Multisite Effects Research Articles

Multi-year and multi-site effects of recurrent glyphosate applications on the wheat rhizosphere microbiome

Glyphosate (N-(phosphonomethyl)glycine) is broad-spectrum herbicide that is extensively used worldwide, but its effects on the soil microbiome are inconsistent. To provide a sound scientific basis for herbicide re-review and registration decisions, we conducted a four-year (2013–2016) study in which we consecutively applied glyphosate to a wheat (Triticum aestivum L.)–field pea (Pisum sativum L.)–canola (Brassica napus L.)–wheat crop rotation at five sites in the Canadian prairies. The glyphosate rates were 0, 1, 2, 4 and 8 kg ae ha−1, applied pre-seeding and post-harvest every year. The wheat rhizosphere was sampled in the final year of the study and analysed for microbial biomass C (MBC), the composition and diversity of the microbiome, and activities of β-glucosidase, N-acetyl-β-glucosiminidase, acid phosphomonoesterase and arylsulphatase. Glyphosate did not affect MBC, the composition and diversity of prokaryotes and fungi, and the activities of three of the four enzymes measured in the wheat rhizosphere. The one effect of glyphosate was a wave-like response of N-acetyl-β-glucosaminidase activity with increasing application rates. The experimental sites had much greater effects, driven by soil pH and organic C, on the soil microbiome composition and enzyme activities than glyphosate. Soil pH was positively correlated with the relative abundance of Acidobacteriota but negatively correlated with that of Actinobacteriota and Basidiomycota. Soil organic C was positively correlated with the relative abundances of Proteobacteriota and Verrucomicrobiota, but negatively correlated with the relative abundance of Crenachaeota. The activity of acid phosphomonoesterase declined with increasing relative abundance of Acidobacteriota, but increased with that of Actinobacteriota and Basidiomycota. The activity of N-acetyl-β-glucosaminidase also increased with increasing relative abundance of Actinobacteriota but decreased with that of Mortierellomycota. β-glucosidase activity also decreased with increasing relative abundance of Mortierellomycota. The core fungal species observed in at least 90% of the samples were Humicola nigrescens, Gibberella tricincta and Giberella fujikuroi. Therefore, this multi-site study on the Canadian prairies revealed no significant effects of 4-year applications of glyphosate applied at different rates on most soil microbial properties despite differences in the properties among sites. However, it is important to keep evaluating glyphosate effects on the soil microbiome and its functioning because it is the most widely used herbicide worldwide.

TreeMap: a structured approach to fine mapping of eQTL variants.

MotivationExpression quantitative trait loci (eQTL) harbor genetic variants modulating gene transcription. Fine mapping of regulatory variants at these loci is a daunting task due to the juxtaposition of causal and linked variants at a locus as well as the likelihood of interactions among multiple variants. This problem is exacerbated in genes with multiple cis-acting eQTL, where superimposed effects of adjacent loci further distort the association signals.ResultsWe developed a novel algorithm, TreeMap, that identifies putative causal variants in cis-eQTL accounting for multisite effects and genetic linkage at a locus. Guided by the hierarchical structure of linkage disequilibrium, TreeMap performs an organized search for individual and multiple causal variants. Via extensive simulations, we show that TreeMap detects co-regulating variants more accurately than current methods. Furthermore, its high computational efficiency enables genome-wide analysis of long-range eQTL. We applied TreeMap to GTEx data of brain hippocampus samples and transverse colon samples to search for eQTL in gene bodies and in 4 Mbps gene-flanking regions, discovering numerous distal eQTL. Furthermore, we found concordant distal eQTL that were present in both brain and colon samples, implying long-range regulation of gene expression.Availability and implementationTreeMap is available as an R package enabled for parallel processing at https://github.com/liliulab/treemap.Supplementary information Supplementary data are available at Bioinformatics online.

P4529Atrioventricular optimization in cardiac resynchronization therapy with quadripolarleads, improves energy handling and quality of life in heart failure patients: HUMVEE Trial

Abstract Background Cardiac resynchronization therapy (CRT) is a well-established technique for symptomatic heart failure (HF) patients, producing significant clinical benefits. Recent studies have revealed the potential role of multipoint pacing (MPP) in improving response and clinical outcomes. The aim of Heart failUre study of Multisite pacing effects on VEntriculoartErial coupling (HUMVEE) trial was to evaluate the association between MPP of the left ventricle vs those of standard biventricular pacing (BVP) on: a) ventriculoarterial coupling (VAC) and energy efficiency of the failing heart, b) diastolic function, c) quality of life, and d) NT-proBNP levels. Methods HUMVEE is a single-center, prospective (13 months) trial (clinicaltrials.gov identifier NCT03189368), of 54 NYHA III patients (69±9 years; 79% men; 50% dilated cardiomyopathy), under optimal tolerated medical therapy, with standard BVP indication, having being implanted with a CRT system able to deliver both modes of pacing. Creatinine and NT-proBNP levels and echocardiographic measurements (VAC calculation, strain rate, diastolic function assessment), as well as 6-min-walking-test and quality of life (MLHF questionnaire) were measured at baseline, 6 months post BVP optimization (right before MPP activation) and at the end of follow-up (6 months post MPP optimization). Cardiac power (CP) was calculated according the equation: CP=Cardiac Output x Mean Aortic Pressure/451. Results Both CRT and MPP improved 6-min-walk (differences at baseline/6 mo/end of FU: 277±27 vs. 345±27 vs 363±27 m, p=0.07); left ventricular ejection fraction (24,2% vs 30,6%vs, 32%, p=0.05); end -diastolic diameters of left ventricle (65±1,4 vs. 63±1.7 vs. 61±1.1, p=0.03); end-systolic volume (150±15 vs. 140±10 vs. 131±13, p=0.08); stroke volume (41.6±9 vs. 53.6±14 vs. 62±9, p=0.0001 for MPP); left atrial volume (76±5 vs. 74±10 vs 61±6, p=0.001 for MPP), E/Emv (14±5 vs. 12±4 vs. 11±3, p=0.05 for MPP); NtproBNP (2782±1000 vs. 2080±2500 vs. 2000±1000, p=0.05 for MPP). VAC was reduced from 1.14±0.27 to 1.1±0.17 (p=0.1) while CP increased from 564.2±142 to 768±103 (p=0.009). Quality of life score (the lower the better) improved from 23.75±17 at baseline to 17.25±10 at end of FU (p=0.05). Conclusions MPP is a new, promising pacing modality with the potential to improve HF patients' outcome, offering additive effects on myocardial energy balance, cardiac power, systolic and diastolic ventricular function and aortoventricular coupling, especially in ischemic patients. HUMVEE trial illustrates those clinical, imaging and biochemical divergences of MPP from standard BVP that reflect significant improvement in quality of life in patients with advanced HF and cardiac dysychronization.

Luminescent features in double-track type II waveguides made in Er/Yb:LiNbO3 by Ultrafast Laser Inscription

This work reports the first double-track type II waveguides fabricated by Ultrafast Laser Inscription (ULI) in a z-cut crystal of Er0.5% Yb0.5%LiNbO3. The light-guiding properties were explored and it was found that both polarization modes, TE and TM, are supported at a wavelength of 1550 nm. Also, a thorough spectroscopic characterization of these structures was performed. All luminescence bands of active ions and their corresponding lifetimes were measured and scanning confocal μ-photoluminescence maps were developed. Slight shifts and broadening were found, relative to the bulk, for some specific emission peaks in waveguides. Particularly, Yb3+ ions luminescence within a region up to 2 μm from to where the laser struck during ULI processing, exhibited changes of their positions, heights and widths. The contribution of ULI to the ion environment distortions could be detected by confocal microscopy and could be decoupled from multi-site effects. This procedure can be taken as a quality control tracking of waveguides fabricated by ULI, if one considers variations in micromachining parameters (energy per pulse, speed of writing, repetition rate or pulse duration) as well as in concentration ratios of Er/Yb, or even annealing treatments. Although spectral modifications were resolved, the bulk spectra of these ions are essentially preserved in the waveguide core and surroundings. Therefore, this gives rise to explore these Er/Yb co-doped waveguides as active photonics devices, considering the rich spectra of Er3+ ions: green, red and NIR (1550 nm) emissions and the doping with Yb3+ ions to improve its efficiency.

High-temperature electronic structure with the Korringa-Kohn-Rostoker Green's function method.

Modeling high-temperature (tens or hundreds of eV), dense plasmas is challenging due to the multitude of non-negligible physical effects including significant partial ionization and multisite effects. These effects cause the breakdown or intractability of common methods and approximations used at low temperatures, such as pseudopotentials or plane-wave basis sets. Here we explore the Korringa-Kohn-Rostoker Green's function method at these high-temperature conditions. The method is all electron, does not rely on pseudopotentials, and uses a spherical harmonic basis set, and so avoids the aforementioned limitations. It is found to be accurate for solid density aluminum and iron plasmas when compared to a plane-wave method at low temperature, while being able to access high temperatures.

Statistical power and prediction accuracy in multisite resting-state fMRI connectivity

Connectivity studies using resting-state functional magnetic resonance imaging are increasingly pooling data acquired at multiple sites. While this may allow investigators to speed up recruitment or increase sample size, multisite studies also potentially introduce systematic biases in connectivity measures across sites. In this work, we measure the inter-site effect in connectivity and its impact on our ability to detect individual and group differences. Our study was based on real, as opposed to simulated, multisite fMRI datasets collected in N=345 young, healthy subjects across 8 scanning sites with 3T scanners and heterogeneous scanning protocols, drawn from the 1000 functional connectome project. We first empirically show that typical functional networks were reliably found at the group level in all sites, and that the amplitude of the inter-site effects was small to moderate, with a Cohen's effect size below 0.5 on average across brain connections. We then implemented a series of Monte-Carlo simulations, based on real data, to evaluate the impact of the multisite effects on detection power in statistical tests comparing two groups (with and without the effect) using a general linear model, as well as on the prediction of group labels with a support-vector machine. As a reference, we also implemented the same simulations with fMRI data collected at a single site using an identical sample size. Simulations revealed that using data from heterogeneous sites only slightly decreased our ability to detect changes compared to a monosite study with the GLM, and had a greater impact on prediction accuracy. However, the deleterious effect of multisite data pooling tended to decrease as the total sample size increased, to a point where differences between monosite and multisite simulations were small with N=120 subjects. Taken together, our results support the feasibility of multisite studies in rs-fMRI provided the sample size is large enough.

Transient Current Behavior through Molecular Bridge Systems; Effects of Intra-Molecule Current on Quantum Relaxation and Oscillation

Transient current behavior through two-site molecular bridge systems is studied using density-matrix calculations in order to clarify the multi-site effects in molecule. It is shown that, as increasing the number of energy-level sites in molecule, the relaxation speed becomes slow and the period of current oscillation increases reflecting the change of electronic states in molecule. Moreover, we found that the intra-molecule quantum electron motion often induces a new oscillation and largely modulates the transient current behavior. This motion is also expected seen as a spike-like vibration in steady-state current when a molecule changes its structure such as by the adsorption and desorption of another molecule. [DOI: 10.1380/ejssnt.2009.606]

A fully integrated GIS-based model of particulate waste distribution from marine fish-cage sites

Modern Geographical Information System (GIS) offers a powerful modelling environment capable of handling large databases. It is a very suitable environment in which to develop a suite of tools designed for environmental management of aquaculture sites, including carrying capacity prediction, land–water interactions and multi-site effects. One such tool, presented here, is a fully integrated and validated particulate fish waste dispersion module which uses mass balance to estimate waste input and takes account of variable bathymetry and variable settling velocity for feed and faecal components. The model also incorporates the effect of cage movement on waste dispersion, the first such model to do so. When tidal range was low (1.67 m), the maximum movement of a 22 m diameter circular cage was 10.1 m and 7.7 m easting and northing, respectively. Highest deposition from particulate fish waste is under the cage and incorporation of cage movement increased the effective area under a cage by 72%. This reduced peak deposition measurements by up to 32% and reduced the average modelled feed and faecal settlement at the cage centre by 23% and 11%, respectively. The model was validated by comparing model predictions with observed deposition measured using sediment traps during three 2-week field trips at a fish farm on the west coast of Scotland. The mean ratio of observed to predicted waste deposition at 5–25 m from the cage centre ranged from 0.9 to 1.06, whilst under the cage the model over-predicts deposition (observed/predicted = 2.21). Although far-field data was seen to be comparable the near-field discrepancies resulted in variable overall accuracy in the model. The overall accuracy based on August 2001 data was ± 50.9%, on February 2002, ± 72.8% and on April 2002, ± 50.6%. Summarizing the data resulted in an overall average predictive accuracy of ± 58.1%.

Multisite Effects on Intervalence Charge Transfer in a Clusterlike Trinuclear Assembly Containing Ruthenium and Osmium

The intervalence charge transfer (IVCT) properties of the mixed-valence forms of the diastereoisomers of the dinuclear [[Ru(bpy)2](mu-HAT)[M(bpy)2]]5+ (M = Ru or Os) complexes and the trinuclear heterochiral [[Ru(bpy)2]2[Os(bpy)2](mu-HAT)]n+ (n = 7, 8; HAT = 1,4,5,8,9,12-hexaazatriphenylene; bpy = 2,2'-bipyridine) species display a marked dependence on the nuclearity and extent of oxidation of the assemblies, while small differences are also observed for the diastereoisomers of the same complex in the dinuclear cases. The mixed-valence heterochiral [[Ru(bpy)2]2[Os(bpy)2](mu-HAT)]n+ (n = 7, 8) forms exhibit IVCT properties that are intermediate between those of the diastereoisomeric forms of the localized hetero-dinuclear complex [[Ru(bpy)2](mu-HAT)[Os(bpy)2]]5+ and the borderline localized-to-delocalized homo-trinuclear complex [[Ru(bpy)2]3(mu-HAT)]n+ (n = 7, 8). The near-infrared (NIR) spectrum of the +7 mixed-valence species exhibits both interconfigurational (IC) and IVCT transitions which are quantitatively similar to those in [[Ru(bpy)2](mu-HAT)[Os(bpy)2]]5+ and are indicative of the localized mixed-valence formulation [[Ru(II)(bpy)2]2[Os(III)(bpy)2](mu-HAT)]7+. The +8 state exhibits a new band attributable to an IVCT transition in the near-infrared region.

INHIBITION OF NITRIC OXIDE SYNTHASE ISOFORMS BY IMMUNOSUPPRESSIVE PEPTIDES

527 Peptides derived from the HLA class I heavy chain (aa 75-84) have immunosuppressive properties as documented in several rodent transplantation models. Based on in vivo data and other physicochemical properties of active peptide derivatives, computer modeling and single amino acid substitutions generated a new set of peptides with 100-fold higher immunosuppressive activity. These peptides were shown to modulate heme oxygenase-1 (HO-1) protein and activity levels in a specific manner. Computer modeling further suggested that these peptide may mimic a porphyrin-like structure and may modify, besides HO-1, the activity of other heme enzymes like nitric oxide synthase (NOS). Peptides RDP1258, DRDP1258, D2, D2RP (negative control) and 2702 were analyzed in enzyme activity assays of all three NOS isoforms in vitro - neuronal NOS (nNOS), endothelial NOS (eNOS) and cytokine-inducible NOS (iNOS). Inhibition of enzyme activity was observed in the presence of peptides with the following IC50 values (in µM) obtained. Inhibitory activity also correlated with immunosuppressive activity observed in vivo.Table With affinity-purified iNOS, inhibition by RDP1258 was non-competitive with both arginine (substrate) and tetrahydrobiopterin (co-factor). The inhibition of iNOS by RDP1258 displayed a positive cooperativity as indicated by a Hill coefficient of 1.8. Using affinity-purified nNOS, RDP1258 displayed an even higher degree of cooperativity with a Hill coefficient of 3.7. Both, cytochrome c reductase activity and NADPH oxidase activity of nNOS were inhibited by RDP1258. Addition of RDP1258, DRDP1258 and D2 dramatically increased the concentration of calmodulin necessary to activate nNOS. These observations are compatible with the proposal that inhibition of NOS by these immunosuppressive peptides may be a result of multi-site effects with binding sites present on both NOS and calmodulin. In conclusion, these findings support the hypothesis that the investigated immunosuppressive peptides mimic a porphyrin-like structure that particularly influences HO-1 and NOS and possibly other heme-containing enzymes in its immunomodulatory activity.

An augmented-space recursion in the k-space representation

We present here a technique for the calculation of configurationally averaged quantities in the reciprocal k-space representation, such as the spectral function and complex band structures. We apply the technique to AgPd alloys in conjunction with the tight-binding linearized muffin-tin orbital basis. We also indicate why the same technique is ideal for application to the more accurate screened KKR and allows us to go beyond the single-site coherent potential approximation and include multi-site effects such as short-ranged ordering and local lattice distortions due to size mismatch of the constituent atoms.

Multisites Cr3+ in GGG and GSGG garnets

The emission and excitation spectra of Cr3+ -doped Gd3Ga5O12 (GGG) and Gd3Sc2Ga3O12 (GSGG) are explained in the light of multisite effects. The situation is particularly complicated in the case of GSGG, where the different sites have2E energy levels near each other which overlap with the4A2 →4T2 absorption bands. The spectra obtained under selective excitations are interpreted on the multisite assumption.

Indirect interactions of H/Ni(111) and H/Pd(100) using embedded atom method

Using the embedded atom method (EAM), we computed lateral interactions between H atoms on Ni(111) and on Pd(100). For H/Ni(111) the binding-energy difference between the two 3-fold sites is very small. As expected due to the very small separation, at nearest neighbor sites there is an extreme repulsion. The only other non-negligible interactions are repulsions of comparable size (a few meV) between H pairs at 2nd and 3rd neighbor separations. Energies for ordered patterns are consistent with isolated pairs: multi-site effects are not significant. Zero-point motion weakens the repulsions for isolated pairs but not for ordered overlayers. Local relaxations are minor. There are no anomalous attractions, but interactions are much smaller than expected from experiment, and (2 × 1) ordering is predicted instead of the observed graphitic (2 × 2). Recent extensions of EAM suggest ways to compute more reliable magnitudes. For H/Pd(100) adsorption is predicted in center sites, but slightly below the surface plane rather than above. The interactions have realistic signs and orders of magnitude, but (2 × 1) ordering is predicted rather than the observed c(2 × 2).

Comment Comparison of the fluorescence lifetimes of Cr 3+ in crystals, glasses and glass ceramics and their use to interpret the effect of pressure on ruby

A correlation has been proposed by Urošević Panić Jovanić, Zeković and Savić between the lifetimes of Cr 3+ in various environments and the Dq parameter of ligand field theory. We show that these observed lifetimes depend on various factors such as multisite effects, reabsorption, thermal excitation or 2E 4T 2 mixing. The correlation between lifetimes and pressure on ruby has to consider these different effects.