Using statistical process control methods to improve herd performance.

Statistical process control (SPC) is a set of analytic methods that uses the theory of variation as a means of explaining with statistical certainty when process performance is improving, staying the same, or getting worse. SPC techniques have been used successfully for 80 years in manufacturing as a quality management tool. It is apparent that these techniques can be applied equally well to livestock production systems. The availability of large amounts of automatically collected data, the advances in computer capability, and the obvious need for more timely fact-based information for day-to-day management make SPC application the next step in improving herd management quality.     

Comparative evaluation of positive tests to Mycobacterium avium subsp. paratuberculosis in clinically healthy sheep and goats in south-west Greece using molecular techniques, serology, and culture

Mycobacterium avium subsp. paratuberculosis (MAP) is the cause of paratuberculosis, which affects mainly ruminants although there is a growing concern about its possible implication in Crohn's disease in humans especially in connection with environmental spread and risks to the food chain. Retail cheese may represent a significant source of human exposure to MAP and the aim of this study was to assess MAP status in clinically healthy sheep and goats in Greece, comparing techniques routinely used in the positive diagnosis of the disease. From a total of 30 flocks, 632 sheep and goats had faecal, serum, and whole-blood samples examined by culture, complement fixation test (CFT), and polymerase chain reaction (PCR) targeted at IS900, IS1245, and IS6110. PCR produced positive results in 21% of the animals tested, with 5.6%, 3.9%, and 11.5% being identified as MAP, Mycobacterium avium subsp. avium, and Mycobacterium tuberculosis complex, respectively. CFT produced positive and suspicious results in 4.4% and 14.4% of the cases. Faecal cultures were negative in all but a single case that was identified as restriction fragment length polymorphism (RFLP)-type BC1. Agreement between results obtained by PCR and CFT was poor with isolated cases although an assessment of the MAP positive tests produced similar results for both methods. The findings indicate the need for additional measures of control, although the costs may be substantial if public health protection justifies elimination of MAP from livestock.     

Optimal Estimation Versus MCMC for $$\mathrm{{CO}}_{2}$$ Retrievals

The Orbiting Carbon Observatory-2 (OCO-2) collects infrared spectra from which atmospheric properties are retrieved. OCO-2 operational data processing uses optimal estimation (OE), a state-of-the-art approach to inference of atmospheric properties from satellite measurements. One of the main advantages of the OE approach is computational efficiency, but it only characterizes the first two moments of the posterior distribution of interest. Here we obtain samples from the posterior using a Markov Chain Monte Carlo (MCMC) algorithm and compare this empirical estimate of the true posterior to the OE results. We focus on 600 simulated soundings that represent the variability of physical conditions encountered by OCO-2 between November 2014 and January 2016. We treat the two retrieval methods as ensemble and density probabilistic forecasts, where the MCMC yields an ensemble from the posterior and the OE retrieval result provide the first two moments of a normal distribution. To compare these methods, we apply both univariate and multivariate diagnostic tools and proper scoring rules. The general impression from our study is that when compared to MCMC, the OE retrieval performs reasonably well for the main quantity of interest, the column-averaged \(\mathrm{{CO}}_{2}\) concentration \(X_{\mathrm{{CO}}_{2}}\), but not for the full state vector \(\mathbf {X}\) which includes a profile of \(\mathrm{{CO}}_{2}\) concentrations over 20 pressure levels, as well as several other atmospheric properties.Supplementary materials accompanying this paper appear on-line.     

Interaction of minerals,organic matter,and microorganisms during biogeochemical interface formation as shown by a series of artificial soil experiments

Our understanding of the interactions between minerals, organic matter, and microorganisms at so-called biogeochemical interfaces in soil is still hampered by the inherent complexity of these systems. Artificial soil maturation experiments can help to bridge a gap in complexity between simple abiotic sorption experiments and larger-scale field experiments. By controlling other soil-forming factors, the effect of a particular variable can be identified in a simplified system. Here, we review the findings of a series of artificial soil incubation experiments with the aim of revealing general trends and conclusions. The artificial soils were designed to determine the effect of mineral composition and charcoal presence on the development of abiotic and biotic soil properties during maturation. In particular, the development of soil aggregates, organic matter (OM) composition and turnover, sorption properties, and the establishment of microbial community composition and function were considered. The main objectives of the research were to determine (1) how surface properties and sorption of chemicals modify biogeochemical interfaces; (2) how much time is required to form aggregates from mixtures of pure minerals, OM, and a microbial inoculum; and (3) how the presence of different mineral and charcoal surfaces affects aggregation, OM turnover, and the development of microbial community composition.     

Impact of climate and lithology on soil phytolith-occluded carbon accumulation in eastern China

Purpose

Occlusion of carbon (C) within phytoliths, biogenic silica deposited in plant tissues and returned to the soil, is an important mechanism for long-term terrestrial biogeochemical C sequestration and might play a significant role in mitigating climate change.

Materials and methods

Subtropical and tropical soil profiles (to 100 cm depth) developed on granite and basalt were sampled using a mass-balance approach to explore the influence of climate and lithology on soil phytolith-occluded carbon (PhytOC) accumulation.

Results and discussion

Soil PhytOC storage in the subtropics was significantly greater than in the tropics, with the soil profiles developed on granite storing greater PhytOC than soils derived on basalt. Phytolith and PhytOC content decreased with depth in all soil profiles. Phytolith content showed a positive correlation with the soil bio-available silicon in the soil profiles developed on basalt, while a negative correlation was observed in soil profiles developed on granite.

Conclusions

Climate and lithology have a significant impact on soil PhytOC sequestration. The management of forests (e.g., afforestation and reforestation) and external silicon amendments (e.g., basalt powder amendment) in soils, especially those developed on granite, have the potential to enhance PhytOC accumulation in forest ecosystems.

     

Sugarcane bagasse biochars impact respiration and greenhouse gas emissions from a latosol

Purpose

A paucity in knowledge remains on the influence of biochar production temperature and the rate of application on greenhouse gas emissions from soil. The objective of this column experiment was to evaluate a biochar thermosequence by doses on CO₂, N₂O, and CH₄ emissions from a latosol following nitrogen fertilizer application following a pre-incubation period.

Materials and methods

Biochar was produced from sugarcane bagasse pyrolyzed at 300, 500, and 700 °C (BC 300, BC 500, and BC 700, respectively). Biochars were added to air-dried latosol columns at rates of 0, 0.5, 1, 2, 5, 10, and 15 % (w/w), and the water content was brought to 95 % of water-filled pore space (WFPS). The emissions from columns were tested on days 1, 3, 7, 15, and 30 following a 30-day pre-incubation.

Results and discussion

All treatments showed a decrease in respiration across the study period. The higher doses of biochar of BC 300 and BC 700 resulted in significantly higher respiration than controls on days 15 and 30. Neither biochar dose nor temperature had a significant effect on CH₄ emissions during the study period. Application of all biochars suppressed the emissions of N₂O at all doses on days 1 and 3, compared to the control. N₂O emissions from higher temperature biochar-amended soil at 2, 5, 10, and 15 % were greater than that from corresponding treatments of lower-temperature biochar-amended soil on days 15 and 30.

Conclusions

Soil respiration and overall greenhouse gas emission from latosol increased with biochar dose and pyrolysis temperature in the 30-day study period due to increasing water retention facilitated by biochar. Careful consideration is needed when applying bagasse biochar as it changes N cycling and soil physical properties.

     

Does closure of traditionally managed open woodlands threaten epigeic invertebrates? Effects of coppicing and high deer densities

The demise of traditional woodland management techniques, such as coppicing or woodland pasture, is causing a gradual closure of formerly sparse lowland woods across Central Europe. It is established that these processes threaten such organisms as butterflies and higher plants. Effects on other groups, such as epigeic invertebrates, are little known, hindering rational conservation decisions. We investigated the effects of stand openness on three epigeic groups, carabids (Carabidae), arachnids (Araneae + Opiliones) and myriapods-isopods (Chilopoda + Diplopoda + Oniscidea), in a lowland deciduous wood in the Czech Republic. Situating some of the traps in an intensive deer park allowed a simultaneous assessment of effects of high vs. low ungulate densities. Carabids reached the highest species richness in either sparse stands with low game or dense stands, high game. More arachnids occurred under low game and in sparse stands than under high game density and in dense stands. The highest richness of myriapods-isopods was in sparse stands with low game. Ordinations revealed that species of conservation concern (‘relic species’ according to C. European authors) tended to be associated with sparse stands and low game. A considerable proportion of epigeic woodland invertebrates, including many species of conservation concern, depends on preserving highly heterogeneous sparse canopy conditions. Restoring such conditions in selected areas will benefit these sensitive open woodland specialists while causing minimum harm to specialists of dense stands, that likely prosper in commercially managed high forests.     

Proanthocyanidins: target compounds as antibacterial agents

Grape seeds accumulate in huge quantities as byproduct during wine production and are therefore a cheap source for pharmacologically active agents. However, studies prove poor antibacterial activity, and results of analyses are sometimes contradictory. The aim of this study was, thus, to determine the antibacterial activity of grape seed extracts with special focus on the chromatographic characterization of active fractions. In the course of these investigations, extraction protocols were optimized so that microwave-assisted extraction (MAE) guaranteed highest preconcentration efficiency. Proanthocyanidins, monomeric flavonoid aglycones, as well as some of their glycosides could be identified within yielded extracts via high-performance liquid chromatography-mass spectrometry (HPLC-MS). By that means the coherence number of possible isomers of procyanidins was approximated by a newly developed equation. As far as antibacterial activity determined via screening tests is concerned, the extracts generally have been found to be positively responsive toward 10 different gram-positive and gram-negative bacteria strains. After fractionation of the raw extracts, proanthocyanidins P2, P3, P4 and gallate esters P2G and P3G (P = proanthocyanidin consisting of catechin and epicatechin units, n = oligomerization degree, G = gallate ester) were determined as active antibacterial agents toward 10 different pathogens. Only moderate activity was found for monomeric flavonoid fractions.     

Modelling the effects of alcohol ethoxylates on diffusion of pesticides in the cuticular wax of Chenopodium album leaves

Cuticular waxes represent the first and, in most cases, the limiting barrier for foliar uptake of pesticides from solution. Sorption of pesticides in reconstituted cuticular wax (wax/water partition coefficients) of Chenopodium album L. and in isolated cuticular membranes (cuticle/water partition coefficients) of Prunus laurocerasus L. was determined. Diffusion coefficients of pesticides in reconstituted cuticular wax of C. album leaves were size-dependent, increasing with increasing molar volume. In the presence of alcohol ethoxylates, diffusion coefficients were enhanced by up to two orders of magnitude, and size selectivity was significantly decreased. The accelerating effect and the decrease in size selectivity were attributed to plasticisation of the cuticular wax by the alcohol ethoxylates increasing the fluidity in the wax. A free volume model adopted from polymer science was successfully applied to predict diffusion coefficients of pesticides on the basis of the transport properties of the wax (size selectivity and crystallinity), the molar volume of the diffusing compound and the accelerator concentration in the wax.     

Trends and change points in surface and bottom thermal environments of the US Northeast Continental Shelf Ecosystem

Temperature is an important factor in defining the habitats of marine resource species. While satellite sensors operationally measure ocean surface temperatures, we depend on in situ measurements to characterize benthic habitats. Ship‐based measurements were interpolated to develop a time series of gridded spring and fall, surface and bottom temperature fields for the US Northeast Shelf. Surface and bottom temperatures have increased over the study period (1968–2018) at rates between 0.18–0.31°C per decade and over a shorter time period (2004–2018) at rates between 0.26–1.49°C per decade. A change point analysis suggests that a warming regime began in the surface waters in 2011 centered on Georges Bank and the Nantucket Shoals; in following years, most of the Northeast Shelf had experienced a shift in surface temperature. A similar analysis of bottom temperature suggests a warming regime began in 2008 in the eastern Gulf of Maine; in following years, change points in temperature occurred further to the west in the Gulf of Maine, finally reaching the Middle Atlantic Bight by 2010. The spatial pattern in bottom water warming is consistent with well‐known oceanographic patterns that advect warming North Atlantic waters into the Gulf of Maine. The varying spatial and temporal progression of warming in the two layers suggests they were actuated by different sets of forcing factors. We then compared these trends and change points to responses of lower and higher trophic level organisms and identified a number of coincident shifts in distribution and biomass of key forage and fisheries species.