The effect of forage management on carbon storage in pastureland and rotation

Non-Peer ReviewedDegraded land with less than 1.5% organic carbon (class 4 and 5 land) in the Parkland of Western Canada has significant potential, from 5 to 15 Mg C ha-1 depending on management, for carbon storage with forages in the Parkland. The potential ranges from 5 to 15 Mg C ha-1, over a period from 15 to 20 years, depending on fertility management of forages in pasture and initial levels of soil organic carbon. Nitrogen fertilizer increased organic carbon stored in reseeded pastures at Pathlow and Brandon relative to paddocks without fertilizer. Over a period of 12 years (1978-1989) in the Pathlow study, 21.9 Mg C ha- 1 (0-15 cm) was stored when N fertilizer was applied at an annual rate of 45 kg ha-1 compared to the control treatment, which was attributed to accumulation of plant debris and roots at the surface. Increases in organic carbon did not persist 10 years after N fertilizer was discontinued at the study at Pathlow, Saskatchewan. At Brandon, Manitoba, fertilized grass pasture stored 16.2 Mg C ha-1 (0-50 cm) compared to unfertilized bromegrass from 1994 to 1999. Long-term forage rotations at Melfort showed no significant difference in the wheat phase of a F-W-W-H-H-W rotation due to nitrogen fertilizer (147.3 Mg C ha-1 150.7 Mg C ha-1) over a period from 1957 to 1994. This was attributed to the high levels of soil carbon in soils at Melfort. Forages in rotation had no significant effect on organic carbon in a study at Glenlea MB conducted from 1992 to 1999, though a range from 110.8 to 145.7 Mg C ha-1 was observed. Significant differences may occur in the long term as organic carbon accumulates in the treatments at Glenlea

Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci

BACKGROUND: DNA methylation (DNAm) is associated with gene regulation and estimated glomerular filtration rate (eGFR), a measure of kidney function. Decreased eGFR is more common among US Hispanics and African Americans. The causes for this are poorly understood. We aimed to identify trans-ethnic and ethnic-specific differentially methylated positions (DMPs) associated with eGFR using an agnostic, genome-wide approach. METHODS: The study included up to 5428 participants from multi-ethnic studies for discovery and 8109 participants for replication. We tested the associations between whole blood DNAm and eGFR using beta values from Illumina 450K or EPIC arrays. Ethnicity-stratified analyses were performed using linear mixed models adjusting for age, sex, smoking, and study-specific and technical variables. Summary results were meta-analyzed within and across ethnicities. Findings were assessed using integrative epigenomics methods and pathway analyses. RESULTS: We identified 93 DMPs associated with eGFR at an FDR of 0.05 and replicated 13 and 1 DMPs across independent samples in trans-ethnic and African American meta-analyses, respectively. The study also validated 6 previously published DMPs. Identified DMPs showed significant overlap enrichment with DNase I hypersensitive sites in kidney tissue, sites associated with the expression of proximal genes, and transcription factor motifs and pathways associated with kidney tissue and kidney development. CONCLUSIONS: We uncovered trans-ethnic and ethnic-specific DMPs associated with eGFR, including DMPs enriched in regulatory elements in kidney tissue and pathways related to kidney development. These findings shed light on epigenetic mechanisms associated with kidney function, bridging the gap between population-specific eGFR-associated DNAm and tissue-specific regulatory context

Risk stratification guided by the index of microcirculatory resistance and left ventricular end-diastolic pressure in acute myocardial infarction

Background: The index of microcirculatory resistance (IMR) of the infarct-related artery and left ventricular end-diastolic pressure (LVEDP) are acute, prognostic biomarkers in patients undergoing primary percutaneous coronary intervention. The clinical significance of IMR and LVEDP in combination is unknown. Methods: IMR and LVEDP were prospectively measured in a prespecified substudy of the T-TIME clinical trial (Trial of Low Dose Adjunctive Alteplase During Primary PCI). IMR was measured using a pressure- and temperature-sensing guidewire following percutaneous coronary intervention. Prognostically established thresholds for IMR (>32) and LVEDP (>18 mm Hg) were predefined. Contrast-enhanced cardiovascular magnetic resonance imaging (1.5 Tesla) was acquired 2 to 7 days and 3 months postmyocardial infarction. The primary end point was major adverse cardiac events, defined as cardiac death/nonfatal myocardial infarction/heart failure hospitalization at 1 year. Results: IMR and LVEDP were both measured in 131 patients (mean age 59±10.7 years, 103 [78.6%] male, 48 [36.6%] with anterior myocardial infarction). The median IMR was 29 (interquartile range, 17–55), the median LVEDP was 17 mm Hg (interquartile range, 12–21), and the correlation between them was not statistically significant (r=0.15; P=0.087). Fifty-three patients (40%) had low IMR (≤32) and low LVEDP (≤18), 18 (14%) had low IMR and high LVEDP, 31 (24%) had high IMR and low LVEDP, while 29 (22%) had high IMR and high LVEDP. Infarct size (% LV mass), LV ejection fraction, final myocardial perfusion grade ≤1, TIMI (Thrombolysis In Myocardial Infarction) flow grade ≤2, and coronary flow reserve were associated with LVEDP/IMR group, as was hospitalization for heart failure (n=18 events; P=0.045) and major adverse cardiac events (n=21 events; P=0.051). LVEDP>18 and IMR>32 combined was associated with major adverse cardiac events, independent of age, estimated glomerular filtration rate, and infarct-related artery (odds ratio, 5.80 [95% CI, 1.60–21.22] P=0.008). The net reclassification improvement for detecting major adverse cardiac events was 50.6% (95% CI, 2.7–98.2; P=0.033) when LVEDP>18 was added to IMR>32. Conclusions: IMR and LVEDP in combination have incremental value for risk stratification following primary percutaneous coronary intervention. Registration: URL: https://www.clinicaltrials.gov. Unique identifier: NCT02257294

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample

A computationally effcient moment-preserving Monte Carlo proton transport method in Geant4

The moment-preserving method, demonstrated as a viable alternative to condensed history for electrons, is extended to protons. Given the generality and the flexibility of the method, a discrete Coulomb scattering and discrete impactionization differential cross-section library for protons was readily developed and existing Geant4 electron discrete process and model classes were extended to make use of the new proton library. It is shown that levels of effciency and accuracy similar to those demonstrated for electrons are obtainable for protons in straight-ahead, energy-loss problems. However, in problems with deflection, agreement is strongly dependent on the proton energy. That is, good agreement was observed in the few MeV range, while unsatisfactory agreement was observed in problems with proton energies above 100-MeV

A computationally effcient moment-preserving Monte Carlo proton transport method in Geant4

The moment-preserving method, demonstrated as a viable alternative to condensed history for electrons, is extended to protons. Given the generality and the flexibility of the method, a discrete Coulomb scattering and discrete impactionization differential cross-section library for protons was readily developed and existing Geant4 electron discrete process and model classes were extended to make use of the new proton library. It is shown that levels of effciency and accuracy similar to those demonstrated for electrons are obtainable for protons in straight-ahead, energy-loss problems. However, in problems with deflection, agreement is strongly dependent on the proton energy. That is, good agreement was observed in the few MeV range, while unsatisfactory agreement was observed in problems with proton energies above 100-MeV