nodules in the thyroid lobe; number of nodules (solitary or multiple), nodule composition (cyst, solid or mixed), calcifications, and nodule size (length and width in centimeters). Out of the 343 participants interviewed in the initial phase of the data collection, 23 participants failed showed up for the thyroid screening in the second phase despite countless attempts to contact them. Hence the current study is based on 320 participants who were successfully interviewed and screened.</p> <p><strong>Statistical analysis</strong></p> <p> The data was captured using SPSS and later exported to STATA 11.0 for further management and analysis. A protocol was designed from the outset for imputing, ensuring data quality and preserving of data for reuse. Descriptive statistics including frequencies, percentages, means and standard deviation were used to summarize participants’ socio-demographic and thyroid characteristics. Bivariate and multivariate logistic regression analyses were conducted to determine factors associated with ATN. Odds ratios and corresponding confidence intervals were reported with statistical significance at p < 0.05</p>
The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover
<p>Zenodo deposit for Pozzi et al (2024) AJB</p> <p>The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover</p> <p><strong> _____________________________________________________________________________________________________________________________________</strong></p> <p><strong>The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover</strong></p> <p>Adrien C.M. Pozzi<sup>1,2</sup>, Ruth G. Shaw<sup>1</sup>, Georgiana May<sup>1,3</sup></p> <p><sup>1</sup> Department of Ecology, Evolution and Behavior, University of Minnesota Twin-Cities, St Paul, MN 55108. <sup>2</sup> Current affiliation: Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622 Villeurbanne, France. ORCID: 0000-0001-6765-4293. <sup>3</sup> Correspondence: Georgiana May (gmay@umn.edu)</p> <p><em><strong>Keywords:</strong></em></p> <p>conservation; <em>Dalea</em> spp.; habitat fragmentation; mutualism; nitrogen-fixing symbiosis; population level variation; native prairie legume; restoration; rhizobia</p> <p><em><strong>Description:</strong></em></p> <p>This Zenodo deposit is part of the MN LCCMR Healthy Prairies project granted to R. Shaw and G. May, UMN Twin-Cities. It contains the following files:</p> <p><span><span>·<span> </span></span></span>“Metadata & data” spreadsheet. <em>Contains metadata and data about the Twin Valley experiment (including the position of plants, an intermediary census, growth and nodulation traits for harvested plants, data on bacterial isolates from root nodules, and source modifiers for GenBank accessions OQ732394-OQ732572).</em></p> <p><span><span>·<span> </span></span></span>“Blast alignments output.txt” text file. <em>Contains ouput of Blastn alignements for the 16S rRNA genes of bacterial isolates against the rRNA_typestrains/16S_ribosomal_RNA 16S ribosomal RNA (Bacteria and Archaea type strains) database, to determine the genus as recommended by GenBank during sequence submission.</em></p> <p><span><span>·<span> </span></span></span>“General script.R”. <em>R script of the general statistical analyses produced for publication.</em></p> <p><span><span>·<span> </span></span></span>“General environment.RData”.<em> The companion RData (environment) of the above R script.</em></p> <p><span><span>·<span> </span></span></span>“Trait model script.R”. <em>R script of the plant trait models produced for publication</em></p> <p><span><span>·<span> </span></span></span>“Trait model environment.RData”. <em>The companion RData (environment) of the above R script.</em></p> <p><strong><em>Acknowledgments:</em></strong></p> <p>The authors thank members of the May Lab (Mai Beauclaire, Em Daily, Mara Demers, Kane Keller, Cedric Ndinga-Muniania, Liam Vertal, Monica Watson) for their help in field and lab work. We thank members of the Healthy Prairies project (Shelby Flint, Anna Peschel, Bill Peterson) who provided much of the infrastructure that made this project possible, as well as help in setting up field experiments. We also thank volunteer undergrads from University of Minnesota Morris (Amelia Nelson, Emily Job, Lily Fulton) for assistance in measuring harvested plants and counting nodules. Funding for this project was provided by the Minnesota Environment and Natural Resources Trust Fund as recommended by the Legislative-Citizen Commission on Minnesota Resources (LCCMR) Project 00086965, Healthy Prairies.</p> <p> </p>
Soil C, N, P, and Frankia nifD-K RFLP genotypes distribution from Alnus tenuifolia nodules in early and late succession 2005
This dataset contains genetic characterizations of Frankia inhabiting Alnus tenuifolia nodules in early and late succession sites in the Bonanza Creek Experimental Forest (BCEF). Characterizations were done using PCR-RFLP on the nifD-K spacer region of the Frankia genome. The position of each plant and each nodule were mapped in order to examine spatial patterns in Frankia distribution within sites. Soil chemistry data, including C, N, P, and pH, were also collected from mineral and organic layers.
Post-fire Variability in Siberian Alder in Interior Alaska: Distribution Patterns, Nitrogen Fixation Rates, and Ecosystem Consequences IV - Nodule Biomass 2015
This data set was collected as a part of Brian Houseman's MS Thesis, Post-fire Variability in Siberian Alder in Interior Alaska: Distribution Patterns, Nitrogen Fixation Rates, and Ecosystem Consequences (December 2017). Data include Siberian alder (Alnus viridis ssp. fruticosa) nodule biomass. Data were collected on study plots established across two burn scars (2004 Boundary Fire and 1971 Wickersham Dome Fire) within the Yukon-Tanana Uplands ecoregion of interior Alaska. The data were collected in 2015.
Counted Nodules dataset used in 'RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation'
<p>Counted Nodules dataset used in the article: 'RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation'</p>
MicroRNA Panel Predicts Lung Adenocarcinoma in Patients Presenting with Ground-Glass Nodules
<p>MicroRNA (miRNA) expression is correlated with tumor histology, differentiation, invasiveness and treatment outcome. We aimed to identify miRNAs whose differential expression might enable early diagnosis of lung adenocarcinoma in patients presenting with ground-glass nodules (GGNs). To identify potential miRNAs of interest, we analyzed the miRNA expression profile of tumor and adjacent non para-tumor tissue in 3 participants by next-generation sequencing (NGS). We then assessed the expression levels of the miRNAs of interest in 73 lung adenocarcinoma presenting with GGNs with matched adjacent non-tumor tissue by quantitative real-time polymerase chain reaction (qRT-PCR). Target genes of our selected miRNA panel were predicted using Miranda with default parameters. Twenty-three miRNAs showed differential expression between tumor and adjacent non-tumor tissue by NGS. Five miRNAs exhibited higher expression in tumor tissue compared to adjacent non-tumor tissue (P＜0.05), eighteen miRNAs demonstrated lower expression in tumor tissue versus adjacent non-tumor tissue (P＜0.05). When qRT-PCR was performed for the 23 miRNAs identified by NGS in the pilot stage, seven were found to have statistically significant expression in tumor versus adjacent non-tumor tissue (P＜0.05). The predicted targets of our miRNAs of interest are frequently associated with cancer signaling pathways. We developed a miRNA panel that could potential predict the presence of lung adenocarcinoma in patients presenting with GGNs. </p>
Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants
<p><span>Supplementary Data 4 from the manuscript "Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants". </span></p> <p><span>A concatenated alignment of all samples and all loci. This file was used for branch length estimation and not directly for phylogeny reconstruction (though an extraction of each subtree taxonomic samples subset from this alignment would be the alignment used to produce the scaffolded subtrees that were described in the paper). Sequences are labeled by well and can be mapped back to taxon for sub-setting and further use using Supplementary Data 1. </span></p>
Text-fig. 2. CT slices on Block 2. Details of other skeletal parts (a). The familiar shape of an ammonite (a, c). Holes, cracks and empty cavities in both the limestone matrix and within the vertebrate fossil (b, c). Heterogeneity of the 'tuffeau' limestone, the more porous areas of the matrix clearly distinguishable from the more compact ones (c). Ferric nodules (c). in Hidden Treasures Uncovered: Successful Detection Of Fossils Below The Surface In Large Limestone Blocks Using A Standard Medical X-Ray Ct Scanner
Text-fig. 2. CT slices on Block 2. Details of other skeletal parts (a). The familiar shape of an ammonite (a, c). Holes, cracks and empty cavities in both the limestone matrix and within the vertebrate fossil (b, c). Heterogeneity of the 'tuffeau' limestone, the more porous areas of the matrix clearly distinguishable from the more compact ones (c). Ferric nodules (c).
FIG. 69. Elytral morphotypes with color patterns and nodules. A, B. Morphotype 68, VMNH 54567. C, D. Morphotype 69, VMNH 95448. E–G. Morphotype 70, VMNH 95487 in Remarkable Diversity Of Beetles (Coleoptera) In The Late Triassic (Norian) "Solite Deposit" Of Virginia And North Carolina
FIG. 69. Elytral morphotypes with color patterns and nodules. A, B. Morphotype 68, VMNH 54567. C, D. Morphotype 69, VMNH 95448. E–G. Morphotype 70, VMNH 95487. Scale bars: A–F: 0.5 mm, G: 0.1 mm.
Fig. 1. Subcutaneous nodules. a in Nodular onchocercosis in red deer (Cervus elaphus) in Sweden
Fig. 1. Subcutaneous nodules. a) in the subcutaneous fascia from the rump of a carcass b) parts of the threadlike O. flexuosa extracted from a subcutaneous nodule.
Text-fig. 1. Bohemian Massif with position of the Prague Basin (in black) and distribution of Ordovician rocks in the Prague Basin, with geographic position of main localities of the siliceous nodules. in Porambonites Havliceki Sp. Nov., A New Brachiopod From The Šárka Formation (Darriwilian) From Bohemia And Its Contribution To Early History Of The Porambonitidae
Text-fig. 1. Bohemian Massif with position of the Prague Basin (in black) and distribution of Ordovician rocks in the Prague Basin, with geographic position of main localities of the siliceous nodules.
Text-fig. 3. Borehole section in the Blansko Graben with lithology, distribution of palynomorphs, macroflora and macrofauna (modified after Čech, unpublished report). 1 – Spesovicornea pacltovae, 2 – Platanus sp., 3 – Myrtophyllum angustum (VEL.) KNOBOCH, 4 – Gleichenia sp.), 5 – percentage of land-derived palynomorphs, 6 – percentages of marine palynomorphs, 7 – glauconite, 8 – pyrite nodules, 9 – macrofauna, 10 – productive palynological samples, 11 – carbonized roots, 12 – conglomerate, 13 – sandstone, 14 – claystone, 15 – coal, 16 – granite and granodiorite of the Brno pluton. in Spesovicornea Pacltovae Gen. Nov. Et Sp. Nov., A New Elateroid Sporomorph From The Bohemian Cenomanian (Czech Republic)
Text-fig. 3. Borehole section in the Blansko Graben with lithology, distribution of palynomorphs, macroflora and macrofauna (modified after Čech, unpublished report). 1 – Spesovicornea pacltovae, 2 – Platanus sp., 3 – Myrtophyllum angustum (VEL.) KNOBOCH, 4 – Gleichenia sp.), 5 – percentage of land-derived palynomorphs, 6 – percentages of marine palynomorphs, 7 – glauconite, 8 – pyrite nodules, 9 – macrofauna, 10 – productive palynological samples, 11 – carbonized roots, 12 – conglomerate, 13 – sandstone, 14 – claystone, 15 – coal, 16 – granite and granodiorite of the Brno pluton.
Linked collectors and determiners for: Abyssal fauna of the UK-1 polymetallic nodule exploration area, Clarion-Clipperton Zone, central Pacific Ocean: Cnidaria.
Natural history specimen data linked to collectors and determiners held within, "Abyssal fauna of the UK-1 polymetallic nodule exploration area, Clarion-Clipperton Zone, central Pacific Ocean: Cnidaria". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/44d7b5dd-7543-4b62-b816-393ce983e0db">https://bionomia.net/dataset/44d7b5dd-7543-4b62-b816-393ce983e0db</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/44d7b5dd-7543-4b62-b816-393ce983e0db">https://gbif.org/dataset/44d7b5dd-7543-4b62-b816-393ce983e0db</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Abyssal fauna of the UK-1 polymetallic nodule exploration claim, Clarion-Clipperton Zone, central Pacific Ocean: Echinodermata.
Natural history specimen data linked to collectors and determiners held within, "Abyssal fauna of the UK-1 polymetallic nodule exploration claim, Clarion-Clipperton Zone, central Pacific Ocean: Echinodermata". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/0751b002-8da2-436d-981f-a02ac44783bf">https://bionomia.net/dataset/0751b002-8da2-436d-981f-a02ac44783bf</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/0751b002-8da2-436d-981f-a02ac44783bf">https://gbif.org/dataset/0751b002-8da2-436d-981f-a02ac44783bf</a>. Formatted as a Frictionless Data package.
Fig. 8 in Neanthes goodayi sp. nov. (Annelida, Nereididae), a remarkable new annelid species living inside deep-sea polymetallic nodules
Fig. 8. Neanthes goodayi sp. nov., live specimens, in situ images. A. Paratype (NHM_2026), burrowing within nodule crevice. B. Detail of paratype (NHM_2026), in burrow. C. Paratype (NHM_512), burrowing within a foraminiferan growing on nodule. D–E. Detail of paratype (NHM_512), in burrow. F. Detail of paratype (NHM_1624), burrowing within a mudball encrusting the nodule surface. G–H. Details of paratype (NHM_1624), in burrow. Scale bars: 1 cm.
Fig. 6 in Neanthes goodayi sp. nov. (Annelida, Nereididae), a remarkable new annelid species living inside deep-sea polymetallic nodules
Fig. 6. Neanthes goodayi sp. nov., epitoke paratype (NHM_1783), preserved specimen. A. Entire specimen, dorsal view. B. Extruded pharynx, dorsal view (left), ventral view (right). C. Detail of prenatatory parapodium 4, with modified dorsal and ventral cirri, posterior view. D. Detail of modified natatory swimming parapodium, chaetiger 31, posterior view. E. Detail of papillated dorsal cirrus, chaetiger 31, posterior view. F. Modified swimming spinigers, subacicular neurocheatal fascicle, chaetiger 32. Abbreviations: DC = dorsal cirrus; VC = ventral cirrus. Lobe at base of dorsal cirrus in D and E outlined with a fine white or black line. Parapodium in C dissected from left side of specimen; parapodium in D dissected from right side of specimen, with images D and E laterally inverted to follow direction of other plates. Scale bars: A = 1 mm; B = 500 µm; C–D = 200 µm; E = 100 µm; F = 50 µm.
Fig. 5 in Neanthes goodayi sp. nov. (Annelida, Nereididae), a remarkable new annelid species living inside deep-sea polymetallic nodules
Fig. 5. Neanthes goodayi sp. nov., juvenile specimens. A. Paratype (1254), entire specimen, dorsal view. B. Paratype (NHM_171) dorsal anterior view. C. Paratype (NHM_127) entire specimen, dorsal view. D. Paratype (NHM_127), close up of dorsal anterior, arrows mark position of anterior eye pair. Scale bars: A, C = 1 mm; B = 500 µm; D = 100 µm.
Fig. 4 in Neanthes goodayi sp. nov. (Annelida, Nereididae), a remarkable new annelid species living inside deep-sea polymetallic nodules
Fig. 4. Neanthes goodayi sp. nov., paratypes. A. Paratype (NHM_1624), preserved specimen; dorsal anterior view, live image (left); lateral anterior view, preserved specimen (right). B. Paratype (NHM_755); dorsal anterior view, live image (left), preserved specimen (right); arrows marking pigmentation. C. Paratype (NHM_238), dorsal anterior view, arrows mark pigmentation. D. Paratype (NHM_512), dorsal anterior view, arrows mark pigmentation. Scale bars = 1 mm.
Fig. 2 in Neanthes goodayi sp. nov. (Annelida, Nereididae), a remarkable new annelid species living inside deep-sea polymetallic nodules
Fig. 2. Neanthes goodayi sp. nov., holotype (NHM_739). A. Live image, entire specimen. B. Preserved entire specimen, dorsal view (left), ventral view (right). C. Live image, anterior view, arrows mark pigmentation. D. Preserved specimen, anterior view, arrows mark pigmentation. E. Dissected pharynx, with pharyngeal areas I, II, III, IV, VI, VII–VIII highlighted. Scale bars: B = 1 mm; D = 500 µm; E = 250 µm.
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