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opencc-by-4.0Aug 2024View details →

Ensemble Learning of Catchment-Wise Optimized LSTMs Enhances Regional Rainfall-Runoff modelling - Case Study: Basque Country, Spain - Data

<div> <div>This data and results are for paper: "Ensemble Learning of Catchment-Wise Optimized LSTMs Enhances Regional Rainfall-Runoff modelling - Case Study: Basque Country, Spain" by Hosseini et al. 2024 (Preprint - Under review J.Hydro 2024) Available at SSRN: <a href="https://ssrn.com/abstract=4918782" target="_blank" rel="noopener">https://ssrn.com/abstract=4918782</a></div> <div> </div> </div>

Figure 9. Sometimes many volunteers are necessary for a in Stakeholder contributions to conservation of threatened Northern Pine Snakes (Pituophis melanoleucus, Daudin, 1803) in the New Jersey Pine Barrens as a case study

Figure 9. Sometimes many volunteers are necessary for a project, either digging up a hibernation site (Fig 9a), clearing open areas for sun penetration, or digging up an old septic line to prevent collapses and injuries to snakes.

Fig. 3 in Stakeholder contributions to conservation of threatened Northern Pine Snakes (Pituophis melanoleucus, Daudin, 1803) in the New Jersey Pine Barrens as a case study

Fig. 3. Typical nesting area of Northern Pine Snakes in New Jersey. They require relatively open areas where there is complete sun penetration to the ground to provide sufficient warmth to the incubating eggs (Burger 1989a, 1991a; Burger and Zappalorti 2011a).

Fig. 5 in Stakeholder contributions to conservation of threatened Northern Pine Snakes (Pituophis melanoleucus, Daudin, 1803) in the New Jersey Pine Barrens as a case study

Fig. 5. Pine Snakes hibernate in communal hibernacula that can contain up to 30 or more Pine Snakes (Burger et al. 1988; Burger and Zappalorti 2011a, b, 2015, 2016). Fig. 5a shows the depth hibernation chambers are below ground, a snake in a natural chamber (Fig 5b) and in cement blocks from an old septic chamber (Fig. 5c, Pine Snake on right, Black Racer on left).

Fig. 1 in Stakeholder contributions to conservation of threatened Northern Pine Snakes (Pituophis melanoleucus, Daudin, 1803) in the New Jersey Pine Barrens as a case study

Fig. 1. Northern Pine Snake (Pituophis melanoleucus) hissing when first encountered in the New Jersey Pine Barrens.

Figure 8 in Stakeholder contributions to conservation of threatened Northern Pine Snakes (Pituophis melanoleucus, Daudin, 1803) in the New Jersey Pine Barrens as a case study

Figure 8. Several Pine Snake females often nest in the same nest. Here we (R. Zappalorti and J. Burger) have removed four clutches (note they are bound together, making it possible to identify the eggs of three different females). Once females lay eggs, they exude a liquid that binds the eggs together. This partly prevents other females from disrupting the clutch and accidentally removing them to the outside while they are digging their own side chambers.

Fig. 7 in Stakeholder contributions to conservation of threatened Northern Pine Snakes (Pituophis melanoleucus, Daudin, 1803) in the New Jersey Pine Barrens as a case study

Fig. 7. Volunteers contribute directly to conservation efforts by helping to remove trees that are obstructing sun penetration to nests or hibernation sites (Fig. 7a), or taking data on snake behavior (Fig. 7b).

Fig. 6 in Stakeholder contributions to conservation of threatened Northern Pine Snakes (Pituophis melanoleucus, Daudin, 1803) in the New Jersey Pine Barrens as a case study

Fig. 6. Volunteers of all ages are involved in our Pine Snake research, and the handling and measuring of snakes contributes to their education, and results in their providing information about conservation to their families, friends, classmates, and others. Following hibernation studies, the children (and adults) put the snakes back into their hibernation chambers.

Fig. 4 in Stakeholder contributions to conservation of threatened Northern Pine Snakes (Pituophis melanoleucus, Daudin, 1803) in the New Jersey Pine Barrens as a case study

Fig. 4. Female Pine Snakes sometimes remain in their nests for several days after egg-laying is complete, perhaps protecting their clutch from being disrupted by other females that lay in the same nest.

Fig. 2 in Stakeholder contributions to conservation of threatened Northern Pine Snakes (Pituophis melanoleucus, Daudin, 1803) in the New Jersey Pine Barrens as a case study

Fig. 2. Female Northern Pine Snakes dig their own nests in the New Jersey Pine Barrens, although in the southern part of their range they do not do so. They bend their neck such that the head forms a scoop capable of bringing sand out the entrance (Fig 2a). While digging their body is hidden below ground, and the dump pile of sand is visible (and serves to attract poachers; Fig 2b).

opencc-by-4.0Aug 2024View details →

Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA

<p>Data deposition for "Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA" published in Nucleic Acids Research. Data includes custom paramaterized nucleobase residues for use in AMBER molecular dyanmics simulations. Initial structures and setup code along with starting structures for generation of simulations in AMBER (pmemd.cuda). A in-house "MD-Generator" script to create nessessary files with our select simulation settings. Lastly, also included are CPPTRAJ analysis commands and scripts with visualizion scripts for use in Pymol 2.5 and above. </p>

Fig. 5 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)

Fig. 5. Neophasis oculata metacercariae (A–F) and sexual adult (G). (A) General view of metacercaria (acetic carmine, DIC). (B–C) Histological sections, Mallory's trichrome stain, encysted metacercaria (B) and some of its inner structures (C). (D–F) SEM, ventral view (D) and magnified spines in the anterior (E) and posterior (F) regions. (G) Sexual adult (acetic carmine, DIC). Scale bars – 100 μm on A, B, D, G; 50 μm on C; 10 μm on E, F.Abbreviations: c – ceca; ci – cirrus; eg – eggs; ev – excretory vesicle; icy – inner cyst layer; ocy – outer cyst layer; os – oral sucker; ot – ootype; ov – ovary; pe – pigmented eyespots; ph – pharynx; sv – seminal vesicle; te – testes; ut – uterus; vi – vitelline follicles; vs – ventral sucker.

Fig. 2 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)

Fig. 2. Neophasis oculata intramolluscan stages: daughter redia (A), infective cercaria body structure (B) and general view (C).

Fig. 8 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)

Fig. 8. Phylogenetic position of Neophasis oculata and N. anarrhichae based on the concatenated 18S and 28S rDNA sequence data, inferred with Bayesian inference. Newly generated sequences are indicated in bold. Posterior probabilities are printed at nodes, followed by bootstrap values for the nodes that were also supported in the tree inferred with Maximum likelihood method. Scale bar shows the substitution rate. GenBank accession numbers for the 18S and 28S rDNA sequences are listed in the Supplementary Table S1.

Fig. 7 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)

Fig. 7. Neophasis anarrhichae successive life cycle stages. (A, B) whole mounts (toluidine blue, DIC) of the anterior end of daughter redia (A) and cercaria embryo (B). (C) Cercaria later embryo, CLSM, TRITC-phalloidin and phospho Y antibody staining. (D, E) whole mounts (toluidine blue, DIC) of cercaria (D) and metacercaria (E). (F) Anterior end of metacercaria with gland ducts, CLSM, acetylated α-tubulin and phospho Y antibody staining. (G) Sagittal section of metacercaria, Heidenhain's iron hematoxylin staining. (H) Sagittal section of metacercaria, Mallory's trichrome stain. (I) progenetic metacercaria (toluidine blue, DIC). (J) sexual adult (acetic carmine, DIC). Scale bars – 50 μm.Abbreviations: aс – anterior collecting duct; bp – birth pore canal; c – ceca; cd – caudal excretory duct; ci – cirrus; eg – eggs; ev – excretory vesicle; os – oral sucker; ot – ootype; ov – ovary; ovd – oviduct; pс – posterior collecting duct; pe – pigmented eyespots; pd – penetration gland ducts; ph – pharynx; sv – seminal vesicle; t – tail; te – testes; vi – vitelline follicles; vs – ventral sucker. Arrow indicate on site of main collecting duct division.. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)

Fig. 1. Consensus (99 threshold) neighbour-joining tree based on the concatenated ITS1 and ITS2 860- b.p. fragment, built with Tamura-Nei genetic distance method and 1000 bootstrap resamples; support values are printed at nodes. Repeat regions of the ITS1 were excluded from the alignment. Scale bar shows substitutions per site. The ingroup includes identified and putative life cycle stages of Neophasis oculata and N. anarrhichae, the numbers of isolates are as listed in Table 1. Brachycladium goliath serves as an outgroup.

Fig. 3 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)

Fig. 3. Neophasis oculata cercariae. (A) Infective cercaria, general structure and mucoid in the tegument (toluidine blue), differential interference contrast (DIC). (B) Ducts of the penetration glands in live cercaria. (C) Sagittal histological section of infective cercaria, Erlich's hematoxylin-eosin. (D–E) Mucoid in underdeveloped cercariae (toluidine blue, whole mount, DIC (D) and Azur II-eosin, histological section (E)). (F) SEM, ventral view. (G–I) CLSM, TRITC-phalloidin, acetylated α-tubulin and phospho Y antibody staining. (G) Infective cercaria, flame cells and nerves. (H–I) Underdeveloped cercariae, excretory ducts (H) and eyespots (I). Scale bars – 50 μm.Abbreviations: aс – anterior collecting duct; cd – caudal excretory duct; ev – excretory vesicle; fc – flame cells; ga – cerebral ganglion; mc – mucoid cytons; os – oral sucker; pс – posterior collecting duct; pe – pigmented eyespots; pg – penetration glands; pd – penetration gland ducts; ph – pharynx; t – tail; ue – unpigmented eyespot; vnc – ventral nerve chords; vs – ventral sucker. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

opencc-by-4.0May 2023View details →

Fig. 8 in Does dredging activity exert an influence on benthic macrofauna in tropical estuaries? Case study on the northern coast of Brazil

Fig. 8. Diagram of Principal Component Analysis during collection periods [Temp(W), water temperature; Sal(W), water salinity; OD(W), water dissolved oxygen; pH(W), pH of water; Fe(W), water iron; Mn(W), water manganese; Cu(S), copper from sediment; Cr(S), chromium from sediment; Ni(S), nickel from sediment; Zn(S), zinc from sediment].

opencc-by-4.0May 2023View details →

Fig. 7 in Does dredging activity exert an influence on benthic macrofauna in tropical estuaries? Case study on the northern coast of Brazil

Fig. 7. Dendrogram of Bray-Curtis similarity between the points sampled in the Port Complex of SÃo LuÍs, MaranhÃo, Brazil.