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Figure 8 in Otolith characteristics of species, subspecies, and populations of Aphanius Nardo, 1827 (Teleostei, Cyprinodontiformes) from Anatolia (Turkey)

Figure 8. Zoogeographic map (after Wildekamp 1993, modified). Identical symbols indicate similar otolith morphologies. Aphanius anatoliae is represented by circles, A. asquamatus by a star, A. danfordii by crosses, and A. villwocki by squares.

Figure 2 in Otolith characteristics of species, subspecies, and populations of Aphanius Nardo, 1827 (Teleostei, Cyprinodontiformes) from Anatolia (Turkey)

Figure 2. Photographs of males (left) and females (right) of Aphanius anatoliae anatoliae (1–8) and A. anatoliae splendens (9, 10).

Figure 3 in Otolith characteristics of species, subspecies, and populations of Aphanius Nardo, 1827 (Teleostei, Cyprinodontiformes) from Anatolia (Turkey)

Figure 3. Left sagittae of Aphanius anatoliae anatoliae of south-west Anatolia (Lake District), except (k) right sagitta, mirrored. Localities: Yeşilova/Lake Salda (a–f), Doğanbaba/Lake Salda (g–j), Düğer (k–m), Lake Avlan (n–u), Işıklı dam (v, w). (a–h, k, n–r) Females; (i, j, l, m, s–w) males.

Figure 4 in Otolith characteristics of species, subspecies, and populations of Aphanius Nardo, 1827 (Teleostei, Cyprinodontiformes) from Anatolia (Turkey)

Figure 4. Left sagittae of Aphanius anatoliae anatoliae of south-west (Lake District) (a–g) and western central Anatolia (h–t), except (a) right sagitta, mirrored. Localities: Kovada Canal (a, b), Lake Eğirdir/Barla (c, d), Lake Eğirdir/Eğirdir (e–g), Eflatunpınarı/Beyşehir (h–m), İnsuyu/Cihanbeyli (n), and Akkaya/Niğde (o–t). (a, c, e, f, h–j, o–q) Females; (b, d, g, k–n, r–t) males.

Population average atlas for BundleSeg

Multi-atlas bundle segmentation This data is made to be used with the following script: <a href="https://github.com/scilus/scilpy/blob/2.1.1/scripts/scil_tractogram_segment_with_bundleseg.pyent_with_bundleseg.py">https://github.com/scilus/scilpy/blob/master/scripts/scil_tractogram_segment_with_bundleseg.py</a> Or the following Nextflow pipeline: <a href="https://github.com/scilus/rbx_flow">https://github.com/scilus/rbx_flow</a> <blockquote> Etienne St-Onge, Kurt Schilling, Francois Rheault, "BundleSeg: A versatile, reliable and reproducible approach to whitte matter bundle segmentation.", arXiv, 2308.10958 (2023) Rheault, François. "Analyse et reconstruction de faisceaux de la matière blanche." Computer Science (Université de Sherbrooke) (2020), https://savoirs.usherbrooke.ca/handle/11143/17255 </blockquote> Usage Here is an example (for more details use `scil_tractogram_segment_with_bundleseg.py -h`) : <code>antsRegistrationSyNQuick.sh -d 3 -f ${T1} -m mni_masked.nii.gz -t a -n 4</code> <code>scil_tractogram_segment_with_bundleseg.py ${TRACTOGRAM} config_fss_1.json atlas/*/ output0GenericAffine.mat --out_dir ${OUTPUT_DIR}/ --log_level DEBUG --minimal_vote 0.4 --processes 8 --seed 0 --inverse -f</code> To facilitate interpretation, all endpoints were uniformized head/tail. To see, which side of a bundle is head or tail, you can load the atlas bundle into the software <a href="https://github.com/imeka/mi-brain">MI-Brain</a> Notes on bundles - AC and PC were added mostly in case the atlas is used for lesion-mapping or figures. Likely, segmentation won't produce good results. This is mostly due to difficult tracking for these bundles. - The CC are split for each lobe. However, for technical consideration, the frontal portion was split in two to facilitate clustering and segmentation. For the same reason, the portion fanning to the pre/post central gyri were separated. - The streamlines present in the CC are homotopic, Recobundles will allow for variation and thus lead to 'some' heterotopy. However, it is expected that the results will be mostly homotopic. - CG has 3 possible endpoint locations. However, the full extent of the tail is difficult to track and is often missing. - FPT and POPT should terminate in the pons. However, to fully capture candidate streamlines and improve segmentation quality even streamlines reaching down the brainstem are selected.  - PYT should reach down the brainstem. For similar reasons to the FPT/POPT, streamlines ending in the pons are selected. Otherwise, fanning is affected and bundles is too skinny.  - OR_ML will most likely have difficulty capturing the full ML. However, this is often due to difficult tracking. - The cerebellum is often cut due to acquisition FOV. In such a case, all projection bundles will be more difficult to recognize and most cerebellum bundles will be missing (ICP, MCP, SCP). See Mosaic of bundles <a href="https://i.ibb.co/n7Ln3Gf/mosaic-local.png">here</a>. Acronym AC - Anterior commisure AF - Arcuate fasciculus CC_Fr_1 - Corpus callosum, Frontal lobe (most anterior part) CC_Fr_2 - Corpus callosum, Frontal lobe (most posterior part) CC_Oc - Corpus callosum, Occipital lobe CC_Pa - Corpus callosum, Parietal lobe CC_Pr_Po - Corpus callosum, Pre/Post central gyri CC_Te - Corpus callosum, Temporal lobe CG - Cingulum FAT - Frontal aslant tract FPT - Fronto-pontine tract FX - Fornix ICP - Inferior cerebellar peduncle IFOF - Inferior fronto-occipital fasciculus ILF - Inferior longitudinal fasciculus MCP - Middle cerebellar peduncle MdLF - Middle longitudinal fascicle OR_ML - Optic radiation and Meyer's loop PC - Posterior commisure POPT - parieto-occipito pontine tract PYT - Pyramidal tract SCP - Superior cerebellar peduncle SLF - Superior longitudinal fasciculus UF - Uncinate fasciculus

opencc-zeroNov 2023View details →

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Male song structure predicts offspring recruitment to the breeding population in a migratory bird

Bird song is a classic example of a sexually selected trait, but much of the work relating individual song components to fitness has not accounted for song typically being composed of multiple, often-correlated components, necessitating a multivariate approach. We explored the role of sexual selection in shaping complex male song of house wrens (Troglodytes aedon) by simultaneously relating its multiple components to fitness using multivariate selection analysis, which is widely used in insect and anuran studies but not in birds. The analysis revealed significant variation in the form and strength of selection acting on song across different selection episodes, from nest-site defense to recruitment of offspring to the breeding population. Males that sang more song typically employed in close communication sired more offspring that were subsequently recruited to the breeding population than those that sang far-communication song. However, this relationship was not consistent across earlier selection episodes, as evidenced by non-linear selection acting on these song components in other contexts. Collectively, our results present a complex picture of multivariate selection on male song structure that would not be evident using univariate approaches and suggest possible trade-offs within and among song components at different points of the breeding season.

opencc-by-4.0Aug 2023View details →

Individual multilocus genotypes from four populations of Helichrysum arenarium (Asteraceae) from Belgium and Germany

Individual multilocus genotypes based on 11 microsatellites loci from four populations of Helichrysum arenarium (Asteraceae) from Belgium and Germany. For more details, see Van Rossum et al. 2024 "Genetic diversity assessment of Helichrysum arenarium (Asteraceae) for the genetic restoration of declining populations" in Ecology and Evolution

Fig. 6 in Phenotypic Study Of Population And Distribution Of The Poecilia Reticulata (Cyprinodontiformes, Poeciliidae) From Kyiv Sewage System (Ukraine)

Fig. 6. Dependence of the area of orange spots (stripes, %) on the body length of male guppies (L) P. reticulata.

Fig. 1 in Phenotypic Study Of Population And Distribution Of The Poecilia Reticulata (Cyprinodontiformes, Poeciliidae) From Kyiv Sewage System (Ukraine)

Fig. 1. Potential (probabilistic) model of P. reticulata current world expansion built in the Maxent program based on the CliMond climatic data and GBIF data (2021). Areas of highest habitat suitability (> 0.5) are colored in red and areas of lowest (<0.1) — in blue.

Fig. 7 in Phenotypic Study Of Population And Distribution Of The Poecilia Reticulata (Cyprinodontiformes, Poeciliidae) From Kyiv Sewage System (Ukraine)

Fig. 7. Dependence of the proportions of the tail (C1/C2) on the body length of P. reticulata: C1/C2 = 1 ("symmetrical tail") is shown by the line.

opencc-by-4.0Jul 2023View details →

Figure 1 in Population fluctuation of some economically important mites on two mango cultivars in Qalyubia governorate, Egypt

Figure 1. Population fluctuation of plant-feeding and predacious mites on "Naomi" mango cultivar at Qalyubia governorate during 2020–2022 seasons.

opencc-by-4.0Jul 2023View details →

Figure 2 in Population fluctuation of some economically important mites on two mango cultivars in Qalyubia governorate, Egypt

Figure 2. Population fluctuation of plant-feeding and predacious mites on "Heidi" mango cultivar at Qalyubia governorate during 2020–2022 seasons.

Supporting data for: Vocal fingerprinting reveals a substantially smaller global population of the Critically Endangered cao vit gibbon (Nomascus nasutus) than previously thought

These data were used in the publication "Vocal fingerprinting reveals a substantially smaller global population of the Critically Endangered cao vit gibbon (Nomascus nasutus) than previously thought", currently in review. The acoustic measurements provided in the file were input to the clustering analyses detailed in the paper. Each row corresponds to a single male song phrase. The columns include:<ul><li>GroupID - the name of the gibbon group, based on manual identification of the song phrase</li><li>MFCC[1-88] - Mel-frequency cepstral coefficients as detailed in the paper</li><li>Delta[89-176] - Delta-cepstral coefficients as detailed in the paper</li><li>Duration - the length of the song phrase (in seconds)</li><li>Freq 5% (Hz) and Freq 95% (Hz) - 5th and 95th percentile frequencies, respectively</li><li>Cao and Vit - the number of "cao" and "vit" components, respectively, present in the song phrase</li><li>CutFileName - the file name of the extracted song phrase (which also acts as a unique identifier)</li><li>Representative - whether the given song phrase was 'representative' ("Yes" or "No") of a typical phrase for that male (as defined by the modal number of 'cao' and 'vit' components for males)</li></ul>All columns (except GroupID, CutFileName and Representative) have been standardised (i.e. centred to the mean and scaled according to the standard deviation).

Germline CpG methylation signatures in the human population inferred from genetic polymorphism

This repository contains data released accompanying the manuscript "Germline CpG methylation signatures in the human population inferred from genetic polymorphism".

Micro-CT image of cell-populated collagen scaffold in the aqueous environment (contrasted with PTA)

A dataset of the collagen scaffold populated with the 3T3 cells scanned in the aqueous environment using Bruker Skyscan 1276 machine (Bruker, Belgium). Scaffold productionThe processes of obtaining and working with collagen scaffolds were conducted in an isolated environment under sterile conditions. The collagen sponge matrix was manufactured at the Center for Collagen Innovation within the Institute of Regenerative Medicine at Sechenov University and provided to us for experimental purposes. In order to obtain the collagen, the authors utilized animal-derived materials sourced from the tendons of large horned cattle. To do this, the tendons were cleaned of excess tissues, cut into pieces with a thickness of 0.5-1 cm, and sequentially treated for 12 hours in a 0.5 M NaCl solution. Subsequently, the mass was homogenized in a 0.83 M acetic acid solution. The resulting suspension was hydrolyzed with 0.24% pepsin for 2 days, after which 1 M NaOH was added to adjust the pH to 7.5, halting the hydrolysis process. The suspension was precipitated with a 12% NaCl solution, the resulting precipitate was redissolved in 0.02 M acetic acid, and then dialyzed. To obtain collagen porous matrices (sponges), the obtained solution was neutralized using 0.1 M NaOH until a pH of 7-7.5 was reached, and the resulting suspension was lyophilized at -40°C for 2 days.Subsequently, the collagen matrix was cut into cubes with sides measuring 0.5 cm. These cubes were placed in 15 ml test tubes filled with 70% ethyl alcohol for sterilization. The test tubes were then placed on a shaker and left in the refrigerator at +4°C for 24 hours. Afterward, the collagen matrices were removed from the alcohol and rinsed five times with 0.9% NaCl.Following the alcohol rinse to confirm the absence of toxicity, an elution test, adapted following the ISO 10993 protocol, was conducted. To obtain collagen cube extracts, they were incubated in a cell culture medium at a volume of 1 ml per sample for 24 hours at 37°C. The 3T3 cell culture was passaged, with 5000 cells seeded in each well of a 96-well plate. After 24 hours, the cells were treated with extract at a volume of 200 µl per well and left in the incubator at 37°C for 24 hours. The following day, extracts were collected, and AlamarBlue reagent (Invitrogen, Waltham, MA, USA) was added according to the manufacturer's instructions to assess the metabolic activity of the cells. Serial dilutions of sodium dodecyl sulfate (SDS) were used as the positive control. Fluorescence intensity was measured using a Victor Nivo spectrofluorimeter (PerkinElmer, Waltham, Massachusetts, USA) at an excitation wavelength of 530 nm and an emission wavelength of 590 nm.Cell seedingAfter confirming the absence of cytotoxic effects, collagen sponges were seeded with the NIH 3T3 cell line at a density of 50,000 cells per sample (cubes of collagen sponge measuring 0.5 cm per side). Staining techniqueFixed specimens in 10% formalin with PBS were washed after 24 hours with distilled water and after that placed in 3% phosphotungstic acid dissolved in distilled water for 24 hours and kept on the rotary shaker at room temperature. After staining, samples were washed and stored in distilled water at 5 °C. Image acquisition and reconstructionA plastic tube filled with distilled water containing the contrasted sample was placed on the sample holder in a SkyScan 1276 micro-CT (Bruker, Kontich, Belgium) and were scanned at 3 μm voxel resolution with 70 kV voltage and 200 uA source power and an aluminum filter with 1 mm of thickness. The rotation was set to 360° around the vertical axis of the sample, with two middle frames for each 0.2° angle step.After scanning, the data were reconstructed using Bruker's NRecon software. During reconstruction, the ring artifact reduction value was set to 20% and the beam hardening correction value to 30%. After that, samples were exported as a series of 16-bit TIFF images which could be opened in the specialized software.

Figure 4 in Longterm study in Leucoptera coffeella population from southern Minas Gerais, Brazil

Figure 4: Correlation between the number of predated larvae and the average monthly temperature between January 2015 and December 2019 (Chi = 62,855, p <0.01) (PL: predated mines; temp: average monthly temperature).

Figure 3 in Longterm study in Leucoptera coffeella population from southern Minas Gerais, Brazil

Figure 3: Correlation between the number of intact larvae and average monthly temperature between January 2015 and December 2019 (Chi = 73.19, p = 0.02701) (IL: intact mines; temp: average monthly temperature).

Figure 1 in Longterm study in Leucoptera coffeella population from southern Minas Gerais, Brazil

Figure 1: A: Variation in observed values of biological parameters (AL, number of attacked leaves; IL, number of intact larvae present on leaves; PL, number of predated larvae observed on leaves). B: Variation in observed values of abiotic parameters (mean monthly temperature; total monthly precipitation).

Figure 6 in Longterm study in Leucoptera coffeella population from southern Minas Gerais, Brazil

Figure 6: Pearson's correlation pyramid showing the degree and value of the correlations between the studied biological and environmental variables (AL, number of attacked leaves; IL, number of intact larvae present on leaves; PL, number of predated larvae observed on leaves; Temp, average monthly temperature; Prec, total monthly rainfall).

Figure 2 in Longterm study in Leucoptera coffeella population from southern Minas Gerais, Brazil

Figure 2: Correlation between the number of attacked leaves and average monthly temperature between January 2015 and December 2019 (F = 6.7135, p = 0.01208) (AL: attacked leaves; temp: average monthly temperature).