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113 results for “pipefish”

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zenodo36/100

Example Inputs for PIPEFISH Spatial Transcriptomics Pipeline Tool

<p>This repository contains example input data, including raw images, codebooks,&nbsp; parameters, and segmentation labels needed to run the FISH spatial transcriptomics pipeline tool <a href="https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline">PIPEFISH</a>. The datasets contained are:</p> <ul> <li><em>in situ</em> sequencing (ISS) of a whole coronal slice of a mouse brain (50 genes). <a href="https://www.biorxiv.org/content/10.1101/2021.10.12.464086v1">Link to publication</a>.</li> </ul> <p>Gataric, M., Park, J.S., Li, T., Vaskivskyi, V., Svedlund, J., Strell, C., Roberts, K., Nilsson, M., Yates, L.R., Bayraktar, O. and Gerstung, M., 2021. PoSTcode: Probabilistic image-based spatial transcriptomics decoder. <em>bioRxiv</em>, pp.2021-10.</p> <ul> <li>MERFISH of human U2-OS cell cultures (130 genes). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047202/">Link to publication</a>.</li> </ul> <p>Moffitt, J.R., Hao, J., Wang, G., Chen, K.H., Babcock, H.P. and Zhuang, X., 2016. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. <em>Proceedings of the National Academy of Sciences</em>, <em>113</em>(39), pp.11046-11051.</p> <ul> <li>seqFISH of a developing mouse embryo (351 genes). <a href="https://www.nature.com/articles/s41587-021-01006-2">Link to publication</a>.</li> </ul> <p>Lohoff, T., Ghazanfar, S., Missarova, A., Koulena, N., Pierson, N., Griffiths, J.A., Bardot, E.S., Eng, C.H., Tyser, R.C.V., Argelaguet, R. and Guibentif, C., 2022. Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. <em>Nature biotechnology</em>, <em>40</em>(1), pp.74-85.</p> <p>In order to correctly format the inputs, run the prep_input.py script for the dataset you wish to run while in the <strong>same</strong> <strong>directory</strong> as the script.</p>

opencc-by-4.0Feb 2023View details →
dryad36/100

Reduced sexual size dimorphism in a pipefish population where males do not prefer larger females

Open the record for dataset details and reuse information.

publicOct 2022View details →
dryad36/100

The population genomics of repeated freshwater colonizations by Gulf Pipefish

Open the record for dataset details and reuse information.

publicJun 2021View details →
dryad36/100

Data from: Mate quality and the temporal dynamics of breeding in a sex-role-reversed pipefish, S. typhle

Open the record for dataset details and reuse information.

publicDec 2017View details →
zenodo32/100

FIGURE 4 in Taxonomic review of the pipefish genus Pseudophallus Herald, with the description of a new species (Syngnathiformes: Syngnathidae)

FIGURE 4: Distribution map of species of Pseudophallus occurring in drainages along the Atlantic coast, based on specimens examined in this study.

opennotspecifiedOct 2020View details →
zenodo32/100

FIGURE 2 in Taxonomic review of the pipefish genus Pseudophallus Herald, with the description of a new species (Syngnathiformes: Syngnathidae)

FIGURE 2: Species of the genus Pseudophallus: A—Pseudophallus brasiliensis (paratype) USNM 212058, 69.1 mm SL, Igarapé Inó, Furo de Panaquera, Rio Tocantins, Pará, Brazil. B—Pseudophallus elcapitanensis MCZ 88623, 110.6 mm SL, Río Picuro, Darien, Panama. C—Pseudophallus mindii (holotype) USNM 81770, 90.3 mm SL, Mindi Creek, Canal Zone, Panama. D—Pseudophallus starksii USNM 208365, 171.1 mm SL, upper tributary of Río Jaque, Província de Darien, Panama. E—Pseudophallus galadrielae. (holotype) FMNH 126156, 63.1mm SL, Lago Izabal, Guatemala. Red arrow indicates the anal papilla.

opennotspecifiedOct 2020View details →
zenodo32/100

FIGURE 6 in Taxonomic review of the pipefish genus Pseudophallus Herald, with the description of a new species (Syngnathiformes: Syngnathidae)

FIGURE 6. Scatterplot of scores of linear discriminant analysis for morphometric and meristic characters of the three species of Pseudophallus occurring in Atlantic drainages. LD1: Linear discriminant 1, LD2: Linear discriminant 2, A: Standard length, B: Head length, C: Snout Length, D: Snout depth, E: Pectoral-fin length, F: Pectoral-fin base length, G: Tail length, H: Dorsal-fin base length, I: Anal ring depth, J: Body depth, K: Head depth, L: Body width, M: Trunk depth, N: Orbital diameter, O: Snout width, P: Dorsal-fin rays, Q: Pectoral-fin rays, R: Trunk rings, S: Caudal rings, T: Subdorsal trunk rings, U: Subdorsal caudal rings, V: Origin of dorsal fin.

opennotspecifiedOct 2020View details →
zenodo32/100

FIGURE 1 in Taxonomic review of the pipefish genus Pseudophallus Herald, with the description of a new species (Syngnathiformes: Syngnathidae)

FIGURE 1. Schematic view of Pseudophallus indicating measurements taken in the present study. Male, lateral view: 1. standard length, 5. brood pouch length, 7. anal-ring depth, 8. body depth, 9. trunk depth, 12. snout depth and 15. head depth. Female, lateral view: 2. head length, 3. tail length, 4. dorsal-fin base length and 13. pectoral-fin length. Anterior part of body, lateral view: 11. snout length, 14. pectoral-fin base length and 16. orbital diameter. Female, anal-papillae region, ventral view: 6. body width and 10. anal-papillae length. In red, trunk rings. In green, tail rings. Hatched pattern: subdorsal rings.

opennotspecifiedOct 2020View details →
zenodo32/100

FIGURE 5 in Taxonomic review of the pipefish genus Pseudophallus Herald, with the description of a new species (Syngnathiformes: Syngnathidae)

FIGURE 5. Distribution map of species of Pseudophallus occurring in drainages along the Pacific coast based on specimens examined in this study.

opennotspecifiedOct 2020View details →
zenodo32/100

FIGURE 3 in Taxonomic review of the pipefish genus Pseudophallus Herald, with the description of a new species (Syngnathiformes: Syngnathidae)

FIGURE 3: Detail of anterior portion of body of species of the genus Pseudophallus A—Pseudophallus brasiliensis (paratype) USNM 212058, 69.1 mm SL, Igarapé Inó Furo de Panaquera, Rio Tocantins, Pará, Brazil. B—Pseudophallus elcapitanensis MCZ 88623, 110.6 mm SL, Río Picuro, Darien, Panama. C—Pseudophallus mindii (holotype) USNM 81770, 90.3 mm SL, Mindi Creek, Canal Zone, Panama. D—Pseudophallus starksii USNM 208365, 171.1 mm SL, upper tributary of Río Jaque, Província de Darien, Panama. E—Pseudophallus galadrielae. (holotype), FMNH 126156, 63.1 mm SL, Lago Izabal, Guatemala.

opennotspecifiedOct 2020View details →
zenodo32/100

FIGURE 7 in Taxonomic review of the pipefish genus Pseudophallus Herald, with the description of a new species (Syngnathiformes: Syngnathidae)

FIGURE 7. Maps of distribution of specimens of Pseudophallus available for study. Left side: distribution of specimens examined for the morphological analysis in this study. Right side map: distribution of voucher specimens with genetic sequences on GenBank (as of April 2020).

opennotspecifiedOct 2020View details →
dryad32/100

Data from: The effects of synthetic estrogen exposure on pre-mating and post-mating episodes of selection in sex-role-reversed Gulf pipefish

Environmental estrogens have been shown to affect populations of aquatic organisms in devastating ways, including feminization of males, alterations in mating behaviors, and disruption of sexual selection. Studies have shown 17α-ethinylestradiol (EE2) exposure to induce female-like secondary sexual traits in male Gulf pipefish, changing how females perceive affected males. We aimed to understand the effects of EE2 exposure on the sex-role-reversed mating system and the strength of selection in Gulf pipefish. We used artificial Gulf pipefish breeding aggregations and microsatellite-based parentage analysis to determine maternity. We then calculated the opportunity for selection and selection differentials on body size for both sexes during three consecutive episodes of selection. Exposure to EE2 did not affect the strength of selection, likely due to the unusual sex-role-reversed mating system found in this species. With respect to multiply mated females, EE2 exposed females produced more eggs with higher embryo survivorship than non-exposed females. Thus, short-term exposure to low concentrations (2.0 ng/L) of EE2 in Gulf pipefish enhanced female reproductive success. However, higher EE2 concentrations (5.0 ng/L) caused complete reproductive failure in Gulf pipefish males. These results call for more work on the long-term effects of EE2 exposure in Gulf pipefish in artificial and natural populations.

opencc-zeroDec 2012View details →
dryad32/100

Data from: Female ornamentation and the fecundity trade-off in a sex-role reversed pipefish

Sexual ornaments found only in females are a rare occurrence in nature. One explanation for this is that female ornaments are costly to produce and maintain and, therefore, females must trade-off resources related to reproduction to promote ornament expression. Here, we investigate whether a trade-off exists between female ornamentation and fecundity in the sex-role reversed, wide-bodied pipefish, Stigmatopora nigra. We measured two components of the disk-shaped, ventral-striped female ornament, body width and stripe thickness. After controlling for the influence of body size, we found no evidence of a cost of belly width or stripe thickness on female fecundity. Rather, females that have larger ornaments have higher fecundity and thus accurately advertise their reproductive value to males without incurring a cost to fecundity. We also investigated the relationship between female body size and egg size and found that larger females suffered a slight decrease in egg size and fecundity, although this decrease was independent of female ornamentation. More broadly, considered in light of similar findings in other taxa, lack of an apparent fecundity cost of ornamentation in female pipefish underscores the need to revisit theoretical assumptions concerning the evolution of female ornamentation.

opencc-zeroDec 2017View details →
dryad32/100

Data from: The "Woman in Red" Effect: pipefish males curb pregnancies at the sight of an attractive female

In an old Gene Wilder movie, an attractive woman dressed in red devastated a man's current relationship. We have found a similar "Woman in Red" effect in pipefish, a group of fish where pregnancy occurs in males. We tested for the existence of pregnancy blocks in pregnant male black-striped pipefish (Syngnathus abaster). We allowed pregnant males to see females that were larger and even more attractive than their original high-quality mates and monitored the survival and growth of developing offspring. After exposure to these extremely attractive females, males produced smaller offspring in more heterogeneous broods and showed a higher rate of spontaneous offspring abortion. Although we did not observe a full pregnancy block, our results show that males are able to reduce investment in current broods when faced with prospects of a more successful future reproduction with a potentially better mate. This "Woman in Red" life history trade-off between present and future reproduction has similarities to the Bruce effect, and our study represents the first documentation of such a phenomenon outside mammals.

opencc-zeroDec 2017View details →
dryad32/100

Data from: Embryo oxygenation in pipefish brood pouches: novel insights

The pipefish brood pouch presents a unique mode of parental care that enables males to protect, osmoregulate, nourish and oxygenate the developing young. Using a very fine O2 probe, we assessed the extent to which males of the broad-nosed pipefish (Syngnathus typhle) oxygenate the developing embryos and are able to maintain pouch fluid O2 levels when brooding in normoxia (100% O2 saturation) and hypoxia (40% O2 saturation) for 24 days. In both treatments, pouch fluid O2 saturation levels were lower compared with the surrounding water and decreased throughout the brooding period, reflecting greater offspring demand for O2 during development and/or decreasing paternal ability to provide O2 to the embryos. Male condition (hepatosomatic index) was negatively affected by hypoxia. Larger males had higher pouch fluid O2 saturation levels compared with smaller males, and levels were higher in the bottom section of the pouch compared with other sections. Embryo size was positively correlated with O2 availability, irrespective of their position in the pouch. Two important conclusions can be drawn from our findings. First, our results highlight a potential limitation to brooding within the pouch and dismiss the notion of closed brood pouches as well-oxygenated structures promoting the evolution of larger eggs in syngnathids. Second, we provide direct evidence that paternal care improves with male size in this species. This finding offers an explanation for the documented strong female preference for larger partners because, in terms of oxygenation, the brood pouch can restrict embryo growth.

opencc-zeroDec 2014View details →
dryad32/100

Data from: The contributions of premating and postmating selection episodes to total selection in sex-role-reversed Gulf pipefish

Empirical studies of sexual selection often focus on events occurring either before or after mating but rarely both and consequently may fail to discern the relative magnitudes and interactions of premating and postmating episodes of selection. Here, we simultaneously quantify premating and postmating selection in the sex-role-reversed Gulf pipefish by using a microsatellite-based analysis of parentage in experimental populations. Female pipefish exhibited an opportunity for selection (I) of 1.64, which was higher than that of males (0.35). Decompositions of I and the selection differential on body size showed that over 95% of the selection on females arose from the premating phase. We also found evidence for a trade-off between selection phases, where multiply mating females had significantly lower offspring survivorship compared to singly mated females. In males, variance in relative fitness arose mainly from the number of eggs received per copulation and a small number of males who failed to mate. Overall, our study exemplifies a general approach for the decomposition of total selection into premating and postmating phases to understand the interplay among components of natural and sexual selection that conspire to shape sexually selected traits.

opencc-zeroDec 2012View details →
zenodo32/100

FIGURE 4 in Syngnathus chihiroe, a new species of pipefish (Syngnathidae) from southern Japan

FIGURE 4. Preserved specimen of Syngnathus schlegeli, BSKU 47138 (1 of 9 specimens), 79.4 mm SL, East China Sea.

opennotspecifiedDec 2017View details →
zenodo32/100

FIGURE 2 in Syngnathus chihiroe, a new species of pipefish (Syngnathidae) from southern Japan

FIGURE 2. Semi-schematic drawings of (A) lateral and (B) dorsal views of head; (C) lateral and (D) dorsolateral views of trunk-tail portion in holotype of Syngnathus chihiroe sp. nov., NSMT-P 106296, 92.0 mm SL. AR: anal ring; DE: dorsal-fin base end; DO: dorsal-fin base origin; ITAR: inferior tail ridge; ITR: inferior trunk ridge; LTAR: lateral tail ridge; LTR: lateral trunk ridge; STAR: superior tail ridge; STR: superior trunk ridge. Dorsal-fin not illustrated in (C) and (D), except for 1st and last rays in (D). Bars indicate 3 mm.

opennotspecifiedDec 2017View details →
zenodo32/100

FIGURE 5 in Syngnathus chihiroe, a new species of pipefish (Syngnathidae) from southern Japan

FIGURE 5. Relationships between snout length (% HL) (A); snout depth (% HL) (B); anal ring depth (% HL); and snout depth (% snout length) (D) to head length (mm) in Syngnathus chihiroe sp. nov. (blue triangle) and S. schlegeli (red circles).

opennotspecifiedDec 2017View details →
zenodo32/100

FIGURE 1 in Syngnathus chihiroe, a new species of pipefish (Syngnathidae) from southern Japan

FIGURE 1. Holotype of Syngnathus chihiroe sp. nov., NSMT-P 106296, female, 92.0 mm SL, southwest of Yakushima Island, Kagoshima Prefecture, Japan. (A) Lateral view of body; (B) lateral and (C) dorsal views of head.

opennotspecifiedDec 2017View details →

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DANDI Archive for NWB datasets

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dandi-nwb
electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.
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International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl
behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.
Last verified 2026-04-29Open record

OpenNeuro

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openneuro
neuroscienceopenPublished datasets are available on demand over the internet.
Last verified 2026-04-29Open record