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FIGURE 1 in Brachiopods from off the San Bernardo Archipelago (Colombian Caribbean), with comments on specific synonymies in Tichosina Cooper, 1977
FIGURE 1.Geographic location of the study area, sectors, and stations sampled during the MARCORAL cruise off the San Bernardo Archipelago, Caribbean of Colombia.
FIGURE 1 in Reinstatement of the independent specific status of Chrysanthemum neo-oreastrum (Asteraceae, Anthemideae)
FIGURE 1. Type specimens of Chrysanthemum neo-oreastrum (A, B) and C. hypargyreum (C, D). A. China, Sichuan, Songpan, E.H. Wilson 3858a (holotype: K). B. Same locality, E.H. Wilson 3858a (isotype: A). C. China, Shaanxi, Baoji, J. Giraldi 2903 (syntype: FI). D. China, Shaanxi, Meixian, J. Giraldi 2902 (syntype: FI).
FIGURE 3 in Reinstatement of the independent specific status of Chrysanthemum neo-oreastrum (Asteraceae, Anthemideae)
FIGURE 3. Chrysanthemum hypargyreum in the wild (Meixian, Shaanxi, China). A. Habitat and habit. B. Portion of stem. C. Leaves (adaxial surface; inset shows abaxial densely argenteous-sericeous leaf blade). D. Capitulum (top view). E. Capitulum (side view). F. Capitulum (back view). G. Phyllaries (abaxial surface). H. Ray florets. I. Tubular florets. All photographs by L. Wang.
FIGURE 2 in Reinstatement of the independent specific status of Chrysanthemum neo-oreastrum (Asteraceae, Anthemideae)
FIGURE 2. Chrysanthemum neo-oreastrum in the wild (Songpan, Sichuan, China). A. Habitat and habit. B. Portion of stem. C. Leaves (adaxial surface; inset shows abaxial slightly araneose leaf blade). D. Capitulum (top view). E. Capitulum (side view). F. Capitulum (back view). G. Phyllaries (abaxial surface). H. Ray florets. I. Tubular florets. All photographs by L. Wang.
Processed Data for Cell type-specific aging clocks to quantify aging and rejuvenation in regenerative regions of the brain
<p>Seurat objects for data accompanying the publication "Cell type-specific aging clocks to quantify aging and rejuvenation in regenerative regions of the brain".</p> <p>Preprint available at <a href="https://doi.org/10.1101/2022.01.10.475747">https://doi.org/10.1101/2022.01.10.475747</a></p> <ul> <li>multi_intergrated_seurat_Dec2020.rds is the data from the SVZ of the cohort of 28 mice across different ages</li> <li>pb_combined.rds is the data from the SVZ of both heterochronic parabiosis mouse cohorts</li> <li>Dulken_svz_celltypes_2019-01-31.rda is the data associated with <a href="https://doi.org/10.1038/s41586-019-1362-5">https://doi.org/10.1038/s41586-019-1362-5</a></li> </ul> <p> </p>
C.Origami: Cell type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening
<p>This data repository includes dataset generated from IMR-90, GM12878 cell lines and C.Origami pre-trained model weights.</p> <p>GitHub page: https://github.com/tanjimin/C.Origami</p>
Species of Acantholichen occurring only in the Neotropics show a high degree of endemism (Dal Forno et al. 2016). Of the seven species now recognized in this genus (Table 2), 71.4% (5) are known only from South America. As with Dictyonema, Acantholichen seem to be specific to substrate type and appears in the Andean small forest occurring on mosses in tree bark inhabiting mostly exposed habitats. Cyphellostereum is also represented by a high number of species restricted to the Neotropics [6 (66.6%)], while one is known only from North America, one from Southeastern United States and Puerto Rico, and another species is known only from Borneo and Fiji (Table 2). It is probably due to their unusual appearance that these lichens are getting confused with free-living cyanobacteria colonies, and that there are still undescribed species in the Neotropics. in Eight new species of lichenized Basidiomycota in the genera Acantholichen, Cyphellostereum and Dictyonema s.str. (Agaricales, Hygrophoraceae) from northern South America
Species of Acantholichen occurring only in the Neotropics show a high degree of endemism (Dal Forno et al. 2016). Of the seven species now recognized in this genus (Table 2), 71.4% (5) are known only from South America. As with Dictyonema, Acantholichen seem to be specific to substrate type and appears in the Andean small forest occurring on mosses in tree bark inhabiting mostly exposed habitats. Cyphellostereum is also represented by a high number of species restricted to the Neotropics [6 (66.6%)], while one is known only from North America, one from Southeastern United States and Puerto Rico, and another species is known only from Borneo and Fiji (Table 2). It is probably due to their unusual appearance that these lichens are getting confused with free-living cyanobacteria colonies, and that there are still undescribed species in the Neotropics.
Figure 2 in Vocal repertoire and group-specific signature in the Smooth-billed Ani, Crotophaga ani Linnaeus, 1758 (Cuculiformes, Aves)
Figure 2. Song structure of the Smooth-billed Ani showing the notes, sillable and harmonic.
Supplementary Videos - Mild paravalvular leak may pose an increased thrombogenic risk in transcatheter aortic valve replacement (TAVR) patients - Insights from patient specific in vitro and in silico studies
<p>Supplementary Videos for manuscript in Bioengineering Special Issue "“Mathematical Modeling of Aortic Diseases " </p> <p>Mild paravalvular leak may pose an increased thrombogenic risk in transcatheter aortic valve replacement (TAVR) patients - Insights from patient specific in vitro and in silico studies</p> <p>Brandon J. Kovarovic PhD<sup>1</sup>, Oren M. Rotman PhD<sup>1</sup>, Puja B. Parikh MD, MPH<sup>2</sup>, Marvin J. Slepian MD<sup>3,4</sup>, and Danny Bluestein PhD<sup>1,</sup> *</p> <p><sup>1</sup> Biofluids Research Group, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA.</p> <p><sup>2</sup> Division of Cardiovascular Medicine, Department of Medicine, Stony Brook University, Stony Brook, NY, USA.</p> <p><sup>3</sup> Department of Medicine, Sarver Heart Center, University of Arizona, Tucson, AZ, USA</p> <p><sup>4</sup> Department of Biomedical Engineering, College of Engineering, University of Arizona, Tucson, AZ USA</p> <p><strong>*</strong> Correspondence: danny.bluestein@stonybrook.edu</p> <p><strong>*</strong> Correspondence: danny.bluestein@stonybrook.edu</p>
Information theoretic evidence for layer- and frequency-specific changes in cortical information processing under anesthesia
<p>Nature relies on highly distributed computation for the processing of information in nervous systems across the entire animal kingdom. Such distributed computation can be more easily understood if decomposed into the three elementary components of information processing, i.e., storage, transfer and modification, and rigorous information theoretic measures for these components exist. However, the distributed computation is often also linked to neural dynamics exhibiting distinct rhythms. Thus, it would be beneficial to associate the above components of information processing with distinct rhythmic processes where possible. Here we focus on the storage of information in neural dynamics and introduce a novel spectrally-resolved measure of active information storage (AIS). Drawing on intracortical recordings of neural activity in ferrets under anesthesia before and after loss of consciousness (LOC), we show that anesthesia-related modulation of AIS is highly specific to different frequency bands and that these frequency-specific effects differ across cortical layers and brain regions. We found that in the high/low gamma band, the effects of anesthesia result in AIS modulation only in the supergranular layers, while in the alpha/beta band, the strongest decrease in AIS can be seen at infragranular layers. Finally, we show that the increase of spectral power at multiple frequencies, in particular at alpha and delta bands in frontal areas, that is often observed during LOC ('anteriorization') also impacts local information processing – but in a frequency-specific way: Increases in isoflurane concentration induced a decrease in AIS in the alpha frequencies, while they increased AIS in the delta frequency range $<2$Hz. Thus, the analysis of spectrally-resolved AIS provides valuable additional insights into changes in cortical information processing under anaesthesia.</p>
Data: Towards understanding specific ion effects in aqueous media using thermodiffusion
<p>Data, which are presented in the following publication: Mohanakumar, Shilpa; Wiegand, Simone (2022): Towards understanding specific ion effects in aqueous media using thermodiffusion. In: The Eur. Phys. J. E 45 (2), S. 10. DOI: 10.1140/epje/s10189-022-00164-8.</p>
Files for: Soft robotic patient-specific hydrodynamic model of aortic stenosis and ventricular remodeling
<p>This repository includes the files necessary to reproduce the digital anatomies, cardiac and aortic sleeves, and multi-material 3D-printed valves from the "Soft robotic patient-specific hydrodynamic model of aortic stenosis and ventricular remodeling" article.</p>
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
<p><span>Cancer cells bypass cell death by changing the expression of the BCL-2 family of proteins, which are apoptotic pathway regulators. Upregulation of pro-survival BCL-2 proteins or downregulation of cell death effectors BAX and BAK interferes with the initiation of the intrinsic apoptotic pathway. In normal cells, apoptosis can occur through pro-apoptotic BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins. When cancer cells over-express pro-survival BCL-2 proteins, a potential remedy is the sequestration of these pro-survival proteins through a class of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic groove of pro-survival BCL-2 proteins. To improve the design of these BH3 mimetics, the packing interface between BH3 domain ligands and pro-survival BCL-2 proteins was analyzed using the Knob-Socket model to identify the amino acid residues responsible for interaction affinity and specificity. A Knob-Socket analysis organizes all the residues in a binding interface into simple 4 residue units: 3-residue sockets defining surfaces on a protein that pack a 4th residue knob from the other protein. In this way, the position and composition of the knobs packing into sockets across the BH3/BCL-2 interface can be classified. A Knob-Socket analysis of 19 BCL-2 protein and BH3 helix co-crystals reveal multiple conserved binding patterns across protein paralogs. Conserved knob residues such as a Gly, Leu, Ala and Glu most likely define binding specificity in the BH3/BCL-2 interface, whereas other residues such as Asp, Asn, and Val are important for forming surface sockets that bind these knobs. These findings can be used to inform the design of BH3 mimetics that are specific to pro-survival BCL-2 proteins for cancer therapeutics.</span></p>
Part 3: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/.</p> <p>The other subdirectories in the directory subtelomere contain instructions and scripts for reproducing many of the results in the manuscript. The subdirectory subtelomere/TwoCopies/ contains two subdirectories of instructions and scripts for reproducing the results in the table on the average coverage of Focb TR4 isolates. The subdirectory subtelomere/TEs/ contains four subdirectories, each of which provides instructions and scripts for estimating the copy numbers of one or two transposons in the table on the copy numbers of five transposons in Focb TR4 isolates. The subdirectory subtelomere/SVs/ explains how the results on SNPs and presence/absence polymorphisms could be reproduced. The subdirectory subtelomere/Fol/ contains three subdirectories, each of which includes information for reproducing one of the three columns in the table on mean SNP rates between Fol D11 and each of Fol4287, Fol069 and Fol072. The subdirectory subtelomere/Forc/ demonstrates how some of the programs and scripts developed by the author are used to analyze a genome assembly of Forc isolate Forc016. The subdirectory subtelomere/pub/ contains the source and executable code of those programs. See the README and z.cmd files in each leaf subdirectory for more information</p>
Permafrost response to temperature rise in carbon and nutrient cycling: Effects from habitat-specific conditions and factors of warming
<p>Permafrost is warming at a rate of two times faster than the rest of the Earth's surface. However, there is still a lack of a quantitative basis for predicting the functional stability of permafrost ecosystems in carbon (C) and nutrient cycling. We compiled the data of 708 observations from 89 air-warming experiments in the Northern Hemisphere and characterized the general effects of temperature increase on permafrost C exchange and balance, biomass production, microbial biomass, soil nutrients, and vegetation N dynamics via a meta-analysis. Also, an investigation was made on how responses may change with habitat-specific (e.g., plant functional groups and soil moisture status) conditions and warming variables (e.g., warming phases, levels, and timing). Warming downregulated net ecosystem C exchange generally via stimulating ecosystem respiration (15.6%) more than photosynthesis (6.2%). Vegetation usually responded to warming by investing more the C to the belowground, as belowground biomass increased much more (30.1%) than aboveground biomass (2.9%). Warming had a minor effect on microbial biomass. Warming increased soil ammonium and nitrate concentrations. What's more, a synthesis of 70 observations from 11 herbs and 9 shrubs revealed a 2.5% decline of N in green leaves. Compared to herbs, shrubs demonstrated a stronger response in respiration and had green leaf N declined by a greater extent. Not only in dry conditions did green leaf N decline with warming but also in wet conditions. Warming in non-growing seasons would negatively affect soil water, C uptake, and biomass production during growing seasons. Permafrost C loss and vegetation N decline may increase with warming levels and timing. Overall, our findings suggest that besides a positive C cycling-climate feedback, there will be negative feedback between permafrost nutrient cycling and climate warming.</p>
Data and code for "The immune regulation and epidemiological consequences of specific immune priming in Drosophila"
<p>Raw data and R code used to analyse and generate all figures in the above manuscript.</p>
Experimental ectoparasite removal has a sex-specific effect on nestling telomere length
<p>Parasites are a strong selective force that can influence fitness-related traits. The length of chromosome-capping telomeres can be used to assess the long-term costs of parasitism, as telomere loss accelerates in response to environmental stressors and often precedes poorer survival prospects. Here, we explored the sex-specific effects of ectoparasite removal on morphology and telomere length in nestling tree swallows (<em>Tachycineta bicolor</em>). To do so, we experimentally removed blowfly (<em>Protocalliphora</em> spp.) larvae from nests using Permethrin, a broad-spectrum insecticide. Compared to water-treated controls, insecticide treatment of nests had a sex-biased effect on blood telomere length: ectoparasite removal resulted in significantly longer telomeres in males but not females. While this treatment did not influence nestling body mass, it was associated with reduced feather development regardless of sex. This may reflect a relaxed pressure to fledge quickly in the absence of parasites, or alternatively, could be a negative side effect of permethrin on morphology. Exploring robust sex-specific telomere dynamics in response to early-life environmental pressures such as parasitism will shed light on sexual dimorphism in adult life histories and ageing.</p>
Input data for "Characterisation of the mechanism of Bile Salt Hydrolase substrate specificity by experimental and computational analyses"
<p>Topologies, coordinates, input and analysis scripts for Amber20 simulations performed in "Characterisation of the mechanism of Bile Salt Hydrolase substrate specificity by experimental and computational analyses", Structure, 2023</p>
Data-specific substitution models improve protein-based phylogenetics - data
<p>Amino-acid sequence data sets, estimated data-specific amino-acid substitution models, and optimal ML trees.</p> <p>Data are divided in five folders, each one with a readme.txt file describing it.</p> <p>├── 1_simulated_data_sets<br> │ ├── 1500-site_alignments<br> │ ├── 400-site_alignments<br> │ └── 8000-site_alignments<br> ├── 2_simulated_data_specific_models<br> │ ├── Codeml_models<br> │ ├── FastMG_models<br> │ ├── IQTREE_models<br> │ ├── P4_BI_models<br> │ └── P4_ML_models<br> ├── 3_optimal_ML_trees_simulated_data<br> │ ├── commonly-used_empirical_models<br> │ │ ├── cpREV_model_analyses<br> │ │ └── WAG_model_analyses<br> │ ├── data_specfic_model_analyses<br> │ │ ├── Codeml-estimated_model_analyses<br> │ │ ├── FastMG-estimated_model_analyses<br> │ │ ├── IQTREE-estimated_model_analyses<br> │ │ ├── P4BI-estimated_model_analyses<br> │ │ └── P4ML-estimated_model_analyses<br> │ └── simulation_model_analyses<br> ├── 4_data_specific_models_empirical_data<br> │ └── Toussaint18_data_specific_models_27partitions<br> └── 5_optimal_ML_trees_empirical_data</p>
Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity
<p>1- workflow for data analysis and figures generation</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.