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opencc-by-4.0Jan 2022View details →

FIG. 2 in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 2. Scheme of plots in a regular grid. A. Study site. B. Brephulopsis cylindrica and Xeropicta derbentina in the field. C. Scheme of plots in a regular grid. РИС. 2. Регулярная сетка плоЩадок. A. РасполоЖение исследуемого участка. B. Brephulopsis cylindrica и Xeropicta derbentina в месте обитания. C. Схема регулярной сетки плоЩадок.

opencc-by-4.0Dec 2018View details →

Рис. 8. СреЗы череЗ гонады моллюска: А – поперечный среЗ череЗ гонаду самки, Б–Д – фолликулы в гонадах самок (Б, В – Зрелые ооциты круглой формы, готовые к вымету; Г – ооциты в период активного гаметогенеЗа на стадии раннего трофоплаЗматического роста, Д – ооциты каплевидной формы в период преднерестовой стадии при ЗаверШении трофоплаЗматического роста), Е, Ж – поперечные среЗы череЗ гонаду самца, З, И – ацинусы в гонадах самцов (З – преднерестоваЯ стадиЯ, просветы в ацинусах практически отсутствуют, стенки ацинусов не раЗличимы, И – нерестоваЯ стадиЯ, имеютсЯ просветы в ацинусах). МасШтабные линейки 300 мкм (А), 200 мкм (Е), 100 мкм (Ж), 50 мкм (Б–Д, З, И). вя – вакуолиЗированное Ядро, сф – стенка фолликула, вм – вителлиноваЯ мембрана, РО – раЗвиваюЩиесЯ иЗ пелликулы ооциты, пг – ресничный проток гонады, с – сперматоциты, па – просветы в ацинусах. Fig. 8. Sections through the gonads of the mollusk: А – transverse section through the female gonad, Б–Д – ovarian acini, follicles (Б, В – mature round-shaped oocytes ready to be swept out; Г – oocytes in the period of active gametogenesis at the stage of early trophoplasmatic growth, Д – tear-shaped oocytes during the pre-spawning stage at the end of trophoplasmatic growth), Е, Ж – transverse sections through the male gonads, З, И – testicular acini (З – pre-spawning stage, with practically absent gaps in the acini and invisible the acini walls, И – spawning stage, with gaps in the acini). Scale bars 300 µm (A), 200 µm (E), 100 µm (Ж), 50 µm (Б–Д, З, И). вя – vacuolated nucleus, сф – follicle wall, вм – vitelline membrane, РО – developing oocytes arising from a pellicle, пг – ciliated gonadal duct, с – spermatocytes, па – gaps in acini. in Nodularia vladivostokensis (Bivalvia: Unionidae) from Razdolnaya River (Primorye, Russia)

Рис. 8. СреЗы череЗ гонады моллюска: А – поперечный среЗ череЗ гонаду самки, Б–Д – фолликулы в гонадах самок (Б, В – Зрелые ооциты круглой формы, готовые к вымету; Г – ооциты в период активного гаметогенеЗа на стадии раннего трофоплаЗматического роста, Д – ооциты каплевидной формы в период преднерестовой стадии при ЗаверШении трофоплаЗматического роста), Е, Ж – поперечные среЗы череЗ гонаду самца, З, И – ацинусы в гонадах самцов (З – преднерестоваЯ стадиЯ, просветы в ацинусах практически отсутствуют, стенки ацинусов не раЗличимы, И – нерестоваЯ стадиЯ, имеютсЯ просветы в ацинусах). МасШтабные линейки 300 мкм (А), 200 мкм (Е), 100 мкм (Ж), 50 мкм (Б–Д, З, И). вя – вакуолиЗированное Ядро, сф – стенка фолликула, вм – вителлиноваЯ мембрана, РО – раЗвиваюЩиесЯ иЗ пелликулы ооциты, пг – ресничный проток гонады, с – сперматоциты, па – просветы в ацинусах. Fig. 8. Sections through the gonads of the mollusk: А – transverse section through the female gonad, Б–Д – ovarian acini, follicles (Б, В – mature round-shaped oocytes ready to be swept out; Г – oocytes in the period of active gametogenesis at the stage of early trophoplasmatic growth, Д – tear-shaped oocytes during the pre-spawning stage at the end of trophoplasmatic growth), Е, Ж – transverse sections through the male gonads, З, И – testicular acini (З – pre-spawning stage, with practically absent gaps in the acini and invisible the acini walls, И – spawning stage, with gaps in the acini). Scale bars 300 µm (A), 200 µm (E), 100 µm (Ж), 50 µm (Б–Д, З, И). вя – vacuolated nucleus, сф – follicle wall, вм – vitelline membrane, РО – developing oocytes arising from a pellicle, пг – ciliated gonadal duct, с – spermatocytes, па – gaps in acini.

The processed clean data of 16S rRNA V4 amplicon sequecnces for the six stage of phenolic microbiome domestication

Open the record for dataset details and reuse information.

Microbial Load on Dental Students' Hands: A Gender and Academic Stage Analysis

This dataset supports a study investigating microbial contamination on the hands of dental students at Al-Hadi University College. The data were collected using impression sampling of the index and thumb fingers of 35 students (17 males, 18 females) from the third, fourth, and fifth academic years. Sampling occurred at the end of academic or clinical activities, and bacterial load was measured using colony-forming units (CFUs) cultured on MacConkey agar. Variables in the dataset include gender, academic stage, handedness, and CFU counts.

Platynereis dumerilii full-length transcriptome of developmental stages

To generate a high-quality full-length transcriptome for the annelid Platynereis dumerilii, we collected samples from representative developmental stages, from unfertilized eggs to 5 days post-fertilization. Each sample consisted of a bulk mix from 1 to 5 batches of embryos fertilized by different parents. We incubated all batches at 18 degrees Celsius until the desired time point, then collected the embryos into a clean tube and snap-froze them in liquid nitrogen with as little seawater as possible. The samples were stored at -80 degrees Celsius until RNA extraction. We extracted total RNA from the samples using a Trizol protocol. After measuring the RNA concentration with NanoDrop, we created a bulk RNA mix by combining 1 µL from each sample into a new tube. We gave the sample to the Sequencing and Genotyping facility of the Max Planck Institute of Molecular Cell Biology and Genetics, who ran aliquots of this bulk mix through a Bioanalyzer and gel electrophoresis. They found no evidence of RNA degradation. From this sample, they prepared PacBio Iso-Seq libraries using the Express Template Prep Kit 2.0 and sequenced full-length transcripts on a SMRT 8M Cell for 30 hours using a PacBio Sequel II System. They processed the raw movie subreads with SMRT Analysis software, following the Iso-Seq v3 workflow to generate representative circular consensus sequences, demultiplex and remove primers, trim poly(A) tails, and remove concatemers. After transcript clustering and merging, the resulting dataset contained 176,122 polished high-quality isoforms. Using Cogent, we removed redundant isoforms and obtained a dataset with 117,524 transcripts. From this, we generated a dataset containing only the longest isoform for each gene, with 70,003 sequences in total. We calculated descriptive metrics using Transrate. To estimate their completeness, we used BUSCO for metazoa and obtained a score of 85%. Finally, we annotated the longest-isoform dataset using EnTAP. About 85% of the transcripts have a coding sequence. We obtained annotations for 67% of the sequences, while 33% have remained unannotated. <h2>Datasets</h2> <table> <tbody> <tr> <td>file name</td> <td>file size (zipped)</td> <td>sequences</td> <td>description</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/0-Pdum_workflow.zip?download=1">0-Pdum_workflow.zip</a> (folder)</td> <td>3.40 GB</td> <td>-</td> <td>entire pipeline with notebook entries and analyses</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/1-Pdum_hq_isoforms.zip?download=1">1-Pdum_hq_isoforms.zip</a> (fasta)</td> <td>180.30 MB</td> <td>176,122</td> <td>polished high-quality isoforms from CCS</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/2-Pdum_co_isoforms.zip?download=1">2-Pdum_co_isoforms.zip</a> (fasta)</td> <td>70.68 MB</td> <td>117,524</td> <td>non-redundant polished high-quality isoforms</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/3-Pdum_co_longest.zip?download=1">3-Pdum_co_longest.zip</a> (fasta)</td> <td>54.85 MB</td> <td>70,003</td> <td>longest of non-redundant polished high-quality isoforms</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/4-Pdum_co_longest_annotations.zip?download=1">4-Pdum_co_longest_annotations.zip</a> (tsv)</td> <td>34.37 MB</td> <td>70,003 (46,635 annotated)</td> <td>annotations for longest-isoform dataset</td> </tr> </tbody> </table>

The initial stages of Ag fluorination: a scanning tunneling microscopy investigation

Low Temperature scanning tunneling microscopy images of Ag(100) and Ag(110) crystals exposed at room temperature for different amounts of time to a fluorine-rich atmosphere. The temperature used for acquiring the STM images is written within the title of the file.  The calibration factors for the STM images are 1.12 in X and Y, 0.867 in Z.  These STM data are the raw images of the results shown in the paper published in ArXiv with the doi number 10.48550/arXiv.2410.04858.

opencc-by-4.0Oct 2021View details →

DeepBacs – Escherichia coli growth stage object detection dataset and YOLOv2 model

Training and test images of E. coli cells for object detection and classification using YOLOv2, as well as a trained YOLOv2 model. Additional information can be found on this <a href="https://github.com/HenriquesLab/DeepBacs/wiki">github wiki</a>. The example shows a bright field image of live E. coli cells and the respective annotation for specific growth stages.   Training and test dataset Data type: Paired microscopy images (bright field) and annotations in PASCAL VOC format Microscopy data type: 2D bright field images recorded at 1 min interval Microscope: Nikon Eclipse Ti-E equipped with an Apo TIRF 1.49NA 100x oil immersion objective Cell type: E. coli MG1655 wild type strain (CGSC #6300). File format: .png (8-bit) Image size: 256 x 256 px² (158 nm / pixel), 100/15 individual frames (training/test dataset) 1024 x 1024 px² (79 nm / pixel), 9 regions of interest with 80 frames @ 1 min time interval (live-cell time series) Image preprocessing: Raw images were recorded in 16-bit mode (image size 512x512 px² @ 158 nm/px). 256 x 256 px² patches were extracted from individual frames and converted into 8-bit .png images after adjusting brightness and contrast. Annotation was performed online using LabelImg (https://github.com/tzutalin/labelImg).   YOLOv2 model The YOLOv2 model was generated using the ZeroCostDL4Mic platform (Chamier et al., 2021). It was trained from scratch for 97 epochs on 100 manually annotated images (image dimensions: (256, 256)) with a batch size of 8 and a custom loss function combining MSE and crossentropy losses, using the YOLOv2 ZeroCostDL4Mic notebook (v 1.12.1). Key python packages used include tensorflow (v 0.1.12), Keras (v 2.3.1), numpy (v 1.19.5), cuda (v 11.0.221). The training was accelerated using a Tesla T4 GPU and data were augmented by a factor of 4 using flipping and rotation. The model weights can be used with the ZeroCostDL4Mic YOLOv2 notebook.   Author(s): Christoph Spahn1,2, Mike Heilemann1,3 Contact email: christoph.spahn@mpi-marburg.mpg.de   Affiliation(s):  1) Institute of Physical and Theoretical Chemistry, Max-von-Laue Str. 7, Goethe-University Frankfurt, 60439 Frankfurt, Germany 2) ORCID: 0000-0001-9886-2263  3) ORCID: 0000-0002-9821-3578

opencc-by-4.0Jan 2006View details →

Fig. 33 in Nesting Biologies and Immature Stages of the Tapinotaspidine Bee Genera Monoeca and Lanthanomelissa and of Their Osirine Cleptoparasites Protosiris and Parepeolus (Hymenoptera: Apidae: Apinae)

Fig. 33. Cocoon of Lanthanomelissa betinae from which larva had been removed, lateral view. Fig. 34. Cocoon of Parepeolus minutus from which larva had bee removed, lateral view. Fig. 35. Inner surface of front end of cocoon of Lanthanomelissa betinae showing complete covering by pale feces. Fig. 36. Inner surface of front end of cocoon of Parepeolus minutus showing central area that is not coated by feces.

opencc-by-4.0Jan 2006View details →

Fig. 1 in Nesting Biologies and Immature Stages of the Tapinotaspidine Bee Genera Monoeca and Lanthanomelissa and of Their Osirine Cleptoparasites Protosiris and Parepeolus (Hymenoptera: Apidae: Apinae)

Fig. 1. Nesting site of Monoeca haemorrhoidalis, showing dense ground cover in foreground. Fig. 2. Closeup of two nest entrances of same. Fig. 3. Main burrow of Monoeca haemorrhoidalis showing repetitive tamping impressions on shiny burrow wall. Fig. 4. Monoeca haemorrhoidalis, spiral inner surface of cell closure. Figs. 5, 6. Closure ends of cells of Monoeca haemorrhoidalis, showing plugged entrance holes made by females of Protosiris gigas; holes are filled by them as they depart.

opencc-by-4.0Nov 2021View details →

Model weights for a Weather4cast 2021 Challenge IEEE Big Data Cup Stage solution

This repository contains the pre-trained model weights for the TensorFlow/Keras models used in the <a href="https://www.iarai.ac.at/weather4cast/2021-competition/challenge/">Weather4cast 2021 Challenge IEEE Big Data Cup Stage</a> by the team "antfugue". The model code can be found in <a href="https://github.com/jleinonen/weather4cast-bigdata">https://github.com/jleinonen/weather4cast-bigdata</a> along with instructions on where to extract the weights.

Figs 25–28. Culicoides insignis Lutz, 1913 in Study of the immature stages of two species of the biting midge genus Culicoides (Diptera: Ceratopogonidae)

Figs 25–28. Culicoides insignis Lutz, 1913, male pupa: 25 – cephalothoracic sensilla; 26 – dorsal setae; 27 – first abdominal segment chaetotaxy; 28 – fourth abdominal segment chaetotaxy. Scale bars: 0.05 mm. Abbreviations: AL-1-T, AL-2-T, AL-3-T – anterolateral sensilla; AM-1-T – anteromedial sensillum; DL-1-H, DL-2-H, DL-3-H – dorsolateral cephalic sclerite sensilla; D-1-T, D-2-T, D-3-T, D-4-T, D-5-T – dorsal setae; SA-2-T – supraalar; D-2-I, D-3-I, D-4-I, D-7-I, D-8-I, D-9-I – dorsal sensilla of first abdominal segment; L-1-I, L-2-I, L-3-I – lateral sensilla of first abdominal segment; D-2-IV, D-3-IV, D-4-IV, D-5-IV, D-7-IV, D-8-IV, D-9-IV – dorsal sensilla of fourth abdominal segment; L-1-IV, L-2-IV, L-3-IV, L-4-IV – lateral sensilla of fourth abdominal segment; V-5-IV, V-6-IV, V-7-IV – ventral sensilla of fourth abdominal segment.

Figs 13–16. Culicoides bambusicola Lutz, 1913 in Study of the immature stages of two species of the biting midge genus Culicoides (Diptera: Ceratopogonidae)

Figs 13–16. Culicoides bambusicola Lutz, 1913, male pupa: 13 – cephalothoracic sensilla and respiratory organ; 14 – dorsal setae; 15 – first abdominal segment chaetotaxy; 16 – fourth abdominal segment chaetotaxy. Scale bars: 0.05 mm. Abbreviations: AL-1-T, AL-2-T, AL-3-T – anterolateral sensilla; AM-1-T – anteromedial sensillum; DL-1-H, DL-2-H – dorsolateral cephalic sclerite sensilla; p – pores; RO – respiratory organ; D-1-T, D-2-T, D-3-T, D-4-T, D-5-T – dorsals; SA-2-T – supraalar; D-2-I, D-3-I, D-4-I, D-7-I, D-8-I, D-9-I – dorsal sensilla of first abdominal segment; L-1-I, L-2-I, L-3-I – lateral sensilla of first abdominal segment; D-2-IV, D-3-IV, D-4-IV, D-5-IV, D-7-IV, D-8-IV, D-9-IV – dorsal sensilla of fourth abdominal segment; L-1-IV, L-2-IV, L-3-IV, L-4-IV – lateral sensilla of fourth abdominal segment; V-5-IV, V-6-IV, V-7-IV – ventral sensilla of fourth abdominal segment.

Figs 9–12. Culicoides bambusicola Lutz, 1913. 9–10 in Study of the immature stages of two species of the biting midge genus Culicoides (Diptera: Ceratopogonidae)

Figs 9–12. Culicoides bambusicola Lutz, 1913. 9–10 – male pupa; 11–12 – female pupa; 9, 11 – dorsal apotome; 10, 12 – ninth segment, ventral view. Scale bars: 0.05 mm. Abbreviations: DA-1-H, DA-2-H – dorsal apotomal sensilla; GL – genital lobe; TP – terminal process; D-5-IX, D-6-IX – campaniform sensilla of terminal process.

Figs 1–4. Culicoides bambusicola Lutz, 1913 in Study of the immature stages of two species of the biting midge genus Culicoides (Diptera: Ceratopogonidae)

Figs 1–4. Culicoides bambusicola Lutz, 1913, larva: 1 – head capsule, ventral view; 2 – head capsule, anteroventral view; 3 – mouthparts (messors and scopae); 4 – head capsule, detail of lateral view of mouthparts (mandible and maxilla) (from RONDEROS & SPINELLI 2000). Abbreviations: AN – antennae; CO – collar; HY – hypostoma; LC1 – lacinial sclerite 1; LB – labrum; MD – mandible; MX – maxilla; MP – maxillary palpus; MS – messors; SC – scopae; PL – palatum; ss – sensilla styloconica; st – sensilla trichoidea. Head capsule chaetotaxy: n – anterolateral pit; o – parahypostomal setae; s – anterior perifrontal setae; v – posterolateral setae; w – anterolateral setae; y – ventral setae.

opencc-zeroFeb 2022View details →

dryad40/100

Imprints of latitude, host taxon and decay stage on fungus-associated arthropod communities

Interactions among fungi and insects involve hundreds of thousands of species. While insect communities on plants have formed some of the classic model systems in ecology, fungus-based communities and the forces structuring them remain poorly studied by comparison. We characterize the arthropod communities associated with fruiting bodies of eight mycorrhizal basidiomycete fungus species from three different orders along a 1200-km latitudinal gradient in northern Europe. We hypothesized that—matching the pattern seen for most insect taxa on plants—we would observe a general decrease of fungal-associated species with latitude. Against this backdrop, we expected local communities to be structured by host identity and phylogeny, with more closely related fungal species sharing more similar communities of associated organisms. As a more unique dimension added by the ephemeral nature of fungal fruiting bodies, we expected further imprints generated by successional change, with younger fruiting bodies harboring communities different from older ones. Using DNA metabarcoding to identify arthropod communities from fungal fruiting bodies, we find that latitude leaves a clear imprint on fungus-associated arthropod community composition, with host phylogeny and decay stage of fruiting bodies leaving lesser but still-detectable effects. The main latitudinal imprint is on a high arthropod species turnover, with no detectable pattern in overall species richness. Overall, these findings paint a new picture of the drivers of fungus-associated arthropod communities, suggesting that latitude will not affect how many arthropod species inhabits a fruiting body, but rather what species occur in it and at what relative abundances (as measured by sequence read counts). These patterns upset simplistic predictions regarding latitudinal gradients in species richness and in the strength of biotic interactions.

opencc-by-4.0Oct 2019View details →

FIGURE 12 in Nest Architecture, Immature Stages, and Ethnoentomology of a New Species of Trigonisca from Northern Colombia (Hymenoptera: Apidae)

FIGURE 12. SEM micrographs of mature larva of Trigonisca (Trigonisca) mepecheu Engel and Gonzalez, new species. A. Entire larva, oblique frontal view. B. Close-up of pro- and mesothoracic segments showing paired segmental dorsolateral tubercles (arrows) and distribution of fine spicules. C. Close-up of meso- and metathoracic segments and of first abdominal segment showing dorsolateral tubercles along left side as well as distribution of fine spicules. D. Head, frontal view, demonstrating extreme width, and showing pronounced, dome-shaped antennae. E. Same, oblique lateral view. F. Close-up of labrum and mandibles, frontal view, showing cluster of multipronged spicules at lower edge of labrum as well as sharp-pointed mandibles. G. Close-up of left side of cluster of multipronged spicules along lower edge of labrum and sharply toothed upper edge of left mandible, possibly used as comb to push provisions through prongs toward esophagus.

opencc-by-4.0Dec 2021View details →

Fig. 1. N in Obtaining Oviparous Grass Snake, Natrix Natrix (Serpentes, Colubridae), Embryos At Early Developmental Stages By Caesarean Section

Fig. 1. N. natrix embryos at developmental stages A. 20. B. 22. C. 24. D. 25. E. 26. F. 27: av —auditory vesicle; cl —crystalline

opencc-by-4.0Jul 2019View details →

Fig. 9 in Intraspecific Morphological Variation In Free- Living Stages Of Strongyloides Papillosus (Nematoda, Strongyloididae) Parasitizing Various Mammal Species

Fig. 9. Morphometric parameters of free-living females of S. papillosus: а — body length; b — body width; c — length of esophagus; d — length of intestine; e — length of tail; f — distance to vulva; g — number of eggs; on the ordinate axis — length in µm, on the abscissa axis — species of host (Ch — Capra hircus, Oc — Oryctolagus cuniculus, Cp — Cavia porcellus).

opencc-by-4.0Jul 2019View details →

Fig. 8 in Intraspecific Morphological Variation In Free- Living Stages Of Strongyloides Papillosus (Nematoda, Strongyloididae) Parasitizing Various Mammal Species

Fig. 8. Morphometric parameters of S. papillosus males: a — body length; b – body width; c — length of esophagus; d — length of intestine; e — length of the tail; f — length of spicules; on the ordinate axis — length in µm, on the abscissa axis — species of host (Ch — Capra hircus, Oc — Oryctolagus cuniculus, Cp — Cavia porcellus).