dataesr/scientific-paragraphs-categorization huggingface dataset:
Recent advances in binning of metagenomic datasets from complex environments now enable the reconstruction of uncultured bacterial genomes from soil microbiomes  18, 52  , allowing for a dissection of soilassociated microbiome function with high taxonomic resolution. In this study, we applied this strategy to understand the underlying functional basis for drought-induced shifts in individual lineages within the rhizosphere microbiome. It represents one of the first studies performed in the plant rhizosphere to employ such a binning strategy  52, 53  and expands on prior successes by making use of paired host transcriptomics across a longitudinal transect of sorghum development and downstream reductionist experiments in controlled growth environments to help validate hypotheses generated through comparative analysis of MAG genetic capacity.
Our recovery of 55 bacterial genomes representing the most dominant phyla in the sorghum rhizosphere offers one clear advantage over traditional isolate sequencing, another standard method of functional assessment within a microbial community. This advantage is the ability to recover genomes from organisms that have been traditionally challenging to culture  48. As part of this study, we recovered four Actinobacterial genomes classified within the class Thermoleophilia, a recently proposed lineage with very few species cultivated and characterized  54  ; to date, there are only 18 reference genomes that belong to this class on the NCBI database (Taxonomy ID: 1497346), and none are closely related to the MAGs identified in this study. As all four of these MAGs were among our five nonenriched Actinobacterial genomes, a comparative analysis across enriched and unenriched lineages within this phylum would not have been possible using only currently available public reference data.
It is worth noting that while only a fraction of the total shotgun dataset mapped to these 55 MAGs, broad trends in microbial composition and functional capacity observed in the complete co-assembled contig dataset were recapitulated in our analyses of the MAGs. We anticipate that future efforts with greater read depth and an increased number of MAGs will decrease discrepancies between these datasets, while enabling our ability to assign functional capacity to individual community members. Unexpectedly, comparative genomics analysis across these Actinobacterial MAGs helped identify an intersection between drought stress enrichment phenotypes and iron metabolism. All living organisms on earth, with few exceptions, require iron to survive due to its inclusion as a co-factor in essential protein complexes  40.
Methods Experiment design and sampling time points. In brief, the field experiments were conducted at the Kearney Agricultural Research Center in Parlier, California. Two sorghum cultivars (RTx430 and BTx642) were planted with a randomized block design and two different types of irrigation (drought stress and watered controls) with three replicate blocks per treatment  6. Plant emergence was recorded on June 1, 2016, which coincides with TP0. All additional sequential time points represent the number of weeks past since plant emergence (eg. , TP3 is exactly 3 weeks after TP0). In this study, rhizosphere and bulk soil samples were collected for shotgun metagenomics samples at TP3, 4, 8, 9, 10, and 11 (Supplementary Fig. 1 ). Sorghum transcriptomics data used in the generation of Fig. 5  were previously published in Varoquaux et al 2019  32  , and were generated for all time points between TP2 and TP17.
CWSI has been described as a relative indicator of the levels of crop water stress, with values closer to 0. 0 indicating non-water-stressed plants that transpire at levels indicating nonlimiting soil water availability, and a value of 1. 0 indicating maximum water stress, with essentially no transpiration. For CWSI determinations, a handheld infrared thermometer (Everest Interscience, Tucson, AZ) was used to evaluate canopy temperature in 15 locations per field replication of each irrigation treatment during the period of 1400-1530 h PST. Air temperature and relative humidity were determined at a height of 2 m to match canopy temperature measurements, recorded on a data logger using air temperature and humidity sensors (Spectrum Technol. , Aurora, IL) to allow determination of vaporpressure deficit.
6. 3. The relative abundance of CDSs was estimated by Kallisto v0. 42. 4  92  by mapping raw reads from each sample to CDS sequences. Reads belonging to each phylum within a sample were summed and calculated the relative abundance. The composition profile of shotgun metagenomic data for each sample was plotted in R. The differential expression level between different treatments for CDSs was calculated by edgeR v3. 24. 3. The CDSs were clustered to different pathways based on the COG database. A hypergeometric test was used to check the enrichment status of pathways and COG categories. Genome binning, dereplication, and taxonomy assignment. In order to reduce the contig heterogeneity for the binning process and while maintaining enough reads to retrieve long contigs, we grouped and performed the second type of coassembly with megahit v1.
1. 2 for four groups of samples: bulk soil under drought, bulk soil under control, rhizosphere under drought, and rhizosphere under control samples, respectively. We filtered and kept the contigs ≥ 1 kb for binning with softwares CONCOCT v1. 1. 0 96 , metaBAT v2. 12. 1  97  , and MaxBin 2. 0  98. The best bin across the output of the three binning software results for each sample was selected using DAS_Tool v1. 1. 1  99. Further, dereplication across all bins was performed with dRep v2. 0. 5 nucleotide 100 according to average nucleotide identity (AN ≥ 99%). The resulting MAGs were assessed for completeness and contamination using CheckM v1. 0. 11  101. Sixty-four MAGs satisfied the conditions of medium-quality genome (completeness > 50%, contamination < 10%) and seven MAGs showed high quality (completeness > 90% and contamination < 10%).
We used the fiftyfive genomes with the quality completeness > 60% and contamination < 10% for further analysis. The taxonomy assignment was predicted with CheckM v1. 0. 11  101 nd GTDB-Tk v1. 3. 0 102. A manual curation was performed to combine the phylogenetic results from these two software packages. We only kept the taxonomy level that shows consistency between the two software packages. The multiplesequence alignment file, which was generated by GTDB-Tk v1. 3. 0, including 55 MAGs and over 20,000 guide genomes, was used for building a phylogenetic tree. An archaea genome was added for tree re-rooting. Differential abundance analysis between the treatment for MAGs. Differential abundance of MAGs between control and preflowering drought treatment was determined using raw-read count data as the input.
The expression level for each CDS was estimated by kallisto v0. 42. 4  92  by mapping raw reads from 52 samples to each CDS. Differential expression patterns for CDSs were calculated by R package edgeR v3. 24. 3  93. Hypergeometric tests were used to test each COG category that includes a group of significant differential expressed CDSs  6. The gene prediction and annotation of MAGs were performed with IMG/ER  28. The function comparison of two groups of genomes was performed with IMG by the 'Statistic Analysis' function. The parameters we used here are as follows: feature type: COG, measurements: gene count, statistical method: default and relative. Exogenous iron-solution treatment. The bacterial inoculation solution and the iron solution were mixed with soil in a laminar flow hood right before planting  6.
The plants grew in a walk-in growth chamber under 16 h of light at 33 °C / 8 h of dark at 28 °C, with 60% humidity for four weeks before harvesting. The sorghum fresh root and shoot weight comparison between different inoculations and iron concentrations was evaluated by a post hoc test with TukeyHSD function in R. Bacterial quantification from microboxes. Quantitative reverse transcription -PCR was performed using QX200 EvaGreen Supermix (Bio Rad, Catalog No. 1864034). Three biological replicates were performed for each reverse transcription-PCR experiment. The Sorghum GAPDH gene is used as the internal reference to normalize the expression data (GAPDH-f: 5′-AAGGCCGGCATTGC TTTGAAT-3′, GAPDH-r: 5′-ACATGTGGCAGATCAGGTCGA-3′). The primers used for Streptomyces quantitation are Actino235 (5′-CGCGGCCTATCAGCTTG TTG-3') and Eub518 (5'-ATTACCGCGGCTGCTGG-3'), and the primers for Pseudomonas quantitation are Eub338 (5′-ACTCCTACGGGAGGCAGCAG-3′) and Bet680 (5′-TCACTGCTACACGYG-3′).
All of the samples were used for 16S sequencing as described above. Root total RNA was isolated using Trizol. For qRT-PCR analysis, cDNA was synthesized from DNase I-treated total RNA by SuperScript ® III First-Strand Synthesis System. Standard deviation was calculated among at least three biological replicates for each sample. The maize GAPDH gene was used as the internal reference to normalize the expression data  105. All of the primers used for qPCR have been listed in Supplementary Table  1. Root tissue collection. Root tissue was collected as previously described above. After isolation, roots were vortexed to remove rhizosphere soil, then rinsed twice in the root washing buffer, the same as the epiphyte removal buffer. The washed roots were then gently dried, placed in aluminum foil bags, and quickly frozen in liquid nitrogen.
Acknowledgements We thank  Feng Yu  for participating in the sample collection, tissue grinding, DNA extraction, and providing thoughtful suggestions. We thank  Nabila Riaz 's help with analysis of iron-regulated gene expression. We thank  Bailey Bonnet  for sharing microbial technology. We thank  Alex Styer  for helping with sample collection and sharing his R color palette. We thank  Joy Hollingsworth  and  Julie A Sievert  for participating in the sample collection. We thank  Matthew Traxler  and  Bridget Hansen  for discussing the project. This work was funded by the  Department of Energy  Grant  DE-SC0014081. This work was also funded by  National Institutes of Health  grant  P42 ES007373  to M. L. G.
0 1. 5 2. 0 Fold enrichment under drought Fig. 4 GO enrichment analysis of enriched Actinobacterial metagenome-assembled genomes (MAGs) at the peak of drought in the rhizosphere. GO enrichment analysis for all COGs showing enrichment within genomes of enriched Actinobacterial MAGs (n = 10) as compared with nonenriched Actinobacterial MAGs (n = 5) under drought for rhizosphere at time point 8 (TP8). The values on the x-axis indicate the fold enrichment ratio of the relative percentages of COGs upregulated under drought in each category relative to the total relative percentage of COGs in the corresponding category within the entire dataset. Solid (filled) circles indicate categories for which the enrichment had a p-value < 0. 05 in a one-sided hypergeometric test and empty circles indicate categories with p values > 0.
Symptomatic patients were defined by the presence of angina or dyspnea on exertion. In the first place, patients with a high-grade > 90% stenosis on CCTA were directly referred for invasive coronary angiography without stress CMR exam. The main exclusion criteria were known CAD, contraindication to CCTA, CMR, or dipyridamole (detailed list in Supplementary Material 1). Clinical data including symptoms were collected according to the medical history and clinical examination on the day of CCTA. All patients gave informed written consent for CCTA, CMR, and enrolment in the clinical research study. The study was approved by the local Ethics Committee of our Institutions and conducted in accordance with the Declaration of Helsinki. This study followed the STROBE reporting guidelines for cohort studies.
Patients Follow-Up and Clinical Outcome The follow-up consisted of a clinical visit as part of usual care (67%) or by direct contact with the patient or the referring cardiologist (33%). Data collection was ended on January 2021. Cardiovascular (CV) events were checked by medical reports collected from the affiliated hospitals. The primary composite endpoint was the occurrence of at least one of the combined major adverse clinical events (MACE), defined as CV mortality or non-fatal MI. The secondary endpoints were CV mortality and all-cause mortality. All these clinical events were defined according to standardized definitions (15, 16), and are detailed in Supplementary Material 2. Three patients who experienced peri-procedural events after percutaneous coronary intervention (PCI) or coronary artery bypass grafting (CABG) < 90 days after the index CCTA examination were excluded.
CCTA Protocol and Analysis Between December 2008 and January 2020, all CCTA studies were performed on multidetector CT scanners with ≥64 detector rows (Brilliance 64, Philips Healthcare, Eindhoven, Netherlands, between 2008 and 2011; Philips iCT 128, between 2012 and 2018; Aquilion One Genesis, Canon Medical Systems, Otawara, Japan from 2019 to 2020), and the imaging protocol adhered to the Society of CV Computed Tomography guidelines on appropriateness and performance of CCTA available at the time of scanning (4, 17-19). Each CCTA protocol is detailed in Supplementary Material 3 and radiation exposure assessment is described in Supplementary Material 4. Coronary computed tomography angiography data were interpreted using multi-planar reconstruction and maximum intensity projections. The data were analyzed based on the 16segment coronary artery model  (20).
Cluster Analysis A total of 44 clinical characteristics and CCTA/CMR imaging data were determined (Supplementary Material 7). The absence of collinearity between those 44 baseline variables was verified by principal component analysis (PCA). After the exclusion of collinear variables, 17 categorical variables were selected for the clustering model and the definition of phenogroups which were as follows: age, gender, obesity (body mass index ≥ 30 kg/m²), dyslipidemia, diabetes mellitus, hypertension, current or former smoker, family history of CAD, presence of typical angina, dyspnea on exertion, presence of atrial fibrillation (AF) on 12-lead ECG, history of peripheral arterial disease (PAD) defined by revascularization procedures involving the peripheral arterial circulation (15), presence of LV dilatation defined by LV enddiastolic volume indexed (LVEDVi > 100 ml/m 2 ) (28), presence of LV systolic dysfunction defined by LV ejection fraction (LVEF) value < 50% (28), ≥1 proximal segment with stenosis > 50%, rate of segments with non-calcified plaques ≥ 50%, the presence of LGE, and the presence of inducible ischemia.
An unsupervised hierarchical clustering of principal components (HCPC function, from FactoMineR package, Vienna, Austria) algorithm was conducted using two steps: a multiple correspondence analysis (MCA) by which the principal components were obtained, followed by a hierarchical clustering analysis using Euclidean distance measures. Notably, the use of MCA was justified by the fact that all continuous variables included for clustering analysis were further classified into categorical variables. In addition, four dimensions were retained in the MCA output. The optimal number of clusters was determined based on the gain in withininertia (inside group variance) and using the Nbclust package (Vienna, Austria). A detailed description of the used cluster analysis methods is provided in Supplementary Material 8.
Patients Characteristics The flowchart of the study is presented in Figure  1. Overall, 2,015 symptomatic patients with newly diagnosed obstructive CAD on CCTA and further referred for stress CMR completed the clinical follow-up and constituted our study cohort. The median (IQR) delay between CCTA and stress CMR was 9 (4-12) days. No patient had non-fatal MI, CV mortality, or death between CCTA and stress CMR. Among the 2,015 patients who were symptomatic at the time of CCTA and further referred to stress CMR, 2,001 (99. 3%) had similar symptoms at the time of stress CMR. No severe adverse events occurred and detailed safety results are presented in Supplementary Material 9. Baseline patient characteristics and imaging data are shown in Table  1. Among the 2,015 patients (46. 3% men, mean age 70 ± 12.
Study Limitations Although patients were included prospectively, the study design was retrospective with 7. 8% of patients lost to follow-up. Baseline data for medications were not collected. In the absence of contraindications, all patients with obstructive CAD on CCTA received optimal medical treatment, including statins, as recommended by current guidelines (2). Although a recent study has emphasized the effects of statins on plaque composition  (35) , the detailed medical regimen was not prospectively collected and this question was beyond the scope of the study. Symptoms were assessed by the sole presence of symptomatic angina or dyspnea on exertion without standardized classification. Patients with a high-grade > 90% stenosis on CCTA were referred for invasive coronary angiography and excluded from analysis, limiting the extrapolation of the findings in this group of patients.
Methods The Early Care After Discharge of Heart Failure patients (ECAD-HF, NCT01820780) was a randomized, multicentre, open-label study to investigate the effectiveness of serial consultations or standard care to prevent hospitalization or death in patients discharged after an acute heart failure event. The protocol and amendments were approved by the French institutional review board ('Comité de Protection des Personnes'). The study was conducted according to French laws, Good Clinical Practice guidelines and the Declaration of Helsinki. All patients provided written informed consent.
Study outcomes The primary outcome was the composite of all-cause deaths or unplanned hospitalizations at 6 months. The secondary outcomes were: all-cause deaths, unplanned hospitalizations or unplanned hospitalizations for HF at 6 and 12 months. Also, evidencebased HF treatment at 6 months, changes in natriuretic peptide BNP or NTproBNP levels between discharge and the second consultation in the intensive group, natriuretic peptide levels between discharge and 6 months in both groups and the cumulative number of days alive and hospitalization-free days at 6 and 12 months. The following sub-group analyses were planned: left ventricular ejection fraction (LVEF) < or ≥ 40%; age < or ≥75 years; previous history of HF or not. Adverse event data was collected during follow-up consultations with investigators or technicians contacted either patients, family or referring doctors by telephone.
Pre-specified subgroup analyses to evaluate variations in treatment effect were done using Cox regression models, with terms for treatment, subgroup, and interaction of treatment with subgroup. All reported subgroup analyses were pre-specified. Assuming an estimated frequency of the composite primary criterion of 35% in the control group, with a reduction in the relative risk of 32% with intensive care, it was estimated that a sample of 554 patients, including a loss to follow-up rate of 10%, would have 80% power to detect a difference in the primary outcome, at a significance level of 0. 05 for a 2-sided test. The two-sided significance level was fixed at 5%. All tests were performed using SAS version 9. 4 statistical software (SAS Institute Inc. , Cary, NC, USA).
Analytical techniques Dilatometry was utilised to determine the in-situ linear thermal expansion of FA/MKPC and GBFS/MKPC binders up to 1200 • C. Dilatometry was performed in a horizontal configuration using a NETZSCH DIL 402C dilatometer between 20 and 1200 • C at 10 • C/min under a constant 50 mN load in air (1 mL/min) on cylindrical samples of 8. 5 ± 0. 1 mm (diameter) and 5. 7 ± 0. 2 mm (length). The linear dimension changes, ΔL, were recorded as a function of temperature and expressed as a percentage of the initial length, L 0. The following analytical techniques were performed on samples after high temperature exposure and air-cooling to room temperature (. i. e. ex-situ). Powder X-ray diffraction (XRD) data were collected between 10 • < 2θ < 50 • using a Bruker D2 PHASER desktop diffractometer with Ni filtered Cu Kα radiation (1.
5418 Å) operating in reflection mode, using a step size of 0. 02 • and time per step of 1 s. Thermal analysis was conducted using a Perkin Elmer DTA 7 instrument, in alumina crucibles under a N 2 atmosphere at 10 • C/min, up to 1000 • C. Blended MKPC samples were polished and carbon coated for SEM analysis, which was performed using a low vacuum Hitachi TM3030 analytical benchtop SEM with an integrated Bruker Quantax 70 EDX (energy dispersive X-ray spectrometer) system   at 15 kV and a 7. 0 mm working distance. Mössbauer spectroscopy was conducted on a Wissel spectrometer (50 Ci 57 Co(Rh) source) using 512 channels and an Fe foil for calibration. Unique Fe species were assigned by fitting Lorentzian doublet and sextets using Recoil software  [39]. Solid-state NMR spectra were collected on a Varian VNMRS 400 (9.
Acknowledgements LJG is grateful to the  Nuclear Decommissioning Authority (NDA)  for sponsorship, under assistance by the  National Nuclear Laboratory. NCH wishes to acknowledge the  Royal Academy of Engineering  and the  Nuclear Decommissioning Authority  for funding and  EPSRC  for part support under grant references  EP/S032959/1 ,  EP/P013600/1 , and  EP/ N017617/1. CLC is grateful to the  University of Sheffield  for the award of a  Vice Chancellor's fellowship  and  EPSRC  for the award of an  Early Career Fellowship  under grant reference  EP/N017374/1. NCH and SAW are grateful to EPSRC for provision of a CDT PhD studentship under grant reference:  EP/G037140/1. Solid-state NMR spectra were obtained at the  EPSRC UK National Solid-state NMR Service at Durham , and we thank  Dr. David Apperley  for his generous assistance in collection and interpretation of the results.
These measurements were averaged for the first three days starting from the colony establishment. During these initial days, the matrix temperature was usually only a little higher than the background temperature, so the heat production in the matrix had negligible effects on the background temperature. Because the matrix enlarged with colony age, and at some time it covered also the soil that surrounded meat, it was impossible to quantify heat production always within the same area. Instead, we quantified the average temperature in the largest possible circular or ellipsoidal area, depending on the shape of the surface covered with the matrix. We used for this purpose in-built tools of the IRSoft 4. 5 software (Testo, Germany).
Results were analysed using ANOVA for repeated measures designs in Statistica 13 (TIBCO Software Inc. , US), with rearing temperature as an independent variable, container type (M + L or M setups) in a pair as a repeated measures variable and the average heat production in the matrix (i. e. heat production averaged across measurement days) as a dependent variable. No outliers were detected. Fisher LSD test was used for post-hoc pairwise comparisons.
Then, it was transferred to a new container and 40 freshly hatched first instar larvae were added to the container. Experiments started on 3 March 2019 (3 replicates), 15 March 2019 (7 replicates), 8 May 2019 (10 replicates) and 5 August 2019 (10 replicates). Once a day colonies were taken out of the chambers to make thermal images. After larvae stopped feeding and began to bury themselves, we counted and weighed them (laboratory scale AS 82/220. R2, Radwag, Poland). Then, larvae were transferred to the soil-filled Petri dishes (3 larvae per dish), where we monitored further development to determine pupation and eclosion times. Results were analysed using ANOVA for repeated measures designs in Statistica 13 (TIBCO Software Inc. , US), with the duration of the prelarval phase as an independent variable and a container type (M/A + L or M + L setups) in a pair as a repeated measures variable.