Dataset Search

Supplemental data sets for the Manuscript entitled " Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats"

Matlab codes for the article "Phage-antibiotic synergy inhibited by temperate and chronic virus competition". Code can be used to reproduce the article figures, perform the parameter sensitivity analysis and simulate the model.

This dataset is derived from the raw dataset (https://doi.org/10.13012/B2IDB-4163883_V1) and collects entity mentions that were manually determined to be noisy, non-chemical entities.

Data in this spreadsheet presents basic information on Cahokia, Mound 72 shell artifacts. This includes taxonomic identifications, provenience, and bead measurements. There are five tabs: 1. Raw data; 2. Disk bead measurements; 3. Columella bead measurements; 4. Data on cups and pendants; and, 5. Information on whole shell beads.

Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar, M. ×giganteus (M×g) ‘1993–1780′, in regions where average annual minimum temperatures are −26.1°C (USDA hardiness zone 5) or lower poses a pressing need to develop new cultivars with superior cold tolerance. To facilitate breeding of Miscanthus, this study characterized phenotypic and genetic variation of overwintering ability in an M. sinensis germplasm panel consisting of 564 accessions, evaluated in field trials at three locations in North America and two in Asia. Genome‐wide association (GWA) and genomic prediction analyses were performed. The Korea/N China M. sinensis genetic group is a valuable gene pool for cold tolerance. The Yangtze‐Qinling, Southern Japan, and Northern Japan genetic groups were also potential sources of cold tolerance. A total of 73 marker–trait associations were detected for overwintering ability. Estimated breeding value for overwintering ability based on these 73 markers could explain 55% of the variation for first winter overwintering ability among M. sinensis. Average genomic prediction ability for overwintering ability across 50 fivefold cross‐validations was high (~0.73) after accounting for population structure. Common genomic regions for overwintering ability were detected by GWA analyses and a previous parallel QTL mapping study using three interconnected biparental F1 populations. One QTL on Miscanthus LG 8 encompassed five GWA hits and a known cold‐responsive gene, COR47. The other overwintering ability QTL on Miscanthus LG 11 contained two GWA hits and three known cold stress‐related genes, carboxylesterase 13 (CEX13), WRKY2 transcription factor, and cold shock domain (CSDP1). Miscanthus accessions collected from high latitude locations with cold winters had higher rates of overwintering, and more alleles for overwintering, than accessions collected from southern locations with mild winters.

This dataset is for the publication "Do Nearctic hover flies (Diptera: Syrphidae) engage in long-distance migration? An assessment of evidence and mechanisms." It consists of 11 Excel spreadsheets and 4 R scripts which correspond to the analyses which were conducted. Paper abstract: Long-distance insect migration is poorly understood despite its tremendous ecological and economic importance. As a group, Nearctic hover flies (Diptera: Syrphidae: Syrphinae), which are crucial pollinators as adults and biological control agents as larvae, are almost entirely unrecognized as migratory despite examples of highly migratory behavior among several Palearctic species. Here, we examined evidence and mechanisms of migration for four hover fly species (Allograpta obliqua, Eupeodes americanus, Syrphus rectus, and Syrphus ribesii) common throughout eastern North America using stable hydrogen isotope (δ2H) measurements of chitinous tissue, morphological assessments, abundance estimations, and cold-tolerance assays. While further studies are needed, non-local isotopic values obtained from hover fly specimens collected in central Illinois support the existence of long-distance fall migratory behavior in Eu. americanus, and to a lesser extent S. ribesii and S. rectus. Elevated abundance of Eu. americanus during the expected autumn migratory period further supports the existence of such behavior. Moreover, high phenotypic plasticity of morphology associated with dispersal coupled with significant differences between local and non-local specimens suggest that Eu. americanus exhibits a unique suite of morphological traits that decrease costs associated with long-distance flight. Finally, compared to the ostensibly non-migratory A. obliqua, Eu. americanus was less cold tolerant, a factor that may be associated with migratory behavior. Collectively, our findings imply that fall migration occurs in Nearctic hover flies, but we consider methodological limitations of our study in addition to potential ecological and economic consequences of these novel findings.

VCF files used to analyze a novel filtering tool VEF, presented in the article "VEF: a Variant Filtering tool based on Ensemble methods".

This dataset contains re-estimated gene trees from the ASTRAL-II [1] simulated datasets. The re-estimated variants of the datasets are called MC6H and MC11H -- they are derived from the MC6 and MC11 conditions from the original data (the MC6 and MC11 names are given by ASTRID [2]). The uploaded files contain the sequence alignments (half-length their original alignments), and the re-estimated species trees using FastTree2. Note: - "mc6h.tar.gz" and "mc11h.tar.gz" contain the sequence alignments and the re-estimated gene trees for the two conditions - the sequence alignments are in the format "all-genes.phylip.splitted.[i].half" where i means that this alignment is for the i-th alignment of the original dataset, but truncating the alignment halving its length - "g1000.trees" under each replicate contains the newline-separated re-estimated gene trees. The gene trees were estimated from the above described alignments using FastTree2 (version 2.1.11) command "FastTree -nt -gtr" [1]: Mirarab, S., & Warnow, T. (2015). ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics, 31(12), i44-i52. [2]: Vachaspati, P., & Warnow, T. (2015). ASTRID: accurate species trees from internode distances. BMC genomics, 16(10), 1-13.

- The objective of this study was to evaluate macronutrient apparent total tract digestibility (ATTD), gastrointestinal tolerance, and fermentative end-products in extruded, canine diets. <br />- Five diets were formulated to be isocaloric and isonitrogenous with either garbanzo beans (GBD), green lentils (GLD), peanut flour (PFD), dried yeast (DYD), or poultry by-product meal (CON) as the primary protein sources. Ten adult, intact, female beagles (mean age: 4.2 ± 1.1 yr, mean 28 weight: 11.9 ± 1.3 kg) were used in a replicated, 5x5 Latin square design with 14 d periods. Total DNA from fresh fecal samples was extracted using Mo-Bio PowerSoil kits (MO BIO Laboratories, Inc., Carlsbad, CA). Amplification of the 292 bp-fragment of V4 region from the 16S rRNA gene was completed using a Fluidigm Access Array (Fluidigm Corporation, South San Francisco, CA). Paired-end Illumina sequencing was performed on a MiSeq using v3 reagents (Illumina Inc., San Diego, CA) at the Roy J. Carver Biotechnology Center at the University of Illinois. <br />- Filenames are composed of animal name identifier, diet (CON=control; DY= dried yeast; GB= garbanzo beans; GL= green lentils; PF= peanut flour) and period replicate number (P1, P2, P3, P4, and P5).

This study acquired publicly available Shell annual reports. Reports were selected for the years since the UN investigation in 2011, resulting in documents from 2012 to 2023.

Photographs and video of two Lesser Chameleons (Furcifer minor) nesting together at the same time near Itremo, Madagascar.

This project evaluates the quality of retraction indexing metadata in Crossref. We investigated 208 DOIs that were indexed as retracted in Crossref in our April 2023 union list (Schneider et al., 2023), but were no longer indexed as retracted in the July 2024 union list (Salami et al., 2024), despite still being covered in the Crossref database. Therefore, we manually checked the current retraction status of these 208 DOIs on their publishers’ websites to ascertain their actual status.

This is a network of 14 systematic reviews on the salt controversy and their included studies. Each edge in the network represents an inclusion from one systematic review to an article. Systematic reviews were collected from Trinquart (Trinquart, L., Johns, D. M., & Galea, S. (2016). Why do we think we know what we know? A metaknowledge analysis of the salt controversy. International Journal of Epidemiology, 45(1), 251–260. https://doi.org/10.1093/ije/dyv184 ). <b>FILE FORMATS</b> 1) Article_list.csv - Unicode CSV 2) Article_attr.csv - Unicode CSV 3) inclusion_net_edges.csv - Unicode CSV 4) potential_inclusion_link.csv - Unicode CSV 5) systematic_review_inclusion_criteria.csv - Unicode CSV 6) Supplementary Reference List.pdf - PDF <b>ROW EXPLANATIONS</b> 1) Article_list.csv - Each row describes a systematic review or included article. 2) Article_attr.csv - Each row is the attributes of a systematic review/included article. 3) inclusion_net_edges.csv - Each row represents an inclusion from a systematic review to an article. 4) potential_inclusion_link.csv - Each row shows the available evidence base of a systematic review. 5) systematic_review_inclusion_criteria.csv - Each row is the inclusion criteria of a systematic review. 6) Supplementary Reference List.pdf - Each item is a bibliographic record of a systematic review/included paper. <b>COLUMN HEADER EXPLANATIONS</b> <b>1) Article_list.csv:</b> ID - Numeric ID of a paper paper assigned ID - ID of the paper from Trinquart et al. (2016) Type - Systematic review / primary study report Study Groupings - Groupings for related primary study reports from the same report, from Trinquart et al. (2016) (if applicable, otherwise blank) Title - Title of the paper year - Publication year of the paper Attitude - Scientific opinion about the salt controversy from Trinquart et al. (2016) Doi - DOIs of the paper. (if applicable, otherwise blank) Retracted (Y/N) - Whether the paper was retracted or withdrawn (Y). Blank if not retracted or withdrawn. <b>2) Article_attr.csv:</b> ID - Numeric ID of a paper year - Publication year Attitude - Scientific opinion about the salt controversy from Trinquart et al. (2016) Type - Systematic review/ primary study report <b>3) inclusion_net_edges.csv:</b> citing_ID - The numeric ID of a systematic review cited_ID - The numeric ID of the included articles <b>4) potential_inclusion_link.csv:</b> This data was translated from the Sankey diagram given in Trinquart et al. (2016) as Web Figure 4. Each row indicates a systematic review and each column indicates a primary study. In the matrix, "p" indicates that a given primary study had been published as of the search date of a given systematic review. <b>5)systematic_review_inclusion_criteria.csv:</b> ID - The numeric IDs of systematic reviews paper assigned ID - ID of the paper from Trinquart et al. (2016) attitude - Its scientific opinion about the salt controversy from Trinquart et al. (2016) No. of studies included - Number of articles included in the systematic review Study design - Study designs to include, per inclusion criteria population - Populations to include, per inclusion criteria Exposure/Intervention - Exposures/Interventions to include, per inclusion criteria outcome - Study outcomes required for inclusion, per inclusion criteria Language restriction - Report languages to include, per inclusion criteria follow-up period - Follow-up period required for inclusion, per inclusion criteria

In a novel approach, metabolically engineered sugarcane “Oilcane” has been investigated for fractionation of lipid and cellulose-rich pulp, using certain Natural deep eutectic solvents (NADES). The exploration of eco-friendly solvents are at the forefront of harnessing the biofuel potential of modern bioenergy crops. For this, six combinations of NADES were prepared using choline chloride (ChCl) as HBA and lactic acid (LA), oxalic acid (OA) and glycerol (Gly) as HBD and were further explored for pretreatment of oilcane bagasse in a molar ratio of 1:1 and 1:2. The impact of NADES ratio, biomass loading (10–50%), residence time (1–2 h), and temperature (90–140 °C) were evaluated for delignification, lipid content, sugar release after enzymatic hydrolysis. The finding demonstrated that under the optimal condition of ChCl: LA (1:2 molar ratio), 140 °C with 2 h retention time, the lipid content in the pre-treated substrate was increased to 2.5-fold (∼8% w/w) and > 80% glucose yield was achieved after 72 h of hydrolysis of pre-treated bagasse. High solid loading (∼50%) during pretreatment resulted in a similar glucose yield. Furthermore, recycling studies demonstrated that nearly 95 to 98% NADES could be recycled after each pretreatment for up to five consecutive cycles without any significant loss in chemical structure as confirmed by 1H NMR and FT IR. FT IR and XRD analyses of native and pre-treated biomass were performed to visualize the morphological changes during NADES pretreatment and their impact on sugar yield. The findings of the study may be used to establish NADES-based biorefinery for the valorization of lipids, and carbohydrates for fuels and chemicals production.

The text file contains the original aligned DNA nucleotide sequence data used in the phylogenetic analyses of Feng et al. (in review), comprising the 3 protein-coding genes (histone H3, cytochrome oxidase I and 2) and 2 ribosomal genes (28S D8 and 16S). The text file is marked up according to the standard NEXUS format commonly used by various phylogenetic analysis software packages. The file will be parsed automatically by a variety of programs that recognize NEXUS as a standard bioinformatics file format. The first six lines of the file identify the file as NEXUS, indicate that the file contains data for 257 taxa (species) and 2995 characters (nucleotide positions), indicate that the characters are DNA sequence, that gaps inserted into the DNA sequence alignment are indicated by a dash, and that missing data are indicated by a question mark. The remainder of the file contains the aligned nucleotide sequence data for the five genes. Data partitions, representing the individual genes and different codon positions of the protein-coding genes, are indicated by the lines beginning "charset" near the end of the file. Two supplementary tables in the provided PDF file provide additional information on the species in the dataset, including the GenBank accession numbers for the sequence data (Table S1) and the DNA substitution models used for each of the data partitions used for analyses in the phylogenetic analysis program IQ-Tree (version 1.6.8) (Table S3), as described in the Methods section of the paper. The supplemental tables will also be linked to the article upon publication at the journal website.

Xylan accounts for up to 40% of the structural carbohydrates in lignocellulosic feedstocks. Along with xylan, acetic acid in sources of hemicellulose can be recovered and marketed as a commodity chemical. Through vibrant bioprocessing innovations, converting xylose and acetic acid into high-value bioproducts via microbial cultures improves the feasibility of lignocellulosic biorefineries. Enzymatic hydrolysis using xylanase supplemented with acetylxylan esterase (AXE) was applied to prepare xylose-acetic acid enriched hydrolysates from bioenergy sorghum, oilcane, or energycane using sequential hydrothermal-mechanical pretreatment. Various biomass solids contents (15 to 25%, w/v) and xylanase loadings (140 to 280 FXU/g biomass) were tested to maximize xylose and acetic acid titers. The xylose and acetic acid yields were significantly improved by supplementing with AXE. The optimal yields of xylose and acetic acid were 92.29% and 62.26% obtained from hydrolyzing energycane and oilcane at 25% and 15% w/v biomass solids using 280 FXU xylanase/g biomass and AXE, respectively.

These datasets are for the four-dimensional scanning transmission electron microscopy (4D-STEM) and electron energy loss spectroscopy (EELS) experiments for cathode nanoparticles at different cutoff voltages and in different electrolytes. The raw 4D-STEM experiment datasets were collected by TEM image & analysis software (FEI) and were saved as SER files. The raw 4D-STEM datasets of SER files can be opened and viewed in MATLAB using our analysis software package of imToolBox available at <a href="https://github.com/flysteven/imToolBox">https://github.com/flysteven/imToolBox</a>. The raw EELS datasets were collected by DigitalMicrograph software and were saved as DM4 files. The raw EELS datasets can be opened and viewed in DigitalMicrograph software or using our analysis codes available at <a href="https://github.com/chenlabUIUC/OrientedPhaseDomain">https://github.com/chenlabUIUC/OrientedPhaseDomain</a>. All the datasets are from the work "Formation and impact of nanoscopic oriented phase domains in electrochemical crystalline electrodes" (2022). The 4D-STEM experiment data include four example datasets for cathode nanoparticles collected at different cutoff voltages and in different electrolytes as described below. Each dataset contains a stack of diffraction patterns collected at different probe positions scanned across the cathode nanoparticle. 1. Pristine cathode particle: "Pristine particle 4D-STEM.ser" 2. Cathode particle at the cutoff voltage of 0.09V during discharge at C/10 in the aqueous electrolyte: "Intermediate cutoff0_09V discharge (aqueous) 4D-STEM.ser" 3. Fully discharged cathode particle at C/10 in the aqueous electrolyte: "Fully discharged particle 4D-STEM.ser" 4. Fully discharged cathode particle at C/10 in the dry organic electrolyte: "Fully discharge particle (dry organic electrolyte).ser" The EELS experiment data includes three example datasets for cathode nanoparticles collected at different cutoff voltages during discharge in the aqueous electrolyte (in "EELS datasets.zip") as described below. Each EELS dataset contains the zero-loss and core-loss EELS spectra collected at different probe positions scanned across the cathode nanoparticle. 1. Pristine cathode particle: "Pristine particle EELS.zip" 2. Cathode particle at the cutoff voltage of 0.09V during discharge at C/10 in the aqueous electrolyte: "intermediate discharge (aqueous) EELS.zip" 3. Fully discharged cathode particle at C/10 in the aqueous electrolyte: "fully discharge (aqueous) EELS.zip" The details of the software package and codes that can be used to analyze the 4D-STEM datasets and EELS datasets are available at: https://github.com/chenlabUIUC/OrientedPhaseDomain. Once our paper is formally published, we will update the relationship of these datasets with our paper.

The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. However, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplexed gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis, which exhibited ~100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As proof of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis.

There is a growing interest in developing cooperative chemoenzymatic reactions to harness the reactivity of chemical catalysts and the selectivity of enzymes for the synthesis of nonracemic chiral compounds. However, existing chemoenzymatic systems with more than one chemical reaction and one enzymatic reaction working cooperatively are rare. Moreover, the application of oxidoreductases in cooperative chemoenzymatic reactions is limited by the necessity of using expensive and unstable redox equivalents such as nicotinamide cofactors. Here, we report a light-driven cooperative chemoenzymatic system comprised of a photoinduced electron transfer reaction (PET) and a photosensitized energy transfer reaction (PEnT) with an enzymatic reduction in one-pot to synthesize chiral building blocks of bioactive compounds. As a proof of concept, ene-reductase was directly regenerated by PET in the absence of external cofactors. Meanwhile, enzymatic reduction worked cooperatively with photocatalyst-catalyzed energy transfer that continuously replenished the reactive isomer from the less reactive one. The whole system stereoconvergently reduced E/Z mixtures of alkenes to the enantiopure products. Additionally, enantioselective enzymatic reduction worked competitively with photocatalyst-catalyzed racemic background reaction and side reactions to channel the overall electron flow to the single enantiopure product. Such a light-driven cooperative chemoenzymatic system holds great potential for asymmetric synthesis using inexpensive petroleum or biomass-derived alkenes.

The photosynthetic capacity or the CO2-saturated photosynthetic rate (Vmax), chlorophyll, and nitrogen are closely linked leaf traits that determine C4 crop photosynthesis and yield. Accurate, timely, rapid, and non-destructive approaches to predict leaf photosynthetic traits from hyperspectral reflectance are urgently needed for high-throughput crop monitoring to ensure food and bioenergy security. Therefore, this study thoroughly evaluated the state-of-the-art physically based radiative transfer models (RTMs), data-driven partial least squares regression (PLSR), and generalized PLSR (gPLSR) models to estimate leaf traits from leaf-clip hyperspectral reflectance, which was collected from maize (Zea mays L.) bioenergy plots with diverse genotypes, growth stages, treatments with nitrogen fertilizers, and ozone stresses in three growing seasons. The results show that leaf RTMs considering bidirectional effects can give accurate estimates of chlorophyll content (Pearson correlation r=0.95), while gPLSR enabled retrieval of leaf nitrogen concentration (r=0.85). Using PLSR with field measurements for training, the cross-validation indicates that Vmax can be well predicted from spectra (r=0.81). The integration of chlorophyll content (strongly related to visible spectra) and nitrogen concentration (linked to shortwave infrared signals) can provide better predictions of Vmax (r=0.71) than only using either chlorophyll or nitrogen individually. This study highlights that leaf chlorophyll content and nitrogen concentration have key and unique contributions to Vmax prediction.

Sugar alcohols are commonly used as low-calorie sweeteners and can serve as potential building blocks for bio-based chemicals. Previous work has shown that the oleaginous yeast Rhodosporidium toruloides IFO0880 can natively produce arabitol from xylose at relatively high titers, suggesting that it may be a useful host for sugar alcohol production. In this work, we explored whether R. toruloides can produce additional sugar alcohols. Rhodosporidium toruloides is able to produce galactitol from galactose. During growth in nitrogen-rich medium, R. toruloides produced 3.2 ± 0.6 g/L, and 8.4 ± 0.8 g/L galactitol from 20 to 40 g/L galactose, respectively. In addition, R. toruloides was able to produce galactitol from galactose at reduced titers during growth in nitrogen-poor medium, which also induces lipid production. These results suggest that R. toruloides can potentially be used for the co-production of lipids and galactitol from galactose. We further characterized the mechanism for galactitol production, including identifying and biochemically characterizing the critical aldose reductase. Intracellular metabolite analysis was also performed to further understand galactose metabolism. Rhodosporidium toruloides has traditionally been used for the production of lipids and lipid-based chemicals. Our work demonstrates that R. toruloides can also produce galactitol, which can be used to produce polymers with applications in medicine and as a precursor for anti-cancer drugs. Collectively, our results further establish that R. toruloides can produce multiple value-added chemicals from a wide range of sugars.

These data were used in the survival and cause-specific mortality analyses of translocated nuisance American black bear in Wisconsin published in Animal Conservation (Bauder, J.M., N.M. Roberts, D. Ruid, B. Kohn, and M.L. Allen. Accepted. Lower survival of nuisance American black bears (Ursus americanus) is not due to translocation. Animal Conservation). Included are CSV files including each bear's capture history and associated covariates and meta-data for each CSV file. Also included is an example R script of how to conduct the analyses (this R script is also included as supporting information with the published paper).

The PhytoplasmasRef_Trivellone_etal.fas fasta file contains the original final sequence alignment used in the phylogenetic analyses of Trivellone et al. (Ecology and Evolution, in review). The 27 sequences (21 phytoplasma reference strains and 6 phytoplasmas strains from the present study) were aligned using the Muscle algorithm as implemented in MEGA 7.0 with default settings. The final dataset contains 952 positions of the F2n/R2 fragment of the 16S rRNA gene. The data analyses are further described in the cited original paper.

These data and code are associated with a study on differences in the rate of hatching failure of eggs across 14 free-living grassland and shrubland birds. We used a device to measure the embryonic heart rate of eggs and found there was variation across species related to factors such as nest type and nest safety. This work is to be published in Ornithology.

This dataset includes structural MRI head scans of 32 piglets, at 28 days of age, scanned at the University of Illinois. The dataset also includes manually drawn brain masks of each of the piglets. The dataset also includes brain masks that were generated automatically using Region-Based Convolutional Neural Networks (Mask R-CNN), trained on the manually drawn brain masks.