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1,657 results for “silencing”
The predator problem and PCR primers in molecular dietary analysis: swamped or silenced; depth or breadth? - Dataset
<p>Raw sequencing data and other metadata files are associated with Cuff et al. (2022), available at https://doi.org/10.5281/zenodo.4708418</p> <p>The associated code, files and description pertain to the non-metric multi-dimensional scaling plot presented in this review (Figure 4). The code and data required for the boxplot (Figure 3) are given at the Zenodo link above (for Cuff et al. 2022).</p> <p>Data were collected and processed according to Cuff et al., (2022) up to the point of aggregating the two primer pair datasets. Binary matrices for prey detections were combined for the two primer pairs, but each sample represented separately for each primer pair (i.e., not aggregated by sample). Instances where taxa were only identified to genus (or lower, e.g., family) level by only one of the primer pairs resulted in aggregation for the other primer pair at that taxonomic level, except for species within those groups that were reliably identified to species level by both primers. Samples for which only one primer pair generated prey data were removed. The non-metric multidimensional scaling spider plot was created using ‘metaMDS’ with a Jaccard distance matrix and 999 tries in the ‘vegan’ package (Oksanen et al., 2016). Outliers that obscured the overall patterns were removed, the final plot having a stress of 0.061. Point colours were assigned using the ‘set1’ palette of the ‘RColorBrewer’ package (Neuwirth, 2014) and the final plot created using ‘ggplot2’ (Wickham, 2016).</p>
Silence Saunders (f2036)
<b>-- <a href="https://doi.org/10.5281/zenodo.11582199">Documentation</a> --</b><br><br><u>Name</u>: Silence Saunders<br><u>musiXplora-ID</u>: f2036<br><u>musiXplora-URI</u>: <a href="https://musixplora.de/mxp/f2036">https://musixplora.de/mxp/f2036</a><br><u>Gender</u>: m<br><u>Date of Birth</u>: 17 January 1706<br><u>Place of Birth</u>: Boston<br><u>Date of Death</u>: 17 April 1790<br><u>Place of Death</u>: Philadelphia<br><u>First Mentioned</u>: 1721<br><u>Professions (Musical)</u>: Instrumentenbauer<br><u>Professions (Non-Musical)</u>: Diplomat, Drucker, Naturwissenschaftler, Physiker, Politiker, Schriftsteller<br><u>Other Places of Activity</u>: Boston, London, New York, Paris, Philadelphia<br><br><br><u>Institutionen:</u><br><table><tbody><tr><th>Role</th><th>Title</th><th>mXp-ID</th></tr><tr><td>Related</td><td>University of Pennsylvania </td><td><a href="https://musixplora.de/mxp/3080310">3080310</a></td></tr></tbody></table><br><u>Titel/Medien:</u><br><table><tbody><tr><th>Role</th><th>Sigel</th><th>Title</th><th>mXp-ID</th></tr><tr><td>Related</td><td>Häffner et al. 2004</td><td>Ewig jung - trotz vieler Falten. 100 Jahre Hohner-Akkordeon in Bildern. History unfolds!. Martin Häffner, Anselm Rössler, Petra Schramböhmer, Haik Wenzel</td><td><a href="https://musixplora.de/mxp/5020585">5020585</a></td></tr></tbody></table><br><br><u>Changelog</u>:<br> - v0.0.1: Initial Upload.<br>
Souls of concrete in silence
<p>Está pintura feita em uma folha A4 (21cm X 29.7cm) e é coberta com tinta das cores verde, pretas, vermelha, branca na base que se mesclam e geram tonalidades diferentes de verde e do preto. Eu pintei em mês de meu aniversário em 2007, na cidade de Feira de Santana na Bahia, Brasil.</p>
H4K20me3 is important for Ash1-mediated H3K36me3 and transcriptional silencing in facultative heterochromatin in a fungal pathogen
<p>Normalized ChIP-seq datasets for visualization in IGV. The tracks contain means of pooled replicate datasets.</p> <p>ChIP-seq data were quality-filtered and adapters removed with trimmomatic v.0.39 (Bolger et al., 2014). Mapping was performed with bowtie2 v.2.4.4 (Langmead and Salzberg, 2012), and sorting and indexing with samtools v.1.9 (Li, 2011). Normalized coverage bigwig files and heatmaps were created with deeptools v.3.5.1 (Ramírez et al., 2016). Wiggletools v.1.2 and the UCSC Genome Browser tools were used to calculate means for replicates and converting wig to bigwig files.</p> <p>Reference genome file is modified from Goodwin et al., 2011. Chromosome 18 was removed from the genome as our reference isolate is missing chromosome 18. </p> <p>Gene annotation file was obtained from FungiDB (release 53) and is based on the annotation published by Grandaubert et al., 2015.</p> <p>In this version, we have added new ChIP-seq bw tracks for ∆ash1::ash1-gfp-V5 and ∆kmt5::kmt5 complementation experiments. All tracks coming from this experiment are labeled *_compl_exp_mean.bw.</p> <p>We also added ChIP peak files (peaks called with HOMER: Heinz et al., 2010) for H4K20me3, H3K36me3 and H3K27me3 in WT, ∆kmt5 and ∆ash1, as well as H3K36me3 peak files for Set2- and Ash1-mediated H3K36me3.</p> <p>We have also added bed files (500 bp windows) containing facultative heterochromatin clusters 1 (Zt09_500bp_K27filtered_K36_K20_cluster1.bed) and 2 (Zt09_500bp_K27filtered_K36_K20_cluster2.bed). </p>
Proteomic analysis of silenced cathepsin B expression suggests non-proteolytic cathepsin B functionality.
<p>A list of human protein uniprot IDs. The proteins were identified by LC-MS/MS in the cellular supernatant of MDA-MB-231 cells, originally published in:</p> <p>F.C. Sigloch, J.D. Knopf, J. Weißer, A. Gomez-Auli, M.L. Biniossek, A. Petrera, et al., Proteomic analysis of silenced cathepsin B expression suggests non-proteolytic cathepsin B functionality, Biochim. Biophys. Acta - Mol. Cell Res. 1863 (2016) 2700–2709. doi:10.1016/j.bbamcr.2016.08.005. https://www.ncbi.nlm.nih.gov/pubmed/27526672</p>
Dataset underlying the study "Enhanced Susceptibility to Tomato Chlorosis Virus (ToCV) in Hsp90- and Sgt1-Silenced Plants: Insights from Gene Expression Dynamics"
<p>This dataset is underlying the scientific publication titled "Enhanced Susceptibility to Tomato Chlorosis Virus (ToCV) in Hsp90- and Sgt1-Silenced Plants: Insights from Gene Expression Dynamics", published in the <a href="https://www.mdpi.com/1999-4915/15/12/2370">Viruses</a> journal. </p><p>The dataset includes a time-course transcriptome analysis using RNA-seq of naïve (no whitefly and no virus), mock (non-viruliferous whiteflies) and ToCV (ToCV_viruliferous whiteflies)-treated tomato samples at 2, 7, and 14 days post-infection (dpi) and viral small RNAs derived from Tomato plants infected with ToCV at 14 dpi. The dataset provided here has been deposited in full by the authors in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB67704 (<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB67704"><strong>https://www.ebi.ac.uk/ena/browser/view/PRJEB67704</strong></a><br><br>The provided information in the dataset are further discussed and interpreted in detail, as well as their subsequent results, in the scientific publication.</p><p>This research was conducted within the VIRTIGATION project, which is part of the EU Open Research Data pilot. This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No. 101000570.</p>
Data from: Not afraid of the Big Bad Wolf: calls from large predators do not silence mesopredators
<p>Large predators are known to shape the behavior and ecology of sympatric predators via conflict and competition, with mesopredators thought to avoid large predators, while dogs suppress predator activity and act as guardians of human property. However, interspecific communication between predators has not been well-explored and this assumption of avoidance may oversimplify the responses of the species involved. We explored the acoustic activity of three closely related sympatric canids: wolves <em>Canis lupus</em>, coyotes <em>Canis latrans</em>, and dogs <em>Canis familiaris</em>. These species have an unbalanced triangle of risk: coyotes, as mesopredators, are at risk from both apex-predator wolves and human-associated dogs, while wolves fear dogs, and dogs may fear wolves as apex predators or challenge them as intruders into human-allied spaces. We predicted that risk perception would dictate vocal response with wolves and dogs silencing coyotes as well as dogs silencing wolves. Dogs, in their protective role of guarding human property, would respond to both. Eleven passive acoustic monitoring devices were deployed across 13 nights in Central Wisconsin, and we measured the responses of each species to naturally occurring heterospecific vocalizations. Against our expectation, silencing did not occur. Instead, coyotes were not silenced by either species: when hearing wolves, coyotes responded at greater than chance rates and when hearing dogs, coyotes did not produce fewer calls than chance rates. Similarly, wolves responded at above chance rates to coyotes and at chance rates when hearing dogs. Only the dogs followed our prediction and responded at above chance rates in response to both coyotes and wolves. Thus, instead of silencing their competitors, canid vocalizations elicit responses from them suggesting the existence of a complex heterospecific communication network.</p>
Rapid sensorimotor adaptation to auditory midbrain silencing in free-flying bats
<p>This dataset accompanies the manuscript entitled "Rapid sensorimotor adaptation to auditory midbrain silencing in free-flying bats".<br>The structures contain the preprocessed data for each bat (individual structures for vocal and flight trajectory, or an overall structure for behavior). <br>The original code that allows for the figure generation associated with this manuscript is included. <br>The data for the audiograms and ABRs is also provided in csv format.</p>
Raw Microscopy and Western Blot Data for "Distinct silencer states generate epigenetic states of heterochromatin"
<p>Raw microscopy and western blot images for "Distinct silencer states generate epigenetic states of heterochromatin"</p>
Can immune gene silencing via dsRNA feeding promote pathogenic viruses to control the globally invasive Argentine ant?
<p><span>Pest control methods that can target pest species with limited environmental impacts are a conservation and economic priority. Species-specific pest control using RNA interference is a challenging but promising avenue in developing the next generation of pest management. We investigate the feasibility of manipulating a biological invader's immune system using double-stranded RNA (dsRNA) in order to increase susceptibility to naturally occurring pathogens. We used the invasive Argentine ant as a model, targeting the immunity-associated genes <em>Spaetzle</em> and <em>Dicer-1</em> with dsRNA. We show that feeding of <em>Spaetzle</em> dsRNA can result in partial target gene silencing for up to 28 days in the laboratory and five days in the field. <em>Dicer-1</em> dsRNA only resulted in partial gene knockdown after two days in the laboratory. Double-stranded RNA treatments were associated with significant gene expression disruptions across immune pathways in the laboratory and to a lower extent in the field. We observed occasional changes in viral loads in dsRNA-treated groups. However, immune pathways disruption did not result in consistent increase in microbial infections, nor did they alter ant abundance in the field. Our study explores the feasibility of lowering a pest's immunity as a control tool. We demonstate that it is possible to alter immune gene expression of pest species and pathogen loads, though in our system the affected pathogens did not appear to influence pest abundance. We provide advice on future directions for dsRNA-mediated immune disruption in pest species, including potential avenues to improve dsRNA delivery as well as the importance of the biology of the pest system and its pathogens.</span></p>
Dataset: Silence Therapeutics plc (SLN) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
Silencing of hippocampal synaptic transmission impairs spatial reward search on a head-fixed tactile treadmill task
<p>Publication data</p> <p>This repository contains the raw data files for the following manuscript:</p> <p>Title: Silencing of hippocampal synaptic transmission impairs spatial reward search on a head-fixed tactile treadmill task<br> Authors: Jake T. Jordan and J. Tiago Gonçalves<br> Pre-print in bioRxiv. doi:10.1101/2021.09.03.458092 (2021)</p> <p>A summary of all experimental groups and data tables and included as two Excel (.xlsx) files: DREADDs_Cued.xlsl and DREADDs_Spatial.xlsl, these correspond to figures 2 and 3 of the publication, respectively.</p> <p>The raw data files were acquired as described in Jordan et al. (2021a) doi:10.1016/j.xpro.2021.100770 <br> Software code for data acquisition and interpretation is available at doi:10.5281/zenodo.5196612</p>
"The place where Idid record the sound "saunan lämmitys" is our family's summerhouse. My father bought it year 1955. He was born nearby in Virojoki village in 1911 and passed away in 2003. As you know Sauna a is very relaxing and important thing to Finns. We like the warm and silence of sauna atmosphere and heating the sauna is almost religious to us. For me it is remembering moments Ispent with my dead father and other relatives. Iam 56 years old internist and living 600 km away from that place but still I visit there for about 2 months yearly." [Timo/timofei]14 in Collecting Sounds. Online Sharing of Field Recordings as Cultural Practice
"The place where Idid record the sound "saunan lämmitys" is our family's summerhouse. My father bought it year 1955. He was born nearby in Virojoki village in 1911 and passed away in 2003. As you know Sauna a is very relaxing and important thing to Finns. We like the warm and silence of sauna atmosphere and heating the sauna is almost religious to us. For me it is remembering moments Ispent with my dead father and other relatives. Iam 56 years old internist and living 600 km away from that place but still I visit there for about 2 months yearly." [Timo/timofei]14
Can immune gene silencing via dsRNA feeding promote pathogenic viruses to control the globally invasive Argentine ant?
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Data from: Not afraid of the Big Bad Wolf: calls from large predators do not silence mesopredators
Open the record for dataset details and reuse information.
Silence is sexy: Soundscape complexity alters mate choice in túngara frogs
Many animals acoustically communicate in large aggregations, producing biotic soundscapes. In turn, these natural soundscapes can influence the efficacy of animal communication, yet little is known about how variation in soundscape interferes with animals that communicate acoustically. We quantified this variation by analyzing natural soundscapes with the mid-frequency cover index and by measuring the frequency ranges and call rates of the most common acoustically communicating species. We then tested female mate choice in the túngara frog (Physalaemus pustulosus) in varying types of background chorus noise. We broadcast two natural túngara frog calls as a stimulus and altered the densities (duty cycles) of natural calls from conspecifics and heterospecifics to form the different types of chorus noise. During both conspecific and heterospecific chorus noise treatments, females demonstrated similar preferences for advertisement calls at low and mid noise densities but failed to express a preference in the presence of high noise density. Our data also suggest that nights with high densities of chorus noise from conspecifics and heterospecifics are common in some breeding ponds, and on nights with high noise density, the soundscape plays an important role diminishing the accuracy of female decision-making.
Expression analysis of targeted genes Sgt1 (A) and Hsp90 (B) in tomato plants subjected to virus-induced gene silencing using Tobacco rattle virus (TRV) vector.
<p><strong>Figure S1</strong>. Expression analysis of targeted genes Sgt1 (A) and Hsp90 (B) in tomato plants subjected to virus-induced gene silencing using Tobacco rattle virus (TRV) vector. (A) Relative expression levels of Sgt1 analyzed by Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR) in tomato plants infected with TRV vector alone (TRV2), TRV carrying Sgt1 silencing constructs (TRV-Sgt1), and mock-inoculated (Mock). Transcript levels were normalized using tomato genes encoding elongation factor 1-α and SAND as internal references, with Mock as the calibrator. (B) Relative expression levels of Hsp90 analyzed by RT-qPCR in tomato plants infected with TRV2, TRV-Hsp90, and Mock. Gene expression levels were normalized using the same reference genes as in (A). (C) Quantification of the relative accumulation of TRV RNA in plants infected with TRV2 and in silenced plants (TRV-Sgt1 and TRV-Hsp90). The expression levels were normalized using tomato genes for elongation factor 1-α and SAND, with TRV2 as the calibrator. All samples were collected at 19 dpi to anticipate the observed decline. Error bars represent standard errors of five biological replicates, and an asterisk indicates a significant difference, as determined by one-way ANOVA with P < 0.05</p>
Understanding piRNA-guided Silencing with Massively Parallel Cellular Assays
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Organizational cynicism, silence, gossip, "onstage communication", "offstage communication"
<p>Three datasets: Study 1, Study2, Study 3 relate to the consequences of organizational cynicism, which are negative gossip about the supervisor and employee silence. The eleven item scale of organizational cynicism developed by Brandes, Dharwadkar and Dean and presented by Kim et al. (2009) was used to measure the three aspects of organizational cynicim. In order to measure employee silence, the Four Forms of Employee Silence Scale (Knoll & van Dick, 2013, adapted by Adamska & Jurek, 2017) was used. To measure negative gossip about a supervisor a subscale of Work Gossip Scale developed by Brady et al. (2017) was used. It consists of five items. </p> <table> <caption>Describtion codes</caption> <tbody> <tr> <td>Variable name</td> <td>Variable </td> <td>Measurement unit</td> <td>Allowed values</td> <td>Description</td> </tr> <tr> <td>Wiek</td> <td>age</td> <td>numeric</td> <td>18-73</td> <td>Age of participants in years</td> </tr> <tr> <td>Płeć</td> <td>sex</td> <td>numeric</td> <td>1=female 2=male</td> <td>Participant's gender</td> </tr> <tr> <td>Wyksztalcenie</td> <td>education</td> <td>numeric</td> <td>1=primary 2=lower secondary 3=vacational 4=secondary 5=higher education</td> <td>Participant's education</td> </tr> <tr> <td>Stażogólny</td> <td>general seniority</td> <td>numeric</td> <td>0,1-53</td> <td>Participant's general seniority</td> </tr> <tr> <td>Stażobecny </td> <td>current seniority</td> <td>numeric</td> <td>0.1-32</td> <td>Participant's seniority in the current place of employment</td> </tr> <tr> <td>C1</td> <td>organizational cynicim item 1</td> <td>numeric</td> <td>1-5</td> <td>cognitive cynicism</td> </tr> <tr> <td>C2</td> <td> </td> <td>numeric</td> <td>1-5</td> <td>affective cynicism</td> </tr> <tr> <td>C3</td> <td>organizational cynicism item 3</td> <td>numeric</td> <td>1-5</td> <td>behavioral cynicism</td> </tr> <tr> <td>C4</td> <td>organizational cynicism item 4</td> <td>numeric</td> <td>1-5</td> <td>cognitive cynicism</td> </tr> <tr> <td>C5</td> <td>organizational cynicism item 5</td> <td>numeric</td> <td>1-5</td> <td>affective cynicism</td> </tr> <tr> <td>C6</td> <td>organizational cynicism item 6</td> <td>numeric</td> <td>1-5</td> <td>behvioral cynicism</td> </tr> <tr> <td>C7</td> <td>organizational cynicism item 7</td> <td>numeric</td> <td>1-5</td> <td>cognitive cynicism</td> </tr> <tr> <td>C8</td> <td>organizational cynicism item 8</td> <td>numeric</td> <td>1-5</td> <td>affective cynicism</td> </tr> <tr> <td>C9</td> <td>organizational cynicism item 9</td> <td>numeric</td> <td>1-5</td> <td>behavioral cynicism</td> </tr> <tr> <td>C10</td> <td>organizational cynicism item 10</td> <td>numeric</td> <td>1-5</td> <td>cognitive cynicism</td> </tr> <tr> <td>C11</td> <td>organizational cynicism item 11</td> <td>numeric</td> <td>1-5</td> <td>affective cynicism</td> </tr> <tr> <td>M1</td> <td>employee silence item 1</td> <td>numeric</td> <td>1-7</td> <td>quiescent silence</td> </tr> <tr> <td>M2</td> <td>employee silence item 2</td> <td>numeric</td> <td>1-7</td> <td>quiescent silence</td> </tr> <tr> <td>M3</td> <td>employee silence item 3</td> <td>numeric</td> <td>1-7</td> <td>prosocial silence</td> </tr> <tr> <td>M4</td> <td>employee silence item 4</td> <td>numeric</td> <td>1-7</td> <td>prosocial silence</td> </tr> <tr> <td>M5</td> <td>employee silence item 5</td> <td>numeric</td> <td>1-7</td> <td>acquiescent silence</td> </tr> <tr> <td>M6</td> <td>employee silence item 6</td> <td>numeric</td> <td>1-7</td> <td>acquiescent silence</td> </tr> <tr> <td>M7</td> <td>employee silence item 7</td> <td>numeric</td> <td>1-7</td> <td>acquiesent silence</td> </tr> <tr> <td>M8</td> <td>employee silence item 8</td> <td>numeric</td> <td>1-7</td> <td>opportunistic silence</td> </tr> <tr> <td>M9</td> <td>employee silence item 9</td> <td>numeric</td> <td>1-7</td> <td>prosocial silence</td> </tr> <tr> <td>M10</td> <td>employee silence item 10</td> <td>numeric</td> <td>1-7</td> <td>opportuistic silence</td> </tr> <tr> <td>M11</td> <td>employee silence item 11</td> <td>numeric</td> <td>1-7</td> <td>quiescence silence</td> </tr> <tr> <td>M12</td> <td>employee silence item 12</td> <td>numeric</td> <td>1-7</td> <td>opportunistic silence</td> </tr> <tr> <td>PL1</td> <td> item1</td> <td>numeric</td> <td>1-7</td> <td>negative gossip about a superviosor</td> </tr> <tr> <td>PL2</td> <td>item 2</td> <td>numeric</td> <td>1-7</td> <td>negative gossip about a supervisor</td> </tr> <tr> <td>PL3</td> <td> item 3</td> <td>numeric</td> <td>1-7</td> <td>negative gossip about a supervisor</td> </tr> <tr> <td>PL4</td> <td> item 4</td> <td>numeric</td> <td>1-7</td> <td>negative gossip about supervisor</td> </tr> <tr> <td>PL5</td> <td> item 5</td> <td>numeric</td> <td>1-7</td> <td>negative gossip about a supervisor</td> </tr> </tbody> </table> <p> </p>
Complete allele-specific silencing of the gain-of-function mutation of Huntington's disease
<p>Dominant gain-of-function mechanism in Huntington's disease (HD) suggests selective inactivation of mutant <em>HTT</em> produces the biggest therapeutic benefit. Here, we developed a complete allele-specific CRISPR/Cas9 strategy to permanently silence mutant <em>HTT</em> through nonsense-mediated decay (NMD), capitalizing on an exonic PAM (protospacer adjacent motif)-Altering SNP (PAS). Comprehensive sequence/haplotype analysis identified PAS-generated NGG PAM sites on exons of common <em>HTT </em>haplotypes in HD patients, revealing a single clinically meaningful PAS-based mutant-specific NMD-CRISPR/Cas9 strategy. The alternative allele of rs363099 eliminates NGG PAM site on the most frequent normal <em>HTT </em>haplotype in HD, permitting mutant <em>HTT-</em>specific CRISPR/Cas9 therapeutics in ~20% of HD patients with European ancestry. Our rs363099-based CRISPR/Cas9 showed perfect allele specificity and good targeting efficiencies in cells derived from HD patients. Dramatically reduced mutant <em>HTT </em>mRNA and complete loss of mutant HTT protein indicate that our allele-specific CRISPR/Cas9 strategy completely inactivates mutant <em>HTT </em>through NMD. RNAseq analysis also supported high levels of on-target gene specificity because no other genes except <em>HTT </em>were altered in clonal lines developed through our NMD-CRISPR/Cas9 strategy. Together, our data demonstrating significant target population, selective inactivation of mutant <em>HTT</em>, good targeting efficiency, and lack of recurrent off-targeting establish its therapeutic value of novel rs363099-based mutant <em>HTT-</em>specific NMD-CRISPR/Cas9 strategy in HD.</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.