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Supplementary material 8 from: Frem M, Fucilli V, Nigro F, El Moujabber M, Abou Kubaa R, La Notte P, Bozzo F, Choueiri E (2021) The potential direct economic impact and private management costs of an invasive alien species: Xylella fastidiosa on Lebanese wine grapes. NeoBiota 70: 43-67. https://doi.org/10.3897/neobiota.70.72280
Table S8
Supplementary material 2 from: Frem M, Fucilli V, Nigro F, El Moujabber M, Abou Kubaa R, La Notte P, Bozzo F, Choueiri E (2021) The potential direct economic impact and private management costs of an invasive alien species: Xylella fastidiosa on Lebanese wine grapes. NeoBiota 70: 43-67. https://doi.org/10.3897/neobiota.70.72280
Table S2
Supplementary material 3 from: Frem M, Fucilli V, Nigro F, El Moujabber M, Abou Kubaa R, La Notte P, Bozzo F, Choueiri E (2021) The potential direct economic impact and private management costs of an invasive alien species: Xylella fastidiosa on Lebanese wine grapes. NeoBiota 70: 43-67. https://doi.org/10.3897/neobiota.70.72280
Table S3
Supplementary material 1 from: Frem M, Fucilli V, Nigro F, El Moujabber M, Abou Kubaa R, La Notte P, Bozzo F, Choueiri E (2021) The potential direct economic impact and private management costs of an invasive alien species: Xylella fastidiosa on Lebanese wine grapes. NeoBiota 70: 43-67. https://doi.org/10.3897/neobiota.70.72280
Table S1
Supplementary material 9 from: Frem M, Fucilli V, Nigro F, El Moujabber M, Abou Kubaa R, La Notte P, Bozzo F, Choueiri E (2021) The potential direct economic impact and private management costs of an invasive alien species: Xylella fastidiosa on Lebanese wine grapes. NeoBiota 70: 43-67. https://doi.org/10.3897/neobiota.70.72280
Field survey questionnaire
Suction feeding by predators limits direct release of alarm cues in fishes
<p>Chemical alarm cues alert aquatic prey to the presence of an actively foraging predator. There is a large literature based upon responses to alarm cues derived from skin extract, because it is anticipated that prey skin is damaged when prey are attacked by a predator. However, many predators feed by suction feeding whereby prey are quickly drawn into the buccal cavity and swallowed whole with little, if any, direct contact between the teeth of the predator and the prey. Here, we test if predation by suction feeding releases chemical information in sufficient quantity to elicit an antipredator response in conspecific prey. In tests of individual zebrafish <i>Danio rerio</i>, we found that odor of crushed zebrafish produced a clear antipredator behavioral response, but water collected immediately adjacent to staged predation events between a largemouth bass <i>Micropterus salmoides</i> (122-145 mm TL) and adult zebrafish (39 mm TL) did not elicit alarm behavior, and did not differ from behavioral responses to blank water or bass odor (on a diet of earthworms). In a second experiment, zebrafish swallowed by largemouth bass, then retrieved seconds later through gastric lavage, produced zebrafish that were alive and completely intact with minimal epidermal damage. Published relationships between bass length, gape size and the geometry of suction feeding suggest that in a hypothetical population of largemouth bass feeding on adult zebrafish, or fathead minnows, the majority of predation events by piscivorous fish probably would not release detectable levels of prey alarm cue. Accounting for the role of feeding mechanics by fish predators requires a recalibration of the literature on risk assessment by small prey fishes. Chemically-mediated antipredator behaviors against suction-feeding predators may occur primarily via post-ingestion dietary cues, or disturbance cues released near the moment of attack.</p>
Supplemental material from: Can transcranial direct current stimulation enhance post-stroke motor recovery? Development of a theoretical patient-tailored model
<p>New treatments that can facilitate neural repair and reduce persistent impairments have significant value in promoting recovery following stroke. One technique that has gained interest is transcranial direct current stimulation (tDCS) as early research suggested it could enhance plasticity and enable greater behavioral recovery. However, several studies have now identified substantial inter-subject variability in response to tDCS and clinical trials revealed insufficient evidence of treatment effectiveness. A possible explanation for the varied and negative findings is that the physiological model of stroke recovery that researchers have used to guide the application of tDCS based treatments in stroke is overly simplistic and does not account for stroke heterogeneity or known determinants that affect the tDCS response. <a name="_Hlk62139152">Here, we propose that tDCS could have a more clearly beneficial role in enhancing stroke recovery</a> if greater consideration is given to individualizing treatment. By critically reviewing the proposed mechanisms of tDCS, stroke physiology across the recovery continuum, and known determinants of tDCS response, we propose a new, theoretical, patient-tailored approach to delivering tDCS after stroke. The proposed model includes a step-by-step principled selection strategy for identifying optimal neuromodulation targets and outlines key areas for further investigation. Tailoring tDCS treatment to individual neuroanatomy and physiology is likely our best chance at producing robust and meaningful clinical benefit for people with stroke and would, therefore, accelerate opportunities for clinical translation.</p>
Influence of Prior Visual Information on Exploratory Movement Direction in Texture Perception
<p>Raw data of all individual participants</p>
Directional ballistic transport in the two-dimensional metal PdCoO2
<p>In an idealized infinite crystal, the material properties are constrained by the symmetries of its unit cell. However, the point-group symmetry is broken by the sample shape of any finite crystal, but this is commonly unobservable in macroscopic metals. To sense the shape-induced symmetry lowering in such metals, long-lived bulk states originating from an anisotropic Fermi surface are needed. Here we show how a strongly facetted Fermi surface and the long quasiparticle mean free path present in microstructures of PdCoO<sub>2</sub> yield an in-plane resistivity anisotropy that is forbidden by symmetry on an infinite hexagonal lattice. We fabricate bar-shaped transport devices narrower than the mean free path from single crystals using focused ion beam milling, such that the ballistic charge carriers at low temperatures frequently collide with both of the side walls that define the channel. Two symmetry-forbidden transport signatures appear: the in-plane resistivity anisotropy exceeds a factor of 2, and a transverse voltage appears in zero magnetic field. Using ballistic Monte Carlo simulations and a numerical solution of the Boltzmann equation, we robustly identify the orientation of the narrow channel as the source of symmetry breaking.</p>
RNA modification detection using direct RNA sequencing and nanoDoc2_2
<p>RNA modification detection using direct RNA sequencing and nanoDoc2_2</p>
targets for Scan-Centric, Frequency-Based Method for Characterizing Peaks from Direct Injection Fourier transform Mass Spectrometry Experiments
<p>_targets folder for the scan-centric, frequency-based peak-characterization manuscript</p>
Direct access to millions of mutations by Whole Genome Sequencing of an oilseed rape mutant population
<p>Induced mutations are an essential source of genetic variation in plant breeding. EMS mutagenesis has been frequently applied, and mutants have been detected by phenotypic or genotypic screening of large populations. In this study, a rapeseed M<sub>2</sub> population was derived from M<sub>1</sub> parent cultivar “Express” treated with EMS. Whole genomes were sequenced from fourfold (4x) pools of 1,988 M<sub>2</sub> plants representing 497 M<sub>2</sub> families. Detected mutations were not evenly distributed and displayed distinct patterns across the 19 chromosomes with lower mutation rates towards the ends. Mutation frequencies ranged from 32/Mb to 48/Mb. On average, 284,442 single nucleotide polymorphisms per M<sub>2</sub> DNA pool were found resulting from EMS mutagenesis. 55% were C→T and G→A transitions, characteristic for EMS induced (‘canonical’) mutations, whereas the remaining SNPs were ‘non-canonical’ transitions (15%) or transversions (30%). Additionally, we detected 88,725 high confidence insertions and deletions (InDels) per pool. On average, each M<sub>2</sub> plant carried 39,120 canonical mutations, corresponding to a frequency of one mutation per 23.6 kb. Roughly 82% of such mutations were located either 5 kb upstream or downstream (~56%) of gene coding regions or within intergenic regions (26%). The remaining 18% were located within regions coding for genes. All mutations detected by whole-genome sequencing could be verified by comparison with known mutations. Furthermore, all sequences are accessible via the online tool “EMS Brassica” (<a href="http://www.emsbrassica.plantbreeding.uni-kiel.de/">http://www.emsbrassica.plantbreeding.uni-kiel.de/</a>), which enables direct identification of mutations in any target sequence. The sequence resource described here will further add value for functional gene studies in rapeseed breeding.</p>
IFNγ-primed periodontal ligament cells regulate T cell responses via IFNγ-inducible mediators and ICAM-1-mediated direct cell contact
<p><span><span><span><span><span><span><span><span><span><span><span>Periodontal ligament (PDL) cells help maintain tissue homeostasis by balancing tissue inflammation and regeneration. However, the mechanisms by which interferon γ (IFNγ) modulates this process are not yet fully understood.The present study aimed to examine the effect of primed and unprimed PDL cells with IFNγ on the viability and differentiation of T lymphocytes and its functional consequences. The results showed that IFNγ-primed PDL cells possessed enhanced immunosuppression by suppressing T lymphocyte viability and directing T lymphocyte differentiation towards a higher Th2/Th1 ratio. Suppression of T cell viability was mainly mediated by IFNγ-inducible secreted mediators, which was prevented in the presence of direct cell contact, likely by intercellular adhesion molecule-1 (ICAM-1)-induced PI3K-mediated TGFβ1 expression in PDL cells. In contrast, ICAM-1 activation augmented IFNγ-induced IFNγ and IL-6 expression in PDL cells, which in turn modulated T cell differentiation. The resulting interaction between these two cell types activated macrophage and suppressed osteoclast differentiation. In conclusion, the results have shown, for the first time, that primed and unprimed PDL cells with IFNγ differentially control T cell responses via IFNγ-inducible mediators and ICAM-1-mediated direct cell contact, suggesting the role of PDL cells in shifting an inflammatory phase towards a regenerative phase.</span></span></span></span></span></span></span></span></span></span></span></p>
Modeled Influence of a Structure Directing Agent on Al Siting Energetics: N,N,N-trimethyl-1-adamantyl ammonium (TMAda+) in Chabazite
<p>Supporting information (zip file) described in the manuscript.</p>
Supplementary material 1 from: Prigot-Maurice C, Depeux C, Paulhac H, Braquart-Varnier C, Beltran-Bech S (2022) Immune priming in Armadillidium vulgare against Salmonella enterica: direct or indirect costs on life history traits? In: De Smedt P, Taiti S, Sfenthourakis S, Campos-Filho IS (Eds) Facets of terrestrial isopod biology. ZooKeys 1101: 131-158. https://doi.org/10.3897/zookeys.1101.77216
Tables S1–S4, Figures S1–S3
Supplementary material 1 from: Premate E, Fišer Ž, Kuralt Ž, Pekolj A, Trajbarič T, Milavc E, Hanc Ž, Kostanjšek R (2022) Behavioral observations of the olm (Proteus anguinus) in a karst spring via direct observations and camera trapping. Subterranean Biology 44: 69-83. https://doi.org/10.3897/subtbiol.44.87295
Figure S1
Text-fig. 5. Anacardiaceae (a–m), Burseraceae (n–q). Scale bars = 1 cm. a–f: Pentoperculum sp. a–c: USNM PAL 772360. a: Lateral view of endocarp, apex up; three germination valves visible, the central clearly displaying the bipartite nature of the valve, reflected light, palladium coated. b: Apical view displaying six locules, with two preserved germination valves at the lower left, reflected light, palladium coated. c: Basal view of the endocarp, the locules suggested by swellings; note point of attachment, micro-CT scan surface rendering. d–f: Pentoperculum sp. USNM PAL 772359, reflected light, palladium coated. d: Lateral view of a probable 6-loculed endocarp, apex up; a single intact germination valve in the center, displaying the central lineation that divides it in two. e: Apical view; two bi-partite germination valves are visible, indicated by arrows to the middle cleavage line of two of the valves. f: Basal view, the locules suggested by the undulations in the margin. g–i: Indet. Spondioideae. USNM PAL 772358, reflected light, palladium coated. g: Lateral view of multi-locular endocarp, apex up. h: Apical view showing finely punctuate surface and peripheral locule cavities. i: Basal view. j–m: Cf. Pleiogynium USNM PAL 772357. j: Lateral view of the multi-locular endocarp, apex up; note intact germination valve on left and exposed locule facing the viewer, micro-CT scan surface rendering. k: Lateral view, rotated about 30° from (j), showing three exposed locules, reflected light, palladium coated; note bipartite locule lining at center. l: Apical view of the multilocular endocarp; the locule with intact germination valve at the upper right, reflected light, palladium coated. Arrows to each locule. m: Basal view showing central point of attachment and prominent radiating ridges aligned with the locules, micro-CT scan surface rendering. n–q: Canarium, USNM PAL 772361. Scale bar = 1 cm. n: Lateral view of endocarp directly facing one germination valve flanked by two strong ridges; apex up; specimen coated in sodium nitrate and photographed by R. A. Scott. o: Lateral view facing one of the three pronounced ridges, flanked to the left and right by two germination valves; apex up. p: Apical view displaying the three strong ridges, arching over the apex and flanking three deep embayments, covered with germination valves. q: Basal view, the three ridges being less pronounced. o–q: Reflected light, palladium coated. in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 5. Anacardiaceae (a–m), Burseraceae (n–q). Scale bars = 1 cm. a–f: Pentoperculum sp. a–c: USNM PAL 772360. a: Lateral view of endocarp, apex up; three germination valves visible, the central clearly displaying the bipartite nature of the valve, reflected light, palladium coated. b: Apical view displaying six locules, with two preserved germination valves at the lower left, reflected light, palladium coated. c: Basal view of the endocarp, the locules suggested by swellings; note point of attachment, micro-CT scan surface rendering. d–f: Pentoperculum sp. USNM PAL 772359, reflected light, palladium coated. d: Lateral view of a probable 6-loculed endocarp, apex up; a single intact germination valve in the center, displaying the central lineation that divides it in two. e: Apical view; two bi-partite germination valves are visible, indicated by arrows to the middle cleavage line of two of the valves. f: Basal view, the locules suggested by the undulations in the margin. g–i: Indet. Spondioideae. USNM PAL 772358, reflected light, palladium coated. g: Lateral view of multi-locular endocarp, apex up. h: Apical view showing finely punctuate surface and peripheral locule cavities. i: Basal view. j–m: Cf. Pleiogynium USNM PAL 772357. j: Lateral view of the multi-locular endocarp, apex up; note intact germination valve on left and exposed locule facing the viewer, micro-CT scan surface rendering. k: Lateral view, rotated about 30° from (j), showing three exposed locules, reflected light, palladium coated; note bipartite locule lining at center. l: Apical view of the multilocular endocarp; the locule with intact germination valve at the upper right, reflected light, palladium coated. Arrows to each locule. m: Basal view showing central point of attachment and prominent radiating ridges aligned with the locules, micro-CT scan surface rendering. n–q: Canarium, USNM PAL 772361. Scale bar = 1 cm. n: Lateral view of endocarp directly facing one germination valve flanked by two strong ridges; apex up; specimen coated in sodium nitrate and photographed by R. A. Scott. o: Lateral view facing one of the three pronounced ridges, flanked to the left and right by two germination valves; apex up. p: Apical view displaying the three strong ridges, arching over the apex and flanking three deep embayments, covered with germination valves. q: Basal view, the three ridges being less pronounced. o–q: Reflected light, palladium coated.
Supplementary material 1 from: Senderov V, Georgiev T, Penev L (2016) Online direct import of specimen records into manuscripts and automatic creation of data papers from biological databases . Research Ideas and Outcomes 2: e10617. https://doi.org/10.3897/rio.2.e10617
A template for an occurrence or specimen record to be imported as a material citation.
Figure 1a from: Ioanas H, Saab B, Rudin M (2017) Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software. Research Ideas and Outcomes 3: e12095. https://doi.org/10.3897/rio.3.e12095
Figure 1a - Minimal (excluding all optional features) dependency graph of the contributed neuroscience package set.
Figure 1b from: Ioanas H, Saab B, Rudin M (2017) Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software. Research Ideas and Outcomes 3: e12095. https://doi.org/10.3897/rio.3.e12095
Figure 1b - Maximal (including all optional features) dependency graph of the contributed neuroscience package set.
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.