Find research datasets worth reusing

A systematic assessment of deep learning methods for drug response prediction: from in-vitro to clinical application

https://github.com/LihongLab/Suppl-data-Benchmark ## GDSC dataset **Table S3.** GDSC gene expression profiles for 966 cancer cell lines, where each column represents a cell line in the form of its name and tissue collection site, and each row represents a gene in the form of the HGNC symbol.   **Table S4.** GDSC gene mutation profiles for 966 cancer cell lines, where each column represents a cell line in the form of its name and tissue collection site, and each row represents a gene in the form of the HGNC symbol. The wild type is coded as 1 and the wild type as 0.   **Table S5.** GDSC copy number variation profiles for 966 cancer cell lines, where each column represents a cell line in the form of its name and tissue collection site, and each row represents a gene in the form of the HGNC symbol. The copy-neutral is coded as 0 and the deletion or amplification as 1.   **Table S6.** GDSC drug response data for 966 cancer cell lines and 282 drugs in the form of the natural logarithm of the IC50 readout. The first column shows the cell line name and tissue collection site, the second column shows the drug name, and the third column shows the drug response readout.   **Table S7.** GDSC annotations for 282 drugs include drug name, PubChem CID, PubChem canonical SMILES, Rdkit canonical SMILES, Target Pathway, standard deviation, bimodality coefficient and density coverage. ## TCGA dataset **Table S8.** TCGA gene expression profiles, where each column represents a patient in the form of TCGA patient ID, and each row represents a gene in the form of the HGNC symbol.   **Table S9.** TCGA gene mutation profiles, where each column represents a patient in the form of TCGA patient ID, and each row represents a gene in the form of the HGNC symbol. The wild type is coded as 1 and the wild type as 0.   **Table S10.** TCGA copy number variation profiles, where each column represents a patient in the form of TCGA patient ID, and each row represents a gene in the form of the HGNC symbol. The copy-neutral is coded as 0 and the deletion or amplification as 1.   **Table S11.** TCGA clinical response data. The first column shows the TCGA patient ID, the second column shows the drug name, the third column shows the clinical response category, the fourth column shows the cancer type, and the last column shows the clinical label as responder or non-responder.

Data from: Responses of invasive and native plants to different forms and availability of phosphorus

Premise—Many studies have assessed the various responses of alien plants to changes in overall nutrient or different nitrogen (N) availabilities. However, in natural soils, nutrients are present as different chemical elements (e.g., N and phosphorus [P]) and forms (e.g., inorganic and organic). Few studies have explored yet whether invasive and native species differ in their responses to varying P availability and forms. Key results—We found that invasive species did not show an overall higher biomass production than that of native species under varied P conditions. However, the biomass response to organic P was, relative to the response to inorganic P, stronger for the invasive species than that for the native species. This coincided with the pattern that invasive species mainly allocated biomass to the root system under organic P conditions. Conclusions—Our study indicates that while invasive species were not more promiscuous than native species were, they took great advantage of the organic-P forms. Therefore, the invasion risk of alien species may increase in habitats with more organic P sources.

opencc-zeroDec 2020View details →

No Escape: The Influence of Substrate Sodium on Plant Growth and Tissue Sodium Responses

This dataset contains data from a systematic review carried out to understand substrate sodium's influence on plant growth and sodium accumulation strategies. Accordingly, we carried out a systematic review of plants' responses to variation in substrate sodium concentrations. We compared biomass and tissue-sodium accumulation among 107 cultivars or populations (67 species in 20 plant families), broadly expanding beyond the agricultural and model taxa for which several generalizations previously had been made. We hypothesized a priori response models for each population's growth and sodium accumulation as a function of increasing substrate NaCl and used Bayesian Information Criterion to choose the best model. Additionally, using a phylogenetic signal analysis, we tested for phylogenetic patterning of responses across taxa. The influence of substrate sodium on growth differed across taxa, with most populations experiencing detrimental effects at high concentrations. Irrespective of growth responses, tissue sodium concentrations for most taxa increased as sodium concentration in the substrate increased. We found no strong associations between type of growth response and type of sodium accumulation response across taxa. Although experiments often fail to test plants across a sufficiently broad range of substrate salinities, non-crop species tended toward higher sodium tolerance than domesticated species. Moreover, some phylogenetic conservatism was apparent, in that evolutionary history helped predict the distribution of total-plant growth responses across the phylogeny, but not sodium accumulation responses. Our study reveals that saltier plants in saltier soils prove to be a broadly general pattern for sodium across plant taxa. Regardless of growth responses, sodium accumulation mostly followed an increasing trend as substrate sodium levels increased.

Physiological responses of fen mosses along a nitrogen gradient point to competition restricting their fundamental niches

Nutrient availability determines vegetation patterns and ecological functioning of intact groundwater-fed peatlands (fens). Bryophytes, commonly referred to as 'brown mosses', dominate calcareous fens (rich fens), are an integral part of their unique biodiversity and contribute significantly to peat formation and carbon sequestration. Brown mosses are replaced by vascular plants as nutrient availability increases. The decline of brown mosses may either be due to their physiological intolerance of high nutrient levels or to them being outcompeted by vascular plants. We aimed to distinguish between these two hypotheses by investigating whether the ecological optima reflect the physiological optima of brown mosses. Eight brown moss species, common in calcareous fens of the northern hemisphere, were grown under a gradient of nitrogen and phosphorus availability. Biomass increment, chlorophyll content and biomass nutrient concentration were measured. All brown moss species studied achieved the highest growth rates and chlorophyll contents when grown under conditions of nitrogen and phosphorus concentrations higher than those where they occur naturally at the highest frequency. Two of the species showed no growth saturation even at the highest levels of nutrient availability, while the others appeared potassium-limited at the highest N and P levels. Brown mosses dominate natural fens at the lower edge of their physiological optimum in terms of nutrient availability, i.e., their realized niche is much narrower than the fundamental one. Based on the literature, we argue that it is the competition for light with vascular plants which limits the occurrence of brown mosses in nutrient-rich habitats and prevents them from occupying their entire fundamental niche.

Heterogeneity of RNA editing in mesothelioma and how RNA editing enzyme ADAR2 affects mesothelioma cell growth, response to chemotherapy and tumor microenvironment

Raw data supporting the manuscript

Data from: A Nonadjuvanted Whole-Inactivated Pneumococcal Vaccine Induces Multiserotype Opsonophagocytic Responses Mediated by Noncapsule-Specific Antibodies

Streptococcus pneumoniae (Spn) remains a major cause of global mortality, with extensive antigenic diversity between capsular serotypes that poses an ongoing challenge for vaccine development. Widespread use of pneumococcal conjugate vaccines (PCVs) targeting Spn capsules has greatly reduced infections by vaccine-included serotypes, but has led to increased infections by non-included serotypes. To date, high cost of PCVs has also limited their usefulness in low-income regions where disease burdens are highest. To overcome these limitations, serotype-independent vaccines are being actively researched. We have developed a whole-cell gamma-irradiated Spn vaccine (termed Gamma-PN) providing serotype-independent protection. We demonstrate that Gamma-PN immunization via the clinically relevant intramuscular route induces protein-specific antibodies able to bind numerous non-vaccine encapsulated serotypes, which mediate opsonophagocytic killing and protection against lethal challenges. Gamma-PN induced comparable or superior OPKA responses to serotypes found in the licensed Prevnar13 (PCV13), and a superior response to non-included serotypes, including emergent 22F and 35B. Additionally, despite a lower observed reactogenicity, administration of Gamma-PN without adjuvant resulted in higher OPKA responses and improved protection compared to adjuvanted Gamma-PN. To our knowledge, this has never been demonstrated for a whole-inactivated Spn vaccine. Eliminating the requirement for adjuvant comes with numerous benefits for clinical applications of this vaccine, and poses interesting questions for the inclusion of adjuvant in similar vaccines in development.

Supplementary data for article "Reduced B-cell antigenicity of Omicron lowers host serologic response"

This repository contains five supplementary data files for the research article "Reduced B-cell antigenicity of Omicron lowers host serologic response". For more information, please refer to the article preprint https://doi.org/10.1101/2022.02.15.480546 and upcoming article at Cell Reports.   <ol> <li>Table_hCoV229E.xlsx: list of hCoV229E RBD sequences, with associated isolate and collection date identifiers, and ScanNet antigenicity score for reproducing Figure 3A. Aligned sequences and templates are also provided.</li> <li>table_artificial_variants.csv: List of artificial RBD sequences generated by an evolutionary-based sequence generative model for reproducing Figure 3B, Supplementary Figure S6H.</li> <li>MSA_RBD.fasta: Multiple Sequence Alignment of RBD sequences and sample weights used for training the sequence generative model used in Figure 3B, Supplementary Figures S2C, S6.</li> <li>table_antibody_hit_rate_RBD.csv: Empirical epitope distribution for the RBD, as determined from the Protein Data Bank and raw data for Supplementary Figure S1).</li> <li>RBD_virtual_DMS.xlsx: virtual Deep Mutational Scan performed with ScanNet and the sequence generative model shown in Supplementary Figure S2.</li> </ol>

Environmentally responsible behavior of community-based tourists in Santo Amaro, Brazil

Data were collected in 2019, with tourists who consumed an alternative tourism experience in Santo Amaro (Maranhao state), Brazil. There were 227 participants. This database has not been processed and its language is Portuguese.

Poroelastic response of water level in Tengchong well aquifer to dynamic stress

Data used in manuscript named "Poroelastic response of water level in Tengchong well aquifer to dynamic stress"

Climate mitigation potential and soil microbial response of cyanobacteria-fertilized bioenergy crops in a cool semi-arid cropland

Bioenergy carbon capture and storage (BECCS) systems can serve as decarbonization pathways for climate mitigation. Perennial grasses are a promising second-generation lignocellulosic bioenergy feedstock, but optimizing their sustainability, productivity, and climate mitigation potential requires an evaluation of how nitrogen (N) fertilizer strategies interact with greenhouse gas (GHG) and soil organic carbon (SOC) dynamics. Further, crop and fertilizer choice can affect the soil microbiome which is critical to soil organic matter turnover, nutrient cycling, and sustaining crop productivity but these feedbacks are poorly understood due to the paucity of data from agroecosystems. Here, we examine the climate mitigation potential and soil microbiome response to establishing two functionally different perennial grasses, switchgrass (Panicum virgatum, C4), and tall wheatgrass (Thinopyrum ponticum, C3), in a cool semi-arid agroecosystem under two fertilizer applications, a novel cyanobacterial biofertilizer (CBF) and urea. Finally, we examine shifts in soil microbial composition resulting from crop establishment and fertilizer regime. We find that in contrast to the C4 crop, the C3 crop achieved 98% greater productivity and had a higher N use efficiency when fertilized and the CBF produced the same biomass enhancement as urea. Non-CO2 greenhouse gas fluxes across all treatments were low and we observed a three-year net loss of SOC under the C4 crop and a net increase under the C3 crop at a 0-30 cm soil depth regardless of fertilization. Further, we detected crop-specific changes in the soil microbiome, including an increased relative abundance of arbuscular mycorrhizal fungi under the C3, and potentially pathogenic fungi in the C4 grass. Taken together, these findings highlight the potential of CBF-fertilized C3 crops as a second-generation bioenergy feedstock in semiarid regions as a part of a climate mitigation strategy.

opencc-by-4.0Aug 2022View details →

Single-cell transcriptome analysis of the in vivo response to viral infection in the cave nectar bat Eonycteris spelaea

Bats are reservoir hosts of many zoonotic viruses with pandemic potential in humans. Here, we utilized single-cell transcriptome sequencing (scRNA-seq) to provide detailed comparative analyses of the immune repertoire and the transcriptional responses in the bat lungs upon in vivo infection with a double-stranded RNA virus, Pteropine orthoreovirus PRV3M. Neutrophils were observed to have basally high IDO1 expression, uniquely amongst mammals currently profiled by scRNA-seq. NK/T cells were the most abundant immune cell type in lung tissue, and included three distinct CD8 + effector T cell populations delineated by the differential expression of KLRB1, GFRA2 and DPP4. We identified NK/T clusters which up-regulated genes involved in T-cell activation and effector function early after viral infection. Alveolar macrophages and classical monocytes were key drivers of antiviral interferon signaling. Infection also resulted in the expansion of a CSF1R + population expressing collagen-like genes, which became the predominant myeloid cell type after infection. This work uncovers novel features relevant to viral disease tolerance in bats, lays a foundation for future in vivo and in vitro experimental investigations, and serves as a key resource for comparative immunology studies across bats and other mammals.   This upload is the transcriptome fasta file used for alignment for the dataset.

Growth, defense, and storage responses of 12 oak (Quercus) species to varying locations and intensities of simulated herbivory

The evolution of plant defenses is often constrained by phylogeny. Many of the differences between competing plant-defense theories hinge upon the differences in the location of meristem damage (apical vs. auxiliary) and the amount of tissue removed. We analyzed the growth and defense responses of 12 Quercus (oak) species from a well-resolved molecular phylogeny using phylogenetically independent contrasts. Access to light is paramount for forest-dwelling tree species, such as many members of the genus Quercus. We therefore predicted a greater investment in defense when apical meristem tissue was removed. We also predicted a greater investment in defense when large amounts of tissue were removed and a greater investment in growth when less tissues were removed. We conducted five simulated-herbivory treatments including a control with no damage and alterations of the location of meristem damage (apical vs. auxiliary shoots) and intensity (25% vs. 75% tissue removal). We measured growth, defense, and nutrient re-allocation traits in response to simulated herbivory. Phylomorphospace models were used to demonstrate the phylogenetic nature of trade-offs between characteristics of growth, chemical defenses, and nutrient re-allocation. We found that growth-defense trade-offs in control treatments were under phylogenetic constraints, but phylogenetic constraints and growth-defense trade-offs were not common in the simulated-herbivory treatments. Growth-defense constraints exist within the Quercus genus, although there are adaptations to herbivory that vary among species.

Decoding the metabolic response of Escherichia coli for sensing trace heavy metals in water

As: Raman spectra from E. coli lysate sample after exposing to As in DI water Cr: Raman spectra from E. coli lysate sample after exposing to Cr in DI water As_TapWater: Raman spectra from E. coli lysate sample after exposing to As in tap water WasteWater_FineTune_Dataset: Raman spectra from E. coli lysate sample after exposing to As in waste water WasteWater 'Unknow' Dataset: Raman spectra from E. coli lysate sample after exposing to waste water

opencc-by-4.0Jun 2022View details →

Evolved transcriptional responses and their trade-offs after long-term adaptation of Bemisia tabaci to a marginally-suitable host

Scripts and data used in the work "Evolved transcriptional responses and their trade-offs after long-term adaptation of Bemisia tabaci to a marginally-suitable host". Abstract: Although generalist insect herbivores can migrate and rapidly adapt to a broad range of host plants, they can face significant difficulties when accidentally migrating to novel and marginally-suitable hosts. What happens, at both the performance and transcriptional levels, if these marginally-suitable hosts must be used for multiple generations before migration to a suitable host can take place, largely remains unknown. In this study, we established multigenerational colonies of the whitefly Bemisia tabaci, a generalist phloem-feeding species, adapted to a marginally-suitable host (habanero pepper) or an optimal host (cotton). We used reciprocal host tests to estimate the differences in performance of the populations on both hosts under optimal (30 oC) and mild-stressful (24 oC) temperature conditions, and documented the associated transcriptomic changes. The habanero pepper-adapted population greatly improved its performance on habanero pepper but did not reach its performance level on cotton, the original host. It also showed reduced performance on cotton, relative to the non-adapted population, and an antagonistic effect of the lower-temperature stressor. The transcriptomic data revealed that most of the expression changes, associated with long-term adaptation to habanero pepper, can be categorized as “evolved” with no initial plastic response. Three molecular functions dominated: enhanced formation of cuticle structural constituents, enhanced activity of oxidation-reduction processes involved in neutralization of phytotoxins and reduced production of proteins from the cathepsin B family. Taken together, these findings indicate that generalist insects can adapt to novel host plants by modifying the expression of a relatively small set of specific molecular functions.

Traits of soil bacteria predict plant responses to soil moisture

Microbes can promote beneficial plant and animal responses to abiotic environments, but the ecological drivers of this benefit remain elusive. Here we investigated byproduct benefits, which occur when traits that increase the fitness of one species provide incidental benefits to another species with no direct cost to the provider species. In experimental mesocosms, microbial traits predicted plant responses to soil moisture such that bacteria with self-beneficial traits in drought increased plant early growth, size at reproduction, and chlorophyll concentration under drought, while bacteria with self-beneficial traits in well-watered environments increased these same plant traits in well-watered environments. Thus, microbial traits that promote microbial success in different soil moisture environments also promote plant success in these same environments. Our results show that the concept of byproduct benefits, originally conceived to explain the evolution of cooperation in pairwise mutualisms, also applies to interactions between plants and non-symbiotic soil microbes.

Metatranscriptomic response of the wheat holobiont to decreasing soil water content

Background This dataset contains processed high throughput metatranscriptomics (RNA) sequencing data related to the scientific article entitled Metatranscriptomic response of the wheat holobiont to decreasing soil water content.  The files available in this archive are described below: Contigs abundance: contigs/qc_mapping_stats.tsv Contains read counts through various steps of the pipeline.   contigs/merged_contigs_abundance.tsv Number of reads that mapped to each contig for each sample. Rows = contig ID; column = sample ID. contigs/merged_contigs_abundance_cpm.tsv Normalized (edgeR) number of reads (Count Per Million - CPM) that mapped to each contig for each sample. Rows = contig ID; column = sample ID. Gene abundance: genes/merged_gene_abundance.tsv Number of reads that mapped to each gene for each sample. Rows = gene ID; column = sample ID. genes/merged_gene_abundance_cpm.tsv Normalized (edgeR) number of reads (Count Per Million - CPM) that mapped to each gene for each sample. Rows = gene ID; column = sample ID. Beta diversity: Beta diversity tables computed (with microbiomeutils v0.9) on gene abundance and contig abundance and bacteria/archaea contigs abundance are available here: betadiv/bray_curtis_contig_abundance/ betadiv/bray_curtis_gene_abundance/ betadiv/bray_curtis_contig_bacteriaArchaea/ Inside each of these directory is an index.html file allowing to visualize an Emperor interactive 3d vizualisation of beta diversity ordinations. ./3d_bray_curtis_plot/index.html Functional annotations: Gene functional annotations procedures are inspired from the JGI annotation workflow and is described in PMID: 31600863. annotations/annotations.tsv Functional annotations and taxonomic lineages (see below) are merged in a single tabular separated file.  Contains the results of  DIAMOND BLASTp of each gene amino acid sequence against KEGG genes database. DIAMOND BLASTp of each gene amino acid sequence against NCBI nr database. HMMSCAN of each gene amino acid sequence against PFAM-A database (in domtblout format). HMMSCAN of each gene amino acid sequence against PFAM-A database (in tblout format). RPS-BLAST of each gene amino acid sequence against COG database. Contigs-based taxonomy: consensus/taxonomy.tsv Contains the taxonomy assignment for each contig. Taxonomy assignment was performed with PMID : 31640809.  consensus/feature_table_<normalized>_L1 to _L7.txt Contigs abundance tables of each contig for each sample. Taxonomy assignment was performed with PMID : 31640809.  consensus/feature_table.tsv Contains the raw reads abundance of each contig across all samples. consensus/feature_table_normalized.tsv Contains the normalized (with edgeR) reads abundance of each bin across all samples.

Different biogeochemical responses to the 1997-98 and 2015-16 El Niño events in the equatorial Pacific: Did PDO play a role?

This dataset contains model outputs simulated by a basin-scale model (OGCM-DEEC V1.4). It is supplementary of the paper "Different biogeochemical responses to the 1997-98 and 2015-16 El Niño events in the equatorial Pacific: Did PDO play a role?". Please let me know if you need any more information

opencc-by-4.0Feb 2022View details →

Predicting emotion from music videos: exploring the relative contribution of visual and auditory information to affective responses.

The dataset to accompany the paper by Phoebe Chua, Dr. Dimos Makris, Prof. Dorien Herremans, Prof. Gemma Roig, and Prof. Kat Agres on Predicting emotion from music videos: exploring the relative contribution of visual and auditory information on affective responses.

RNA-seq of green hydra strains' ( Hydra viridissima) response to the removal or exchange of symbionts

The symbiotic hydra Hydra viridissima has a stable symbiotic relationship with the green alga Chlorella. This hydra appears to cospeciate with the symbiotic alga, and some strains are known to have strain-specific host/symbiont combinations. To investigate the mechanism of the specificity between host and symbiont, we explored the effect of the removal or exchange of symbionts in two distantly related H. viridissima strains (K10 and M9). In this study, we compared the gene expression of symbiont-removed, symbiont-exchanged hosts for each strain. The data include the raw read fastaq, assembled sequences, and read counts of RNA-seq. We also attached the results of differential gene expression analyses for all combinations of the hosts.

Data from: Evidence for divergence in phenology over morphology in response to limiting similarity in montane communities of Rhododendron

1. The coexistence of closely related species is key to understanding the nature of biodiversity hotspots where in situ diversification has yielded rich communities of close relatives. Limiting similarity predicts that co-occurring species are differentiated in their niches; identifying the axes of differentiation in sympatric close relatives can thus help reveal the eco-evolutionary dynamics of community assembly. For flowering plants, these axes may be temporal (related to reproductive phenology) or morphological (related to functional traits). 2. We collected fine-scale data on abundance, morphology, and phenology over a flowering season for 34 species of Rhododendron (Ericaceae) spanning a 2700 m elevation gradient in a nature reserve in the eastern Hengduan Mountains, China. We used null models to test for patterns of clustering versus overdispersion in species' abundances, phylogenetic relatedness, and functional traits across sites, and applied joint distribution models to examine the correlates of pairwise associations. 3. We found that species tended to be spatially aggregated, indicating that communities are not strongly structured by competitive exclusion. At higher elevation sites, species tended to be vegetatively more similar (clustered) and closely related. Environmental variables, including climate and topography, were strong predictors of species' ranges. No evidence of niche differentiation was detected along spatial or morphological (functional) axes, but along the temporal axis, the phenology of co-occurring species showed significant divergence, and was less phylogenetically conserved compared to morphological traits. 4. Synthesis. Local communities of Rhododendron in its center of diversity are structured by environmental filtering and the effects of limiting similarity. Evidence for the latter is apparent in the pervasive phenological divergence of co-occurring species, likely driven by reproductive interference from shared pollinators. The evolutionary lability of flowering time appears to render it the quickest path to coexistence for recently diverged species that experience secondary contact in this biodiversity hotspot.