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opencc-by-4.0Aug 2022View details →

Fig. 5 in First step towards understanding the specific identity of fish muscle parasites of the genus Sarcotaces (Copepoda: Philichthyidae)-New species and first molecular ID in the genus

Fig. 5. SEM micrographs of Sarcotaces izawai sp. nov.; male; (A) Antenna, mandible and maxillule, ventral, (B) Mandibular claw and maxillule, ventral, (C) Maxillae, ventral, (D) Exopod of first thoracopod (left side), (E) Caudal rami of other male specimens, ventral, (F) Caudal ramus of another male specimens, ventral.

opencc-by-4.0Aug 2022View details →

Fig. 2 in First step towards understanding the specific identity of fish muscle parasites of the genus Sarcotaces (Copepoda: Philichthyidae)-New species and first molecular ID in the genus

Fig. 2. Line drawings of Sarcotaces izawai sp. nov.; (A) Female (allotype), habitus, semi-ventral view; small black silhouettes on the right represent the males at the same scale (the highest number found in a single gall), (B) Male (holotype), habitus, ventral, (C, D, E) Other males, habitus, ventral, (F, G) Caudal rami of other male specimens; Abbreviations: M = mouth area, T IV–T VII = thoracic somites, A I–A IV = abdominal somites; Scale bars: A = 10 mm, B–E = 0.5 mm, F–G = 0.1 mm.

opencc-by-4.0Aug 2023View details →

Fig. 3 in Association of bat flies (Diptera: Streblidae) and bats: Richness and host specificity in Western Mexico

Fig. 3. Taxonomic trees with the STD value for the hosts that presented more than two species of parasites. *The value represents the number of steps to get from one host to another since there are only two host species.

opencc-by-4.0Aug 2023View details →

Fig. 2 in Association of bat flies (Diptera: Streblidae) and bats: Richness and host specificity in Western Mexico

Fig. 2. Interaction network between bats and ectoparasites captured in Western Mexico. The lines represent interactions between species, and the width of the line indicates the strength of the interactions.

opencc-by-4.0Mar 2021View details →

FIGURE 2 in Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci

FIGURE 2 | Results of Structure (A, B) and Discriminant analysis of principal components (C) for Pseudoplatystoma magdaleniatum. A: K = 1; B: K = 2; M: Margento, PC: Punta Cartagena, PB: Puerto Berrío, SN: Samaná Norte.

opencc-by-4.0Jun 2024View details →

Neonate germ free and specific pathogen free plethysmography recordings and metadata files

This repository contains recordings of neonate mice during our autoresuscitation assay. Also included is a metadata sheet with additional information about the mice and settings to be used with out accompanying software for analysis.

opencc-by-4.0Feb 2024View details →

Annual crop-specific management history of phosphorus fertilizer input (CMH-P) in the croplands of United States from 1850 to 2022: Application rate, timing, and method

This dataset presents spatiotemporal dynamics of phosphorus (P) fertilizer management (application rate, timing, and method) at a 4km × 4 km resolution in agricultural land of the contiguous U.S. from 1850 to 2022. By harmonizing multiple data sources, we reconstructed the county-level crop-specific P fertilizer use history. We then spatialized and resampled P fertilizer use data to 4 km × 4 km gridded maps based on historical U.S. cropland distribution and crop type database developed by Ye et al. (2024). This dataset contains (1) P fertilizer total consumption and mean application rate at the national level (Tabular); (2) P fertilizer consumption of 11 crops at the state level (Tabular); (3) P fertilizer consumption of permanent pasture (Tabular); (4) P fertilizer consumption of non-farm at the state level (Tabular); (5) P fertilizer application rate of 11 crop types at the state level (Tabular); (6) P fertilizer application rate of 11 crop types at the county level (Tabular); (7) P fertilizer application timing ratio at the state level (Tabular); (8) P fertilizer application method ratio at the state level (Tabular); (9) Gridded maps of P fertilizer application rate based on state-level data; (10) and (11) Gridded maps of P fertilizer application rate based on county-level data; (12)-(20) Gridded maps of P fertilizer application rate for each crop. A detailed description of the data development processes, key findings, and uncertainties can be found in Cao, P., Yi, B., Bilotto, F., Gonzalez Fischer, C., Herrero, M., Lu, C.: Crop-specific Management History of Phosphorus fertilizer input (CMH-P) in the croplands of United States: Reconciliation of top-down and bottom-up data sources, is under review for the journal Earth System Science Data (ESSD). https://essd.copernicus.org/preprints/essd-2024-67/#discussion.  This work is supported by the Iowa Nutrient Research Center, the ISU College of Liberal Arts and Sciences Dean's Faculty Fellowship, and NSF CAREER grant (1945036).

opencc-by-4.0Feb 2024View details →

Gliding motility of the diatom Craspedostauros australis correlates with the intracellular movement of raphid-specific myosins

Abstract: Raphid diatoms are one of the few eukaryotes capable of gliding motility, which is remarkably fast and allows for quasi-instantaneous directional reversals. Besides other mechanistic models, it has been suggested that an actomyosin system provides the force for diatom gliding. However, in vivo data on the dynamics of actin and myosin in diatoms are lacking. In this study we demonstrate that the raphe-associated actin bundles required for diatom movement do not exhibit a directional turnover of subunits and thus their dynamics do not contribute directly to force generation. By phylogenomic analysis we identified four raphid diatom-specific myosins in Craspedostauros australis (CaMyoA-D) and investigated their in vivo localization and dynamics through GFP-tagging. Only CaMyoB-D but not CaMyoA exhibited coordinated movement during gliding, consistent with a role in force generation. The characterization of raphid diatom-specific myosins lays the foundation for unraveling the molecular mechanisms that underlie the gliding motility of diatoms. This dataset contains all microscopy data used for confocal and TIRFM imaging, with all additional elements required to reproduce figures in the manuscript "Gliding motility of the diatom Craspedostauros australis correlates with the intracellular movement of raphid-specific myosins". The dataset also contains code used to generate plots and analyze microscopy data, as well as protein sequences and code used to generate the phylogenomic tree in the paper.

opencc-by-4.0Aug 2024View details →

Form-specific prospective environmental risk assessment of graphene-based materials in European Freshwaters

This dataset is related to the following publication: Title: Form-specific prospective environmental risk assessment fo graphene-based materials in European freshwaters Authors: Hyunjoo Hong, Bernd Nowack  The files contain input files and final codes of the fs-MFA and fs-PSSD models.

FIG. 4 in Pterygoneurum sampaianum (Guim.) Guim.: range extension to Africa, first mentions in France, confirmation of specific status and improved morphological circumscription

FIG. 4. — Habitat of Pterygoneurum sampaianum (Guim.) Guim. (11 March 2020, Tunisia, Siliana Governorate, Sidi Ameur).

FIG. 3. — Bayesian consensus tree inferred from concatenated chloroplast rps4 in Pterygoneurum sampaianum (Guim.) Guim.: range extension to Africa, first mentions in France, confirmation of specific status and improved morphological circumscription

FIG. 3. — Bayesian consensus tree inferred from concatenated chloroplast rps4-trnS and trnM-trnV sequence data of the analysed dataset of Pottiaceae subfam. Pottioideae, partitioned between DNA sequence and indel data. Posterior probability from BI is displayed above the branches; bootstrap support (656 replications) from ML analysis is displayed below the branches.

FIG. 2 in Pterygoneurum sampaianum (Guim.) Guim.: range extension to Africa, first mentions in France, confirmation of specific status and improved morphological circumscription

FIG. 2. — Pterygoneurum sampaianum (Guim.) Guim.: A, habit; B-F, urn; G, gametophytes; H, leaf; I, hair-point; J-L, marginal areolation at leaf base. Scale bars: A-C, E, F, 200 µm; D, G, H, 100 µm; I, J, L, 30 µm; K, 50 µm.

FIG. 1 in Pterygoneurum sampaianum (Guim.) Guim.: range extension to Africa, first mentions in France, confirmation of specific status and improved morphological circumscription

FIG. 1. — Pterygoneurum ovatum (Hedw.) Dixon: A, habit; B, C, urn; D, gametophyte; E, leaf; F, hair-point; G, leaf base; H, marginal areolation at leaf base. Scale bars: A, D, 200 µm; B, C, F, G, 100 µm; E, 300 µm; H, 30 µm.

opencc-by-4.0Jun 2024View details →

DYNA: Disease-Specific Language Model for Variant Pathogenicity

For coding variant effect predictions (VEPs), our approach centers on clinical variant sets specifically related to inherited cardiomyopathies (CM) and arrhythmias (ARM). We utilize a pre-compiled dataset comprised of rare missense pathogenic and benign variants, categorized using a cohort-based approach for diseases such as cardiomyopathy and arrhythmias, as detailed in the previous report by Zhang et al. ClinVar CM and ARM datasets include all missense variants in CM and ARM, respectively, are extracted from ClinVar (Landrum et al.). In the realm of non-coding VEPs, our focus shifts to splicing-related variants, utilizing a dataset from the multiplexed assay for exon recognition by Chong et al., which highlights the significant impact of rare genetic variants on splicing disruptions. Similarly, the ClinVar Splicing dataset, compiled from ClinVar, encompasses all benign sequences and pathogenic variants pertinent to splicing.   For the ClinVar CM and ARM datasets, we translate the DNA sequences into protein sequences using the human genome assembly hg38 from https://www.ncbi.nlm.nih.gov/grc/human. We employed the GFF file, MANE.GRCh38.v1.1.ensembl\_genomic.gff.gz from https://www.ncbi.nlm.nih.gov/refseq/MANE, to annotate coding versus non-coding regions for each gene, as only coding DNA sequences are translated into proteins. Additionally, protein domains, cataloged in the Pfam database (Finn et al.), are essential for the functional characterization of proteins. These domains are identified by aligning the translated sequences to known domain structures, thereby facilitating deeper insights into protein function.

Fig. 5 in Two parasitoids of Diaphorina citri (Hemiptera: Liviidae) have shared, stage-specific preference for host nymphs that does not impact pest mortality rates

Fig. 5. Mean (± SE) development time of parasitoid eggs to adult emergence of (A) Diaphorencyrtus aligarhensis and (B) Tamarixia radiata that developed on different Diaphorina citri instars in no-choice experiments. Treatment means with the same letters are not significantly different (P> 0.05).

Fig. 3 in Two parasitoids of Diaphorina citri (Hemiptera: Liviidae) have shared, stage-specific preference for host nymphs that does not impact pest mortality rates

Fig. 3. Mean (± SE) emergence of adult Diaphorencyrtus aligarhensis from second through fifh instar Diaphorina citri nymphs in no-choice experiments when females foraged alone or with hetero- and conspecific competitors. Foraging scenario only affected parasitoid emergence when D. aligarhensis foraged for fourth instar D. citri nymphs (means with the same letters are not significantly different; P> 0.05).

Fig. 2 in Two parasitoids of Diaphorina citri (Hemiptera: Liviidae) have shared, stage-specific preference for host nymphs that does not impact pest mortality rates

Fig. 2. The effect of foraging scenario on mean (± SE) Diaphorina citri mortality when (A) second, (B) third, (C) fourth, and (D) fifh instar Diaphorina citri nymphs were exposed to female parasitoids in no-choice experiments. In each panel, means with the same letters are not significantly different (P> 0.05).

Fig. 1 in Two parasitoids of Diaphorina citri (Hemiptera: Liviidae) have shared, stage-specific preference for host nymphs that does not impact pest mortality rates

Fig. 1. Mean (± SE) proportion of oviposition events (αi), indicating preference of female parasitoids for second through fifh instar Diaphorina citri nymphs in choice arenas. For each parasitoid species, means with the same letters are not significantly different (P> 0.05).

Fig. 4 in Two parasitoids of Diaphorina citri (Hemiptera: Liviidae) have shared, stage-specific preference for host nymphs that does not impact pest mortality rates

Fig. 4. Mean (± SE) adult Tamarixia radiata emergence from second through fifh instar Diaphorina citri nymphs in no-choice experiments. Means with the same letters are not significantly different (P> 0.05). *Only 1 F1 Tamarixia radiata emerged from second instar D. citri nymphs (mean [± SE] = 0.028 ± 0.028 F1 adults).

Fig. 6 in Two parasitoids of Diaphorina citri (Hemiptera: Liviidae) have shared, stage-specific preference for host nymphs that does not impact pest mortality rates

Fig. 6. The survival probability of adult (A) Diaphorencyrtus aligarhensis and (B) Tamarixia radiata that emerged from second, third, fourth, and fifh instar Diaphorina citri nymphs in no-choice experiments.