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Text-fig. 29. Scanning electron microscope (SEM) images of stamens and pollen grains of cf. Endressistemon sp. 1 (a, b), cf. Endressistemon sp. 2 (c, d) and cf. Endressistemon sp. 3 (e–g); Catefica locality, Portugal. a) Two adhering stamens, each with a long, pointed extension of the connective; b) Monocolpate, reticulate pollen in situ in stamen from stamen pair in (a); c) Fragment of stamen with prominent apical extension of the connective; d) Reticulate, apparently monocolpate, pollen in situ in stamen fragment in (c); e) Stamen with basifixed anther, perhaps sessile, and with prominent, wing-like apical extensions of the connective; note the dehisced thecae with the anther wall curved back; f, g) Monocolpate, reticulate pollen in situ in stamen in (e). Specimens, Catefica 49-S107780 (a, b), Catefica 49-S107784 (c, d), Catefica 49-S107781 (e–g). Scale bars = 600 Μm (a, c, e), 6 Μm (b, d, f, g). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 29. Scanning electron microscope (SEM) images of stamens and pollen grains of cf. Endressistemon sp. 1 (a, b), cf. Endressistemon sp. 2 (c, d) and cf. Endressistemon sp. 3 (e–g); Catefica locality, Portugal. a) Two adhering stamens, each with a long, pointed extension of the connective; b) Monocolpate, reticulate pollen in situ in stamen from stamen pair in (a); c) Fragment of stamen with prominent apical extension of the connective; d) Reticulate, apparently monocolpate, pollen in situ in stamen fragment in (c); e) Stamen with basifixed anther, perhaps sessile, and with prominent, wing-like apical extensions of the connective; note the dehisced thecae with the anther wall curved back; f, g) Monocolpate, reticulate pollen in situ in stamen in (e). Specimens, Catefica 49-S107780 (a, b), Catefica 49-S107784 (c, d), Catefica 49-S107781 (e–g). Scale bars = 600 Μm (a, c, e), 6 Μm (b, d, f, g).

Text-fig. 8. Scanning electron microscope (SEM) images of staminate inflorescences and pollen of Proencistemon portugallicus gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminate inflorescences composed of numerous tetrasporangiate stamens; each stamen lacks a filament and there is no clear indication of other floral organs; note apparently paired arrangement of stamens in (b) (asterisks); c) Pollen in situ in anther from specimen in (a) showing poorly defined trichotomocolpate aperture and semitectate-reticulate tectum; d) Detail of pollen from specimen in (a) showing narrow muri with beaded surface ornamentation; e) Distal and proximal views of pollen in situ in an anther fragment; f) Orbicules attached to surface of in situ pollen from anther fragment. Specimens, Catefica M282-P0341 (holotype, a, c, d), Catefica 150-S174257 (b), Catefica 50-S170393 (e, f). Scale bars = 600 Μm (a, b), 6 Μm (c, e), 1.5 Μm (d, f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 8. Scanning electron microscope (SEM) images of staminate inflorescences and pollen of Proencistemon portugallicus gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminate inflorescences composed of numerous tetrasporangiate stamens; each stamen lacks a filament and there is no clear indication of other floral organs; note apparently paired arrangement of stamens in (b) (asterisks); c) Pollen in situ in anther from specimen in (a) showing poorly defined trichotomocolpate aperture and semitectate-reticulate tectum; d) Detail of pollen from specimen in (a) showing narrow muri with beaded surface ornamentation; e) Distal and proximal views of pollen in situ in an anther fragment; f) Orbicules attached to surface of in situ pollen from anther fragment. Specimens, Catefica M282-P0341 (holotype, a, c, d), Catefica 150-S174257 (b), Catefica 50-S170393 (e, f). Scale bars = 600 Μm (a, b), 6 Μm (c, e), 1.5 Μm (d, f).

Text-fig. 9. Scanning electron microscope (SEM) images of stamens and pollen of Proencistemon portugallicus gen. et sp. nov. (a–g) and Proencistemon sp. (h–j); Catefica locality, Portugal. a) Fragment of stamen whorl from staminate inflorescence showing almost sessile anthers; note short bracts at the base of the stamen whorl (arrow) and apparent paired arrangement of the stamens; b) Fragment of stamen whorl showing almost sessile anthers and apparent paired arrangement of the stamens; c) Pollen in situ from stamen whorl in (b) showing poorly defined trichotomocolpate aperture and semitectate-reticulate tectum; d–g) Distal views of pollen in situ from pollen clump showing poorly defined trichotomocolpate aperture, semitectate-reticulate tectum (d–f), and fractured pollen wall with long, scattered columellae supporting narrow muri (g); h) Fragment of staminate inflorescence with narrow, almost sessile, stamens; i, j) Pollen from fragment of staminate inflorescence in (h) showing poorly defined trichotomocolpate aperture (i), semitectate-reticulate tectum (i, j) and long, scattered columellae supporting narrow muri (j). Specimens, Catefica 49-S266015 (a), Catefica 342-S122086 (b, c), Catefica 50-S170394 (d–g), Catefica 49-S107783 (h–j). Scale bars = 600 Μm (a, b, h), 6 Μm (c–f, i), 1.5 Μm (g, j). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 9. Scanning electron microscope (SEM) images of stamens and pollen of Proencistemon portugallicus gen. et sp. nov. (a–g) and Proencistemon sp. (h–j); Catefica locality, Portugal. a) Fragment of stamen whorl from staminate inflorescence showing almost sessile anthers; note short bracts at the base of the stamen whorl (arrow) and apparent paired arrangement of the stamens; b) Fragment of stamen whorl showing almost sessile anthers and apparent paired arrangement of the stamens; c) Pollen in situ from stamen whorl in (b) showing poorly defined trichotomocolpate aperture and semitectate-reticulate tectum; d–g) Distal views of pollen in situ from pollen clump showing poorly defined trichotomocolpate aperture, semitectate-reticulate tectum (d–f), and fractured pollen wall with long, scattered columellae supporting narrow muri (g); h) Fragment of staminate inflorescence with narrow, almost sessile, stamens; i, j) Pollen from fragment of staminate inflorescence in (h) showing poorly defined trichotomocolpate aperture (i), semitectate-reticulate tectum (i, j) and long, scattered columellae supporting narrow muri (j). Specimens, Catefica 49-S266015 (a), Catefica 342-S122086 (b, c), Catefica 50-S170394 (d–g), Catefica 49-S107783 (h–j). Scale bars = 600 Μm (a, b, h), 6 Μm (c–f, i), 1.5 Μm (g, j).

Text-fig. 7. Ammonoids from the Mospyne Formation. a: Anthracoceratites sp., lateral view; specimen IGSU-4/3634. b, c: Cymoceras sp., lateral view (b), fragment of the suture line in a 42 mm diameter conch (c); specimen IGSU-4/573. d, e: Neodimorphoceratidae indet., lateral view (d), surface ornamentation on the flank (e); specimen IGSU-4/5350. Scale bars 10 mm. in Late Bashkirian Ammonoids From The Mospyne Formation Of The Donets Basin, Ukraine

Text-fig. 7. Ammonoids from the Mospyne Formation. a: Anthracoceratites sp., lateral view; specimen IGSU-4/3634. b, c: Cymoceras sp., lateral view (b), fragment of the suture line in a 42 mm diameter conch (c); specimen IGSU-4/573. d, e: Neodimorphoceratidae indet., lateral view (d), surface ornamentation on the flank (e); specimen IGSU-4/5350. Scale bars 10 mm.

Text-fig. 4. Taphonomic features of the studied localities of ammonoids. a: Sandstone slab with fragmentary remains of productid and spiriferid brachiopods, orthocerids, coiled nautiloids and ammonoids (stratigraphic level No. 3). b: Shell debris cluster and fragment of crushed ammonoid conch (stratigraphic level No. 1). c: Epibionts on the surface of an ammonoid conch (stratigraphic level No. 5). d: Cluster of bivalves, gastropods and cephalopods remains in a siderite nodule (stratigraphic level No. 5). e: Fragment of an ammonoid conch (stratigraphic level No. 3). f: Fragment of an ammonoid conch (?) with terminal aperture and brachiopod valve (stratigraphic level No. 3). g: Specimen of?Anthracoceratites sp. with conch injuries (shown by arrows) (stratigraphic level No. 8). h, i: Bioerosion trace fossils Cyclopuncta girtyi ELIAS, 1958 on the fragments of cephalopod conchs (stratigraphic level No. 5). j: Limonitized conchs of the ammonoid (stratigraphic level No. 7). k: Fragment of an ammonoid conch (stratigraphic level No. 5). Scale bars 10 mm. in Late Bashkirian Ammonoids From The Mospyne Formation Of The Donets Basin, Ukraine

Text-fig. 4. Taphonomic features of the studied localities of ammonoids. a: Sandstone slab with fragmentary remains of productid and spiriferid brachiopods, orthocerids, coiled nautiloids and ammonoids (stratigraphic level No. 3). b: Shell debris cluster and fragment of crushed ammonoid conch (stratigraphic level No. 1). c: Epibionts on the surface of an ammonoid conch (stratigraphic level No. 5). d: Cluster of bivalves, gastropods and cephalopods remains in a siderite nodule (stratigraphic level No. 5). e: Fragment of an ammonoid conch (stratigraphic level No. 3). f: Fragment of an ammonoid conch (?) with terminal aperture and brachiopod valve (stratigraphic level No. 3). g: Specimen of?Anthracoceratites sp. with conch injuries (shown by arrows) (stratigraphic level No. 8). h, i: Bioerosion trace fossils Cyclopuncta girtyi ELIAS, 1958 on the fragments of cephalopod conchs (stratigraphic level No. 5). j: Limonitized conchs of the ammonoid (stratigraphic level No. 7). k: Fragment of an ammonoid conch (stratigraphic level No. 5). Scale bars 10 mm.

Text-fig. 1. Zamites pateri J.KVAČEK sp. nov.; Pecínov locality, holotype, No. NM-F 5185. a: Holotype overview showing fragment of simply pinnate leaf, scale bar 20 mm. b: Abaxial cuticle showing costal and intercostal scale zones and stomata in ill-defined rows, LM micro-photograph, scale bar 100 µm. c: Pinnule detail showing venation pattern, scale bar 5 mm. d: Abaxial cuticle showing costal and intercostal zones, LM micro-photograph, scale bar 500 µm. e: Fragmentary preserved adaxial cuticle showing in New Species Of Zamites From The Cenomanian Of The Bohemian Cretaceous Basin

Text-fig. 1. Zamites pateri J.KVAČEK sp. nov.; Pecínov locality, holotype, No. NM-F 5185. a: Holotype overview showing fragment of simply pinnate leaf, scale bar 20 mm. b: Abaxial cuticle showing costal and intercostal scale zones and stomata in ill-defined rows, LM micro-photograph, scale bar 100 µm. c: Pinnule detail showing venation pattern, scale bar 5 mm. d: Abaxial cuticle showing costal and intercostal zones, LM micro-photograph, scale bar 500 µm. e: Fragmentary preserved adaxial cuticle showing

opencc-by-4.0Jan 2023View details →

New database of fragments of medieval codices of the 11th-12th centuries

The database currently has 117 codex fragments with the number of samples between 11 and 39, with an average of 17, which gives 2040 writing samples. The resolution of the width of the manuscripts varies between two thousand pixels and almost nine thousand pixels.

opencc-by-4.0Sep 2022View details →

A Database of Ultrastable MOFs Reassembled from Stable Fragments with Machine Learning Models

Dataset of MOFs constructed from building blocks of stable MOFs. Note: the columns labeled "rho" in features_and_properties are actually cell volume and not density.

opencc-by-4.0Mar 2023View details →

MALDI-TOF-MS spectra of archaeological bone fragments from Klipdrift Shelter (South Africa) for ZooMS

MALDI-TOF-MS spectra for archaeological bone fragments from Klipdrift Shelter (South Africa). All spectra are uploaded in .mzml format.

opencc-by-4.0May 2023View details →

RVFV data aligning only to M-Fragment to test the PARANOiD pipeline

PARANOiD is a versatile software for fully automated analysis of iCLIP and iCLIP2 data. It contains all steps necessary for preprocessing, the determination of cross-link locations and several additional steps, which can be used to detect specific characteristics, e.g. definite distances between cross-link events or identify binding motifs. The cross-link sites are presented as WIG files that can be easily visualized e.g. using IGV, for which a config file is offered. Additionally, results are offered as statistical plots for a quick overview and as standardized bioinformatics file formats or TSV files, which can be used for further analysis steps. The data provided are used as a test case for PARANOiD. The data was extracted from RVFV MP-12 virions (virion-reads-M-fragment-only.fastq) and BHK cells infected with RVFV (BHK-reads-M-fragment-only.fastq) applying the iCLIP2 method for RVFV N iCLIP. Three independent biological replicates were performed for each sample. Sequencing was performed using the MiSeq Sequencer (Illumina) with MiSeq Reagent Kit v2 Micro (Illumina) for N-iCLIP from virus particles and MiSeq Reagent Kit v3 (Illumina) for N-iCLIP from infected BHK cells. The original reads have been aligned to the RVFV MP-12 reference genome and only reads aligning to the M-fragments were extracted. The whole dataset will be publish at a later date File description: virion-reads-M-fragment-only.fastq - Reads obtained from RVFV virions BHK-reads-M-fragment-only.fastq - Reads obtained from BHK cells infected with RVFV reference_RVFV.fasta - RVFV MP-12 reference genome barcodes-RVFV.tsv - Barcodes for virion-reads-M-fragment-only.fastq barcodes-RVFV-merge-all.tsv - Barcodes for merging all samples of virion-reads-M-fragment-only.fastq barcodes-BHK.tsv - Barcodes for BHK-reads-M-fragment-only.fastq barcodes-BHK-merge-all.tsv - Barcodes for merging all relevant samples of BHK-reads-M-fragment-only.fastq

opencc-by-4.0Feb 2023View details →

Potential aboveground biomass increase in Brazilian Atlantic Forest fragments with climate change

This file collection contains the estimated spatial distribution of the above-ground biomass density (AGB) by the end of the 21st century across the Brazilian Atlantic Forest domain and the respective uncertanty. To develop the models, we used the maximum entropy method with projected climate data to 2100, based on the Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathway (RCP) 4.5 from the fifth Assessment Report (AR5). The dataset is composed of four files in GeoTIFF format: calibrated-AGB-distribution.tif: raster file representing the present spatial distribution of the above-ground biomass density in the Atlantic Forest from the calibrated model. Unit: Mg/ha  estimated-uncertanty-for-calibrated-agb-distribution.tif: raster file representing the estimated spatial uncertanty distribution of the calibrated above-ground biomass density. Unit: percentage. projected-AGB-distribution-under-rcp45.tif: raster file representing the projected spatial distribution of the above-ground biomass density in the Atlantic Forest by the end of 2100 under RCP 4.5 scenario. Unit: Mg/ha  estimated-uncertanty-for-projected-agb-distribution.tif: raster file representing the estimated spatial uncertanty distribution of the projected above-ground biomass density. Unit: percentage. Spatial resolution: 0.0083 degree (ca. 1 km) Coordinate reference system: Geographic Coordinate System - Datum WGS84

opencc-by-sa-4.0Mar 2023View details →

3D models of bead, pendant and softstone vessel fragments found during the 2021 excavations at Kalba (K4)

The 3D models of the three objects were created within the joint excavations project at Kalba (K4), United Arab Emirates, of the Sharjah Archaeology Authority (SAA), the Austrian Archaeological Institute (OeAI) of the Austrian Academy of Sciences (OeAW) and the Leibniz-Zentrum für Archäologie (LEIZA). For each object the following data are available: 3D model with colour values reflecting the curvature (MSII filter) in ply format, texture image for the 3D model in png format, metadata of the 3D acquisition and processing in ttl and json format. The 3D models were created with the Structure from Motion (SfM) technique using Agisoft Metashape software. The images were taken with a Nikon Z50 mirrorless camera and a 90 mm lens. The models obtained were post-processed using GigaMesh (https://gigamesh.eu) to calculate curvature with the MSII built-in filter and to create scaled 2D views. The export of the 3D metadata with information about the 3D model and the 3D acquisition and processing was done with pyhton scripts in agisoft metashape (https://doi.org/10.5281/zenodo.7468298).

opencc-by-4.0Jan 2023View details →

High-throughput crystallography for rapid early-stage fragment growth from crude arrays by low-cost robotics

Data to support the paper - High-throughput crystallography for rapid early-stage fragment growth from crude arrays by low-cost robotics. Data includes a summary of X-ray and LCMS results for the reactions executed on the OpenTrons, output reports and summaries from MSCheck (semi-automated LCMS analyzer tool) and the Python scripts used to execute single and multistep chemistry on the OpenTrons. Abstract We demonstrate that a simple workflow of array synthesis, combining low-cost robotics with analytic techniques to deconvolute crude reaction mixtures, is an effective way to collect structural data on a binding site.  Starting from the high information content of the crystallographic fragment screens on PHIP(2) (second bromodomain of the pleckstrin homology domain interacting protein), a collection of more than 1800 compounds was enumerated. Several thousand Crude Reaction Mixtures (CRMs) were synthesized on one robotic platform, an OpenTrons OT-1 liquid handler, using reaction sequences of up to 5 chemical steps. Analysis via MScheck, an algorithm-based system for finding a m/z in a CRM, significantly shortened product identification protocol times. 957 usable X-ray diffraction datasets were acquired, which resolved as 22 reaction products binding to the protein, 19 with conserved poses relative to the original fragment and 3 with a new, unexpected binding pose. The 22 crystallographic hit compounds were subsequently tested with peptide displacement alpha-screen assay and time-resolved grating-coupled interferometry-based biosensor assays, which confirmed one molecule with an IC50 = 34 μM and KD = 50 μM, from an inactive fragment.  The procedures described are entirely formulaic and engineerable and the method is eminently scalable. We anticipate that this cheap, low solvent-use approach will yield vast amounts of data, enabling rapid SAR landscape exploration around fragments, leading to faster fragment to lead times.

FIG. 7 in Multi-aged forest fragments in Atlantic France that are surrounded by meadows retain a richer epiphyte lichen flora

FIG. 7. — The beta diversity indicated significant lichen species replacement on larger trees in the interiors of the FFs surrounded by meadows (A). In contrast, lichen species replacement was significant on thinner trees from the exteriors of the FFs surrounded by meadows (B).

FIG. 6 in Multi-aged forest fragments in Atlantic France that are surrounded by meadows retain a richer epiphyte lichen flora

FIG. 6. — The gamma diversity indicated that the highest number of lichen species was recorded on larger trees in the interiors of the FFs surrounded by meadows (legend is as in Fig. 2).

FIG. 3 in Multi-aged forest fragments in Atlantic France that are surrounded by meadows retain a richer epiphyte lichen flora

FIG. 3. — The significant effect of host tree species (A) and shrub cover (B) on lichen species abundance according to a summary of the GLMMs. The GLMM results are presented for the interior forest at the tree level within FFs surrounded by meadows, taking into account the larger tree category (trees that range in circumference between 0.56 and 2.97).

FIG. 5 in Multi-aged forest fragments in Atlantic France that are surrounded by meadows retain a richer epiphyte lichen flora

FIG. 5. — The significant effect of tree circumference on the number of lichen species according to the summary of the GLMMs. The GLMM results are presented at the tree level within FFs surrounded by crops, taking into account the larger tree category (details as in Fig. 2).

FIG. 2 in Multi-aged forest fragments in Atlantic France that are surrounded by meadows retain a richer epiphyte lichen flora

FIG. 2. — The significant effects of: A, B, moss coverage; C, D, tree circumference; and E, F, host tree species on lichen abundance according to a summary of the GLMMs. The values of the estimator (E), standard error (SE), and Wald chi-squared test (chisq), the degrees of freedom (dfs) and significance (p) are presented. The GLMM results are presented for the larger tree category (trees that range in circumference between 0.56 and 2.97) at the tree and forest levels at the exteriors of the FFs surrounded by crops.

FIG. 1 in Multi-aged forest fragments in Atlantic France that are surrounded by meadows retain a richer epiphyte lichen flora

FIG. 1. — The location of the study area within the Poitou-Charentes region (western France). Source: Google Earth Pro V 7.3.2.5776. (14 December 2015). France. 45°21'34.14"N, 0°12'32.38"W, Eye alt 340.93 km. SIO, NOAA, U.S. Navy, NGA, GEBCO. US Dept of State Geographer. Landsat/Copernicus 2018. http://www. earth.google.com (13 February 2019).