10 research outputs found
MOESM1 of Sewage sludge for sustainable agriculture: contaminants’ contents and potential use as fertilizer
Additional file 1. NP, NP1EO, NP2EO, DEHP range (min, max values) and median concentration in sewage sludge during the present study (2013-2014)
Taxonomy classification depth comparisons among V region datasets and the FL variants.
<p>Taxonomy classification depth comparisons among V region datasets and the FL variants.</p
Classification of the full-length sequences and their trimmed to the examined V region variants.
<p>Classification of the full-length sequences and their trimmed to the examined V region variants.</p
Pearson correlation tests between corresponding sequence distances of examined V regions and FL variants.
<p>All tests were significant (P<001). Test correlation index (r) values and linear models (presented with solid lines) used to describe overall trends are provided above and below each plot. Local relationships between corresponding sequence distances of the FL and other datasets are expressed with the non-parametric LOWESS (locally weighted regression and smoothing scatterplots) regression analysis plotting (dot-dashed lines), while the ideal y = x correlation is also plotted (dashed lines).</p
16S rRNA gene sequence conservation of soil derived sequences.
<p>A) Nucleic acid base composition of the 16S rRNA gene consensus sequence of the 41,109 RDP database soil derived sequences for 90% conservation cutoff value. Red background positions include hypervariable stretches as reported in reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042671#pone.0042671-Baker1" target="_blank">[24]</a> and expanded in the current study, while green background positions are proposed primer designing sites in reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042671#pone.0042671-Wang1" target="_blank">[11]</a>. The IUPAC system was used for denoting per base variability (degeneracies) and lower-case letters are used for nucleotide positions where gaps participated by more than 10% in the position throughout the sequence alignment. B) Comparison of present study results for 95% sequence conservation with the ones provided in reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042671#pone.0042671-Wang1" target="_blank">[11]</a> for 90% sequence conservation. Letter color coding referring to differences found on sequences of this study compared to that of reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042671#pone.0042671-Wang1" target="_blank">[11]</a>: red) increased variability; blue) altered degeneracy without variability increase; green) reduced variability; grey) although presence of two nucleotides in that position is implied in reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042671#pone.0042671-Wang1" target="_blank">[11]</a>, these are missing in the published table.</p
Taxonomy, OTU (3% sequence distance) analysis and Unifrac results of the performed simulation.
<p>A) PCA results of matrix generated by sample distances based on classified sequence relative abundance (left) and presence absence (right) for the V regions and FL datasets. B) Similarly to A for OTU relative abundance (left) and presence absence (right). C) PCA results for matrices generated using the weighted (left - phylotype relative abundance based) and unweighted (right - phylotype occurrence based) Unifrac analysis result distances between samples for the V regions and FL datasets.</p
Distribution of commonly screened V region fragment lengths.
<p>Fragment lengths including the examined hypervariable regions for all screened (41,109) sequences. Sequence fragments were plotted according to length ascending order.</p
Data_Sheet_1_Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community.DOCX
<p>Pesticides are intentionally applied to agricultural fields for crop protection. They can harm non-target organisms such as soil microorganisms involved in important ecosystem functions with impacts at the global scale. Within the frame of the pesticide registration process, the ecotoxicological impact of pesticides on soil microorganisms is still based on carbon and nitrogen mineralization tests, despite the availability of more extensive approaches analyzing the abundance, activity or diversity of soil microorganisms. In this study, we used a high-density DNA microarray (PhyloChip) and 16S rDNA amplicon next-generation sequencing (NGS) to analyze the impact of the organophosphate insecticide chlorpyrifos (CHL), the phenyl-urea herbicide isoproturon (IPU), or the triazole fungicide tebuconazole (TCZ) on the diversity and composition of the soil bacterial community. To our knowledge, it is the first time that the combination of these approaches are applied to assess the impact of these three pesticides in a lab-to-field experimental design. The PhyloChip analysis revealed that although no significant changes in the composition of the bacterial community were observed in soil microcosms exposed to the pesticides, significant differences in detected operational taxonomic units (OTUs) were observed in the field experiment between pesticide treatments and control for all three tested pesticides after 70 days of exposure. NGS revealed that the bacterial diversity and composition varied over time. This trend was more marked in the microcosm than in the field study. Only slight but significant transient effects of CHL or TCZ were observed in the microcosm and the field study, respectively. IPU was not found to significantly modify the soil bacterial diversity or composition. Our results are in accordance with conclusions of the Environmental Food Safety Authority (EFSA), which concluded that these three pesticides may have a low risk toward soil microorganisms.</p
Development and Validation of Prediction Models of Adverse Kidney Outcomes in the Population With and Without Diabetes.
ObjectiveTo predict adverse kidney outcomes for use in optimizing medical management and clinical trial design.Research design and methodsIn this meta-analysis of individual participant data, 43 cohorts (N = 1,621,817) from research studies, electronic medical records, and clinical trials with global representation were separated into development and validation cohorts. Models were developed and validated within strata of diabetes mellitus (presence or absence) and estimated glomerular filtration rate (eGFR; ≥60 or ResultsThere were 17,399 and 24,591 events in development and validation cohorts, respectively. Models predicting ≥40% eGFR decline or kidney failure incorporated age, sex, eGFR, albuminuria, systolic blood pressure, antihypertensive medication use, history of heart failure, coronary heart disease, atrial fibrillation, smoking status, and BMI, and, in those with diabetes, hemoglobin A1c, insulin use, and oral diabetes medication use. The median C-statistic was 0.774 (interquartile range [IQR] = 0.753, 0.782) in the diabetes and higher-eGFR validation cohorts; 0.769 (IQR = 0.758, 0.808) in the diabetes and lower-eGFR validation cohorts; 0.740 (IQR = 0.717, 0.763) in the no diabetes and higher-eGFR validation cohorts; and 0.750 (IQR = 0.731, 0.785) in the no diabetes and lower-eGFR validation cohorts. Incorporating the previous 2-year eGFR slope minimally improved model performance, and then only in the higher-eGFR cohorts.ConclusionsNovel prediction equations for a decline of ≥40% in eGFR can be applied successfully for use in the general population in persons with and without diabetes with higher or lower eGFR