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Distinguishing between canonical and non-canonical tRNA genes reveals that Thermococcaceae adhere to the standard archaeal tRNA gene set
<p><strong>Abstract</strong></p> <p>Automated genome annotation is an essential tool for extracting biological information from sequence data. The identification and annotation of tRNA genes is frequently performed by the software package tRNAscan-SE, the output of which is listed – for selected genomes – in the Genomic tRNA database (GtRNAdb). Given the central role of tRNA in molecular biology, the accuracy and proper application of tRNAscan-SE is important for both interpretation of the output, and continued improvement of the software. Here, we report a manual annotation of the predicted tRNA gene sets for 20 complete genomes from the archaeal taxon Thermococcaceae. According to GtRNAdb, these 20 genomes contain a number of putative deviations from the standard set of canonical tRNA genes in Archaea. However, manual annotation reveals that only one represents a true divergence; the other instances are either (i) non-canonical tRNA genes resulting from the integration of horizontally transferred genetic elements, or CRISPR-Cas activity, or (ii) attributable to errors in the input DNA sequence. To distinguish between canonical and non-canonical archaeal tRNA genes, we recommend using a combination of automated pseudogene detection by tRNAscan-SE and the tRNAscan-SE isotype score, greatly reducing manual annotation efforts and leading to improved predictions of tRNA gene sets in Archaea.</p> <p> </p> <p><strong>Repository contents</strong></p> <p><strong>01_workflow_tRNAscanSE_predictions_210archaea.html </strong>contains the workflow and graphical output for tRNA gene set predictions in 20 Thermococcaceae genomes and 210 archaeal genomes. Files 03 to 06 below are the files quoted in this workflow.</p> <p><strong>02_workflow_tRNAscanSE_predictions_210archaea.Rmd </strong>contains the markdown file associated with 01_workflow_tRNAscanSE_predictions_210archaea.html above.</p> <p><strong>03_thermo_trnas_GtRNAdb.txt</strong><strong> </strong>contains the predicted tRNA gene sets of 20 Thermococcaceae genomes as listed on GtRNAdb (Data Release 19 (June 2021)).</p> <p><strong>04_Archaea_genome_list.txt </strong>contains the details of all 217 archaeal genomes listed on GtRNAdb (Data Release 19 (June 2021)). The seven genomes for which the NCBI genome sequences were no longer available are indicated by #### preceding the name.</p> <p><strong>05_thermo_tRNAs_genome.txt</strong><strong> </strong>contains the predicted tRNA gene sets of 20 Thermococcaceae genomes as predicted by locally run tRNAscan-SE (version 2.0.6), with standard settings for Archaea (option -A). To display the output, options -H and --detail were added. We note that pseudogene detection is active under these conditions.</p> <p><strong>06_Archaea_210_GtRNAdb_tRNAs.txt </strong>contains the predicted tRNA gene sets of the 210 archaeal genomes as listed on GtRNAdb (Data Release 19 (June 2021)).</p> <p><strong>07_Archaea_210genomes_tRNAs.txt</strong> contains the predicted tRNA gene sets of the 210 archaeal genomes as predicted by locally run tRNAscan-SE (version 2.0.6), with standard settings for Archaea (option -A). To display the output, options -H and --detail were added. We note that pseudogene detection is active under these conditions.</p> <p><strong>08_NCBI_genomes.zip</strong> contains the NCBI GenBank genome sequence files used in this study. These include the 20 Thermococcaceae genomes, the wider 210 archaeal genomes, and several others of interest. </p> <p><strong>09_phylogeny.tar.zip</strong> contains the data used to draw a phylogenetic tree for the 20 Thermococcaceae organisms. The folder includes a file listing the details of all data in the folder (Readme.md), a workflow file (workflow_UndinMarkers_v2.md), and data folders.</p> <p> </p> <p><strong>Notes</strong></p> <p>The extended TIGRFAM database referred to in the phylogenetic tree construction process can be found at <a href="https://zenodo.org/record/3839790#.YjByaVzMI3g">https://zenodo.org/record/3839790#.YjByaVzMI3g</a></p> <p>The perl script used during phylogenetic tree construction, catfasta2phyml.pl, is available in the GitHub repository <a href="https://github.com/nylander/catfasta2phyml">https://github.com/nylander/catfasta2phyml</a></p> <p>tRNAscan-SE is a freely available resource available online (<a href="http://lowelab.ucsc.edu/tRNAscan-SE/">http://lowelab.ucsc.edu/tRNAscan-SE/</a>)</p> <p>GtRNAdb is a publicly accessible resource available online (<a href="http://gtrnadb.ucsc.edu/">http://gtrnadb.ucsc.edu/</a>)</p> <p>NCBI is a publicly accessible resource available online (<a href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</a>)</p> <p>rrnDB is a publicly accessible resource available online (<a href="https://rrndb.umms.med.umich.edu/">https://rrndb.umms.med.umich.edu/</a>)</p> <p>BLAST is a publicly accessible resource available online (<a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi">https://blast.ncbi.nlm.nih.gov/Blast.cgi</a>)</p>
Young people's media use and adherence to preventive measures in the "infodemic": Is it masked by political ideology?
<p>Data to replicate the publication "Young people's media use and adherence to preventive measures in the “infodemic”: Is it masked by political ideology?". This publication examines the role of political ideology and political extremism for COVID-19 information seeking and preventive behaviour with data of the COVIDisc project. COVIDisc investigates how young people aged 15 to 34 years perceive the discussion in the Coronavirus Pandemic, which messages reach them, what media they use to inform themselves and how they experience the situation. en</p>
Extended data of the project "A survey exploring biomedical editors' perceptions of editorial interventions to improve adherence to reporting guidelines"
<p>Figure S1: Survey questionnaire</p> <p>Table S2: Barriers, facilitators and possible improvements of the interventions included in the survey</p>
Influence of conspiracy theories and distrust of community health volunteers on adherence to COVID-19 guidelines and vaccine uptake in Kenya
<p>This cross-sectional study collected data between 25 May –27 June 2021 n=447. It involved all registered community health volunteers (CHVs) who had participated in the COVID-19 vaccine hesitancy study. This data was collected as part of an Epidemic Ethics/WHO initiative that FCDO/Wellcome Grant 214711/Z/18/Z has supported. WHO’s specific grant number was 2020/1077878-0). The funders had no role in study design, data collection and analysis, decision to publish, or manuscript preparation. No authors received a salary from the funders.</p>
Text-fig. 10. Carpolithes (a–j). a–d: Carpolithes sp. 10. USNM PAL 772375. Scale bar = 5 mm, reflected light, palladium coated. a: Lateral view of one face of structure; note adherent mineral material. Longitudinal groove is to right. b: Lateral view of one edge of the structure. c: Opposite view from (b), note groove in upper half of the specimen, facing viewer. d: Apical view. e–j: Carpolithes sp. 11. USNM PAL 772376. Scale bar = 5 mm, micro-CT scan surface views. e: Structure in face view showing central protuberance. f: Same, lateral view. g: Opposite face from (e). h: Opposite face from (f). i: View from one end. j: View from opposite end from (i). in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 10. Carpolithes (a–j). a–d: Carpolithes sp. 10. USNM PAL 772375. Scale bar = 5 mm, reflected light, palladium coated. a: Lateral view of one face of structure; note adherent mineral material. Longitudinal groove is to right. b: Lateral view of one edge of the structure. c: Opposite view from (b), note groove in upper half of the specimen, facing viewer. d: Apical view. e–j: Carpolithes sp. 11. USNM PAL 772376. Scale bar = 5 mm, micro-CT scan surface views. e: Structure in face view showing central protuberance. f: Same, lateral view. g: Opposite face from (e). h: Opposite face from (f). i: View from one end. j: View from opposite end from (i).
Figure 1 in Effect of Mauritia flexuosa L. leaf extract on Staphylococcus aureus and Staphylococcus haemolyticus biofilms adhered to stainless steel surface
Figure 1. Gas chromatographic profile of extracts from Mauritia flexuosa L. leaves. (A) Ethanolic extract and (B) Aqueous extract. The peaks numbers correspond to the phenolic compounds and carbohydrates listed in Table 1.
Underlying data of the project "A survey exploring biomedical editors' perceptions of editorial interventions to improve adherence to reporting guidelines"
<p><em><strong>Survey dataset.xlsx</strong></em> contains the anonymised responses to the survey.</p>
ASSESSMENT OF ADHERENCE TO NEW ORAL ANTICOAGULANTS IN ATRIAL FIBRILLATION PATIENTS WITHIN THE OUTPATIENT REGISTRY PROFILE. PROSPECTIVE OBSERVATIONAL STUDY (ANTEY study)
<p><strong>Rationale</strong></p> <p>Prevention of stroke and thromboembolic complications in non-valvular atrial fibrillation is one of the most common indications for the use of all NOACs and warfarin in cardiology. The issue of regular intake of all OACs, i.e. the issue of adherence to anticoagulation therapy, is paramount for better treatment. The problem of assessment of different aspects of adherence to OACs in patients with atrial fibrillation within an outpatient registry is of current interest.</p> <p><strong>Primary</strong> <strong>Study</strong> <strong>Objectives</strong></p> <p>The aim of the present study is to assess adherence to therapy and factors associated with adherence in patients with CV disease complicated by non-valvular atrial fibrillation requiring OAC treatment within the outpatient registry PROFILE (prospective, observational study).</p> <ol> <li>Data collection in patients with non-valvular atrial fibrillation requiring OAC treatment included in the registry</li> <li>Evaluation of actual patient adherence to OACs</li> </ol> <p><strong>Secondary Study Objective(s)</strong></p> <ol> <li>Evaluation of potential patient adherence to OACs</li> <li>Determination of most significant factors associated with adherence to OACs in patients with non-valvular AF</li> <li>Validation of new original questionnaire</li> <li>Evaluation of doctor’s adherence to OAC prescription according to Guidelines (ESC). Management of atrial fibrillation,2016)</li> </ol> <p><strong>Material and methods</strong></p> <p>.The study included 201 patients with nonvalvular AF from the outpatient "PROFILE" registry, 118 (58,7%) males. The mean age was 71,1 ±8,7 years. The study protocol consisted of the inclusion visit (V0), 6-month follow-up visit (V1), and phone contact 1 year after V0 (follow-up, FU). In V0, all patients were prescribed one of the NOACs. At V1 doctors could recommend warfarin or another NOAC to patients, who have refused to take prescribed NOAC. Medical adherence was determined using the original questionnaire</p> <p><strong>Inclusion Criteria (detailed)</strong></p> <ul> <li>Men and women above 18 years of age who were included in the "PROFILE" registry by the start of the observational study</li> <li>Presence of written informed consent to participate in the study, fill in the study questionnaires, and have personal data analyzed</li> <li>Presence of any form of non-valvular atrial fibrillation with CHA<sub>2</sub>DS<sub>2</sub>-VASc score of ≥1 or patients with CHA<sub>2</sub>DS<sub>2</sub>-VASc score = 0, who are already taking OAK</li> </ul> <p><strong>Exclusion Criteria</strong></p> <p>Patients with high bleeding risk, including patients with:</p> <ul> <li>Congenital or acquired bleeding disorders</li> <li>Uncontrolled resistant hypertension</li> <li>Exacerbation of gastric and duodenal ulcer</li> <li>Vascular retinopathy</li> <li>Recent history of intracranial or intracerebral hemorrhage</li> <li>Pathology of the brain and spinal cord vessels</li> <li>Recent history of the brain, spinal cord, or eye surgery</li> <li>History of bronchiectasis or pulmonary hemorrhage</li> <li>A CHA<sub>2</sub>DS<sub>2</sub>-VASc score of 0 (OACs are not indicated)</li> <li>Pregnancy, lactation</li> <li>Planned surgery</li> <li>Known hypersensitivity to ingredients of medications used in the study</li> </ul> <p><strong>Visit schedule</strong></p> <p>Visit schedule</p> <p>Two visits at 6-month intervals are scheduled for each patient as part of routine clinical practice:</p> <p>Visit 0– visit at study entry:</p> <ul> <li>receiving written informed consent to participate in research from patients</li> <li>inclusion in the program</li> <li>assessment of inclusion and exclusion criteria</li> <li>verification of non-valvular atrial fibrillation diagnosis (according to medical documentation, confirming the history of atrial fibrillation: ECG, Holter monitoring, etc..)</li> <li>collecting information on received medication therapy, including OACs</li> <li>physical examination of patients (measurements of blood pressure, heart rate, height, weight, waist circumference)</li> <li>questioning of patients to determine potential and actual adherence to OACs</li> <li>computation of points on the scale CHA<sub>2</sub>DS<sub>2</sub>-VASc and HAS-BLED to determine the indications for the appointment of the OACs and the identification of an increased risk of bleeding</li> <li>to determine the INR in patients who agreed to replace the use of warfarin with one of the NOACs</li> <li>prescription of OACs according to routine clinical practice and official labels for these medications</li> <li>instructing patients (according to the specifically designed scheme) to regularly take prescribed medications, be aware of precautionary measures when taking OACs, telling them about the pros and cons of treatment with OACs</li> </ul> <p>Visit 1 – visit at 6 months after the Visit 0:</p> <ul> <li>collecting information on patients’ compliance with doctor’s recommendations</li> <li>collecting information on patients’ actual medication therapy</li> <li>collecting information on the safety of treatment with OACs (in case the patient has been taking them), recording all adverse events that occurred during the study period</li> <li>measurements of blood pressure, heart rate as a part of routine clinical practice</li> <li>questioning of patients to determine potential and actual adherence to OACs</li> </ul> <p>FU - follow-up calls to patients (one year)</p> <p>Phone contact to determine patient’s life status, possible (fatal and non-fatal complications of non-valvular atrial fibrillation) and fill (after receiving patient’s consent) the original questionnaire.</p> <p><strong>Primary Outcome</strong></p> <p>The proportion of complete, partial adherent and non-adherent patients according to the original questionnaire</p> <p><strong>Secondary Outcomes </strong></p> <ul> <li>The proportion of potentially adherent patients (according to the original questionnaire)</li> <li>Identification of baseline characteristics associated with adherence</li> <li>The proportion of doctors prescribed OAC according to guidelines.</li> </ul> <p><strong>Safety Outcomes </strong></p> <p>Adverse events and outcomes were recorded from the start of treatment with the OAC until the end of the observational study period. The doctor evaluated the severity of adverse events and outcomes if necessary took measures for their medical treatment according to current clinical practice.</p> <p> </p> <p> </p>
Text-fig. 40. Scanning electron microscope (SEM) images of monocolpate pollen of Eckhartiopsis parva gen. et sp. nov. from an anther; Torres Vedras locality, Portugal. a) Holotype; elongated anther that yielded the pollen in this Text-figure; b–e) Pollen grains showing dense reticulate tectum supported by short columellae that are only loosely attached to the smooth surface of the foot layer: note dentate orbicules on inner surface of anther wall (b, arrowhead); f) Reticulate tectum showing smooth muri with small adhering orbicules (arrowhead); g) Pollen grains showing one in which the reticulum has been lost exposing the smooth surface of the foot layer; h) Fractured pollen wall showing reticulum, short columellae and thick foot layer; note granules on the inner surface of the apertural region (arrow). Specimen, TV39-S170217 (holotype). Scale bars 300 Μm (a), 6 Μm (b–e, g), 3 Μm (f, h). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 40. Scanning electron microscope (SEM) images of monocolpate pollen of Eckhartiopsis parva gen. et sp. nov. from an anther; Torres Vedras locality, Portugal. a) Holotype; elongated anther that yielded the pollen in this Text-figure; b–e) Pollen grains showing dense reticulate tectum supported by short columellae that are only loosely attached to the smooth surface of the foot layer: note dentate orbicules on inner surface of anther wall (b, arrowhead); f) Reticulate tectum showing smooth muri with small adhering orbicules (arrowhead); g) Pollen grains showing one in which the reticulum has been lost exposing the smooth surface of the foot layer; h) Fractured pollen wall showing reticulum, short columellae and thick foot layer; note granules on the inner surface of the apertural region (arrow). Specimen, TV39-S170217 (holotype). Scale bars 300 Μm (a), 6 Μm (b–e, g), 3 Μm (f, h).
Text-fig. 24. Scanning electron microscope (SEM) images (a, c, d) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images (b, e) of fruits and seeds of Serialis antiqua (a, b) and Serialis parva (c–e); Torres Vedras locality, Portugal. a, b) Serialis antiqua lateral view of fruit showing smooth partly abraded fruit wall (a) and longitudinal section (b, SRXTM orthoslice yz0862) showing six closely adhering seeds, some of which are mature with well-preserved nutritive tissue; c–e) Serialis parva lateral view of fruit showing faint ribs (c), finely pitted seed surface with undulate anticlinal walls of the exotestal cells (d), and transverse section showing two closely adhering seeds (SRXTM orthoslice xy0913, e). Specimens, TV43-S174480 (a, b), TV43-S170076 (c), TV43-S170079 (d), TV43-S174477 (e). Scale bars 300 Μm (a–c, e), 50 Μm (d). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 24. Scanning electron microscope (SEM) images (a, c, d) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images (b, e) of fruits and seeds of Serialis antiqua (a, b) and Serialis parva (c–e); Torres Vedras locality, Portugal. a, b) Serialis antiqua lateral view of fruit showing smooth partly abraded fruit wall (a) and longitudinal section (b, SRXTM orthoslice yz0862) showing six closely adhering seeds, some of which are mature with well-preserved nutritive tissue; c–e) Serialis parva lateral view of fruit showing faint ribs (c), finely pitted seed surface with undulate anticlinal walls of the exotestal cells (d), and transverse section showing two closely adhering seeds (SRXTM orthoslice xy0913, e). Specimens, TV43-S174480 (a, b), TV43-S170076 (c), TV43-S170079 (d), TV43-S174477 (e). Scale bars 300 Μm (a–c, e), 50 Μm (d).
Text-fig. 5. Scanning electron microscope (SEM) images of megaspores with possible affinities to Isoetales (a–d) and megaspores of uncertain affinity (e–i); Torres Vedras locality, Portugal. a) Paxillitriletes reticulatus megaspore in lateral view showing long appendages on the flanges of the laesurae and the reticulate-spiny distal surface; b) Dijkstraisporites sp. megaspore in oblique lateral view showing long, sometimes dichotomizing, appendages on the equatorial flanges and bordering the laesurae; c, d) Tenellisporites sp. megaspore in proximal view (c) showing equatorial flanges and laesurae with short, broad, flattened and unbranched appendages; note numerous, spiny microspores adhering to the proximal face of the megaspore (d); e) Megaspore type sp. 2 in lateral view showing apical gula and ornamentation of scattered spines; f, g) Megaspore type sp. 3 in lateral (f) and proximal (g) view showing broad, often dichotomously branched appendages covering the megaspore surface; h, i) aff. Flabellisporites sp. megaspores in proximal (h) and lateral (i) view showing long, narrow appendages covering the megaspore surface. Specimens, TV39-S174619 (a), TV38-S170220 (b), TV38-S170221 (c, d), TV44-S174574 (e), TV44-S174575 (f), TV44-S174577 (g), TV38-S170223 (h), TV38-S170222 (i). Scale bars 100 Μm (a–c, e–i), 25 Μm (d). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 5. Scanning electron microscope (SEM) images of megaspores with possible affinities to Isoetales (a–d) and megaspores of uncertain affinity (e–i); Torres Vedras locality, Portugal. a) Paxillitriletes reticulatus megaspore in lateral view showing long appendages on the flanges of the laesurae and the reticulate-spiny distal surface; b) Dijkstraisporites sp. megaspore in oblique lateral view showing long, sometimes dichotomizing, appendages on the equatorial flanges and bordering the laesurae; c, d) Tenellisporites sp. megaspore in proximal view (c) showing equatorial flanges and laesurae with short, broad, flattened and unbranched appendages; note numerous, spiny microspores adhering to the proximal face of the megaspore (d); e) Megaspore type sp. 2 in lateral view showing apical gula and ornamentation of scattered spines; f, g) Megaspore type sp. 3 in lateral (f) and proximal (g) view showing broad, often dichotomously branched appendages covering the megaspore surface; h, i) aff. Flabellisporites sp. megaspores in proximal (h) and lateral (i) view showing long, narrow appendages covering the megaspore surface. Specimens, TV39-S174619 (a), TV38-S170220 (b), TV38-S170221 (c, d), TV44-S174574 (e), TV44-S174575 (f), TV44-S174577 (g), TV38-S170223 (h), TV38-S170222 (i). Scale bars 100 Μm (a–c, e–i), 25 Μm (d).
Text-fig. 13. Scanning electron microscope (SEM) images of pollen or spore clump with pollen grains or spores of unknown affinity that occur separately or adhering together in dyads, triads and tetrads; Torres Vedras locality, Portugal. a) Clump of pollen or spores that yielded the pollen or spores in this Text-figure; b–f) Grains adhering together in twos, threes or fours (b–e) or occurring singly and apparently with a proximal trilete mark (f); note that the adhering grains are connected by a smooth bandlike covering, perhaps remains of the microspore mother cell; note also abundant orbicules of various sizes among and over the grains. Specimen, TV44-S148149. Scale bars 300 Μm (a), 30 Μm (b–f). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 13. Scanning electron microscope (SEM) images of pollen or spore clump with pollen grains or spores of unknown affinity that occur separately or adhering together in dyads, triads and tetrads; Torres Vedras locality, Portugal. a) Clump of pollen or spores that yielded the pollen or spores in this Text-figure; b–f) Grains adhering together in twos, threes or fours (b–e) or occurring singly and apparently with a proximal trilete mark (f); note that the adhering grains are connected by a smooth bandlike covering, perhaps remains of the microspore mother cell; note also abundant orbicules of various sizes among and over the grains. Specimen, TV44-S148149. Scale bars 300 Μm (a), 30 Μm (b–f).
Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f).
Text-fig. 44. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c, d) images of "Hexacarpellate flower". a) Lateral view of flower showing epigynous organization with remains of tepals inserted at top of the hypanthium; b) Detail of apical part of flower showing laminar structures (arrows) that may be stamen bases, adhering to, or fused with, the tepals; c) Longitudinal section (orthoslice yz0540) of flower through the median plane showing the epigynous organization and central axis with ovules (arrows); d) Transverse section (orthoslice xy1250) through the ovary of the flower showing the hexagonal outline, the six locules and ovules (arrows) borne near the center of the gynoecium. Specimen, Catefica 153-S174313 (a–d). Scale bars = 300 Μm (a, c), 100 Μm (b, d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 44. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c, d) images of "Hexacarpellate flower". a) Lateral view of flower showing epigynous organization with remains of tepals inserted at top of the hypanthium; b) Detail of apical part of flower showing laminar structures (arrows) that may be stamen bases, adhering to, or fused with, the tepals; c) Longitudinal section (orthoslice yz0540) of flower through the median plane showing the epigynous organization and central axis with ovules (arrows); d) Transverse section (orthoslice xy1250) through the ovary of the flower showing the hexagonal outline, the six locules and ovules (arrows) borne near the center of the gynoecium. Specimen, Catefica 153-S174313 (a–d). Scale bars = 300 Μm (a, c), 100 Μm (b, d).
Text-fig. 32. Scanning electron microscope (SEM) images of "Stamen with monocolpate, reticulate pollen"; Catefica locality, Portugal. a) Stamen with four pollen sacs and an adhering bract (arrow); b) Pollen grains from stamen showing the large gaping, almost circular, aperture with a distinct aperture margin; c) Detail of pollen wall showing finely verrucate supratectal ornamentation and bases of broken columellae; d) Pollen grain showing the large gaping, rounded aperture; e) Pollen grains showing large, rounded aperture (left) and abraded reticulum exposing the surface of the foot layer and long columellae (right). Specimen, Catefica 49-S170144 (a–e). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (d, e), 1.5 Μm (c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 32. Scanning electron microscope (SEM) images of "Stamen with monocolpate, reticulate pollen"; Catefica locality, Portugal. a) Stamen with four pollen sacs and an adhering bract (arrow); b) Pollen grains from stamen showing the large gaping, almost circular, aperture with a distinct aperture margin; c) Detail of pollen wall showing finely verrucate supratectal ornamentation and bases of broken columellae; d) Pollen grain showing the large gaping, rounded aperture; e) Pollen grains showing large, rounded aperture (left) and abraded reticulum exposing the surface of the foot layer and long columellae (right). Specimen, Catefica 49-S170144 (a–e). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (d, e), 1.5 Μm (c).
Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d).
Text-fig. 30. Scanning electron microscope (SEM) images of anther and pollen of Kempia longicolpites; Catefica locality, Portugal. a) Transverse section through an anther showing the four pollen sacs with in situ pollen; b) Pollen in situ from anther in (a) showing very long colpus and loosely attached reticulum; c) Detail of reticulum showing smooth muri supported by short, scattered columellae; d) Pollen grain from anther in (a) enlarged showing colpus extended beyond the equator and loosely attached reticulum; e) Detail of pollen wall showing thick, homogeneous foot layer, columellae and reticulate tectum; note remains of granular endexine (arrows) in the apertural region of the grain; f) Internal view of reticulum showing the short columellae adhering to the muri detached from the foot layer. Specimen, Catefica 49-S101208 (a–f). Scale bars = 100 Μm (a), 20 Μm (b), 6 Μm (d), 3 Μm (c, e, f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 30. Scanning electron microscope (SEM) images of anther and pollen of Kempia longicolpites; Catefica locality, Portugal. a) Transverse section through an anther showing the four pollen sacs with in situ pollen; b) Pollen in situ from anther in (a) showing very long colpus and loosely attached reticulum; c) Detail of reticulum showing smooth muri supported by short, scattered columellae; d) Pollen grain from anther in (a) enlarged showing colpus extended beyond the equator and loosely attached reticulum; e) Detail of pollen wall showing thick, homogeneous foot layer, columellae and reticulate tectum; note remains of granular endexine (arrows) in the apertural region of the grain; f) Internal view of reticulum showing the short columellae adhering to the muri detached from the foot layer. Specimen, Catefica 49-S101208 (a–f). Scale bars = 100 Μm (a), 20 Μm (b), 6 Μm (d), 3 Μm (c, e, f).
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. 28. Scanning electron microscope (SEM) images of stamens and pollen of Endressistemon cateficensis gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminal structure with two lateral stamens and one median structure seen in ventral and dorsal view (orientation unknown) showing that each stamen has a prominent apical extension and two pairs of pollen sacs separated by a narrow connective; both stamens are borne on a common base together with the median structure and their anthers are sessile on the common stalk; note the apical projection of the median structure (asterisk) between the two stamens and the ribs over probable vascular bundles that extend from the common base into the apical projections of both stamens and the median structure (arrows); c) Staminal structure showing two stamens with prominent apical projections and median axis-like structure between the two stamens (arrow); d) Staminal structure showing two stamens with prominent apical projections borne on a common base; e) Staminal structure in (a) and (b), from the same orientation as (b), showing the ribs over probable vascular bundles (yellow) that extend into the apical projections; f) Detail of staminal structure in (a) and (b) showing the fused or strongly adhering apical projections of the two lateral stamens and the median structure (asterisk); g) Monocolpate, reticulate pollen grains from the pollen sacs of stamen in (d). Specimens, Catefica 49-S107778 (holotype, a, b, e, f), Catefica 49-S107769 (c), Catefica 49-S107751 (d, g). Scale bars = 600 Μm (a–d), 300 Μm (e), 100 Μm (f), 6 Μm (g). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 28. Scanning electron microscope (SEM) images of stamens and pollen of Endressistemon cateficensis gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminal structure with two lateral stamens and one median structure seen in ventral and dorsal view (orientation unknown) showing that each stamen has a prominent apical extension and two pairs of pollen sacs separated by a narrow connective; both stamens are borne on a common base together with the median structure and their anthers are sessile on the common stalk; note the apical projection of the median structure (asterisk) between the two stamens and the ribs over probable vascular bundles that extend from the common base into the apical projections of both stamens and the median structure (arrows); c) Staminal structure showing two stamens with prominent apical projections and median axis-like structure between the two stamens (arrow); d) Staminal structure showing two stamens with prominent apical projections borne on a common base; e) Staminal structure in (a) and (b), from the same orientation as (b), showing the ribs over probable vascular bundles (yellow) that extend into the apical projections; f) Detail of staminal structure in (a) and (b) showing the fused or strongly adhering apical projections of the two lateral stamens and the median structure (asterisk); g) Monocolpate, reticulate pollen grains from the pollen sacs of stamen in (d). Specimens, Catefica 49-S107778 (holotype, a, b, e, f), Catefica 49-S107769 (c), Catefica 49-S107751 (d, g). Scale bars = 600 Μm (a–d), 300 Μm (e), 100 Μm (f), 6 Μm (g).
Gilman-Adhered FilmClip Emotion Dataset (GAFED): Tailored Clips for Emotional Elicitation
<p><strong>Gilman-Adhered FilmClip Emotion Dataset (GAFED): Tailored Clips for Emotional Elicitation</strong></p> <p><strong>Description</strong>:</p> <p>Introducing the Gilman-Adhered FilmClip Emotion Dataset (GAFED) - a cutting-edge compilation of video clips curated explicitly based on the guidelines set by Gilman et al. (2017). This dataset is meticulously structured, leveraging both the realms of film and psychological research. The objective is clear: to induce specific emotional responses with utmost precision and reproducibility. Perfectly tuned for researchers, therapists, and educators, GAFED facilitates an in-depth exploration into the human emotional spectrum using the medium of film.</p> <p><strong>Dataset Highlights</strong>:</p> <ul> <li><strong>Gilman's Guidelines</strong>: GAFED's foundation is built upon the rigorous criteria and insights provided by Gilman et al., ensuring methodological accuracy and relevance in emotional elicitation.</li> <li><strong>Film Titles</strong>: Each selected film's title provides an immersive backdrop to the emotions sought to be evoked.</li> <li><strong>Emotion Label</strong>: A focused emotional response is designated for each clip, reinforcing the consistency in elicitation.</li> <li><strong>Clip Duration</strong>: Standardized duration of every clip ensures a uniform exposure, leading to consistent response measurements.</li> <li><strong>Curated with Precision</strong>: Every film clip in GAFED has been reviewed and handpicked, echoing Gilman et al.'s principles, thereby cementing their efficacy in triggering the intended emotion.</li> </ul> <p><strong>Emotion-Eliciting Video Clips within Dataset</strong>:</p> Film Targeted Emotion Duration (seconds) The Lover Baseline 43 American History X Anger 106 Cry Freedom Sadness 166 Alive Happiness 310 Scream Fear 395 <p>The crowning feature of GAFED is its identification of "key moments". These crucial timestamps serve as a bridge between cinema and emotion, guiding researchers to intervals teeming with emotional potency.</p> <p><strong>Key Emotional Moments within Dataset</strong>:</p> Film Targeted Emotion Key moment timestamps (seconds) American History X Anger 36, 57, 68 Cry Freedom Sadness 112, 132, 154 Alive Happiness 227, 270, 289 Scream Fear 23, 42, 79, 226, 279, 299, 334 <p><strong>Based on</strong>: Gilman, T. L., et al. (2017). A film set for the elicitation of emotion in research. Behavior Research Methods, 49(6).</p> <p>GAFED isn't merely a dataset; it's an amalgamation of cinema and psychology, encapsulating the vastness of human emotion. Tailored to perfection and adhering to Gilman et al.'s insights, it stands as a beacon for researchers exploring the depths of human emotion through film.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.