An R Package to Compute the Energy Balance for Ruminants under Both Grazing and Pen-Fed Conditions

Grassland degradation is a serious environmental problem around the world, with off-site impacts of soil erosion affecting wider communities beyond those engaging in livestock farming (Kemp and Michalk, 2007). In order to operationalise an alternative farming system that is beneficial to both producers and the ecological environment, the energy and nutritional demands for animal production must be met, either through grassland production, supplementary feeding or the combination of the two, in an efficient manner (Kemp et al., 2013). The use of specialized biophysical models to estimate the energy balance of livestock is a well-proven solution to find such an economically efficient yet environmentally friendly production system. However, the initial cost borne by the user is known to be high, in terms of the financial outlay as well as the learning time. The objective of the present paper is to introduce a newly developed tool to compute the energy balance of ruminants under both grazing and pen-fed conditions. The proposed tool takes the form of a publicly available package to be loaded onto the R platform (R Core Team, 2015). Because this platform is open-source, there is no acquisition cost associated to the introduction of the package. In addition, the high penetration rate of the platform, especially in developing regions that are amongst the most susceptible to grassland degradation, makes the learning cost of the package significantly lower than that of typical specialized software

Quantifying the Economic Value of Evidence-Based Animal Selection on the inner Mongolian Desert Steppe

Inner Mongolian desert steppe in northwestern China suffers from significant grassland degradation, causing a decrease in producers\u27 income as well as negative off-site impacts (Kemp et al., 2013). Recent studies attribute this problem to a sudden increase in the stocking rate over the last half century, and thus development of an alternative farming system to reduce the animal number is urgently needed (Wang et al., 2011). Scientific experiments and modelling analyses have shown the potential of innovative systems that could deliver a win-win solution to local producers and environment (Li et al., 2015). However, the uptake of the proposed new technologies is generally slow because of the scepticism amongst producers, which is often augmented by the traditional herding culture whereby a large flock of animals is a symbol of social success (Kemp and Michalk, 2007). The objective of the present paper is to quantify the economic value of evidenced-based ewe selection, vis-à-vis random selection, the former of which could reduce the negative economic impact to producers due to the reduced stocking rate or, in some cases, even improve their long-term income (Kemp et al., 2011). A particular attention is paid to the carryover effect of an ewe\u27s body condition at an early stage of pregnancy on her lamb\u27s bodyweight at the annual sales time, a relationship relatively understudied in the preceding literature. Because lambs\u27 bodyweight is the most closely linked to economic benefits enjoyed by local producers specializing in meat production, a positive result from this study would be valuable information to convince them to adopt an alternative farming strategy

Reducing Residual-Mass Effects for Domain-Wall Fermions

It has been suggested to project out a number of low-lying eigenvalues of the four-dimensional Wilson--Dirac operator that generates the transfer matrix of domain-wall fermions in order to improve simulations with domain-wall fermions. We investigate how this projection method reduces the residual chiral symmetry-breaking effects for a finite extent of the extra dimension. We use the standard Wilson as well as the renormalization--group--improved gauge action. In both cases we find a substantially reduced residual mass when the projection method is employed. In addition, the large fluctuations in this quantity disappear.Comment: 18 pages, 10 figures, references updated, comments adde

A multi-decade record of high quality fCO2 data in version 3 of the Surface Ocean CO2 Atlas (SOCAT)

The Surface Ocean CO2 Atlas (SOCAT) is a synthesis of quality-controlled fCO2 (fugacity of carbon dioxide) values for the global surface oceans and coastal seas with regular updates. Version 3 of SOCAT has 14.7 million fCO2 values from 3646 data sets covering the years 1957 to 2014. This latest version has an additional 4.6 million fCO2 values relative to version 2 and extends the record from 2011 to 2014. Version 3 also significantly increases the data availability for 2005 to 2013. SOCAT has an average of approximately 1.2 million surface water fCO2 values per year for the years 2006 to 2012. Quality and documentation of the data has improved. A new feature is the data set quality control (QC) flag of E for data from alternative sensors and platforms. The accuracy of surface water fCO2 has been defined for all data set QC flags. Automated range checking has been carried out for all data sets during their upload into SOCAT. The upgrade of the interactive Data Set Viewer (previously known as the Cruise Data Viewer) allows better interrogation of the SOCAT data collection and rapid creation of high-quality figures for scientific presentations. Automated data upload has been launched for version 4 and will enable more frequent SOCAT releases in the future. High-profile scientific applications of SOCAT include quantification of the ocean sink for atmospheric carbon dioxide and its long-term variation, detection of ocean acidification, as well as evaluation of coupled-climate and ocean-only biogeochemical models. Users of SOCAT data products are urged to acknowledge the contribution of data providers, as stated in the SOCAT Fair Data Use Statement. This ESSD (Earth System Science Data) “living data” publication documents the methods and data sets used for the assembly of this new version of the SOCAT data collection and compares these with those used for earlier versions of the data collection (Pfeil et al., 2013; Sabine et al., 2013; Bakker et al., 2014). Individual data set files, included in the synthesis product, can be downloaded here: doi:10.1594/PANGAEA.849770. The gridded products are available here: doi:10.3334/CDIAC/OTG.SOCAT_V3_GRID

Priorities for mitigating greenhouse gas and ammonia emissions to meet UK policy targets

Agriculture is essential for providing food and maintaining food security while concurrently delivering multiple other ecosystem services. However, agricultural systems are generally a net source of greenhouse gases and ammonia. They, therefore, need to substantively contribute to climate change mitigation and net zero ambitions. It is widely acknowledged that there is a need to further reduce and mitigate emissions across sectors, including agriculture to address the climate emergency and emissions gap. This discussion paper outlines a collation of opinions from a range of experts within agricultural research and advisory roles following a greenhouse gas and ammonia emission mitigation workshop held in the UK in March 2022. The meeting identified the top mitigation priorities within the UK’s agricultural sector to achieve reductions in greenhouse gases and ammonia that are compatible with policy targets. In addition, experts provided an overview of what they believe are the key knowledge gaps, future opportunities and co-benefits to mitigation practices as well as indicating the potential barriers to uptake for mitigation scenarios discussed

Analysis of Transcriptional Regulatory Pathways of Photoreceptor Genes by Expression Profiling of the Otx2-Deficient Retina

In the vertebrate retina, the Otx2 transcription factor plays a crucial role in the cell fate determination of both rod and cone photoreceptors. We previously reported that Otx2 conditional knockout (CKO) mice exhibited a total absence of rods and cones in the retina due to their cell fate conversion to amacrine-like cells. In order to investigate the entire transcriptome of the Otx2 CKO retina, we compared expression profile of Otx2 CKO and wild-type retinas at P1 and P12 using microarray. We observed that expression of 101- and 1049-probe sets significantly decreased in the Otx2 CKO retina at P1 and P12, respectively, whereas, expression of 3- and 4149-probe sets increased at P1 and P12, respectively. We found that expression of genes encoding transcription factors involved in photoreceptor development, including Crx, Nrl, Nr2e3, Esrrb, and NeuroD, was markedly down-regulated in the Otx2 CKO at both P1 and P12. Furthermore, we identified three human retinal disease loci mapped in close proximity to certain down-regulated genes in the Otx2 CKO retina including Ccdc126, Tnfsf13 and Pitpnm1, suggesting that these genes are possibly responsible for these diseases. These transcriptome data sets of the Otx2 CKO retina provide a resource on developing rods and cones to further understand the molecular mechanisms underlying photoreceptor development, function and disease

Confinement, chiral symmetry, and the lattice

Two crucial properties of QCD, confinement and chiral symmetry breaking, cannot be understood within the context of conventional Feynman perturbation theory. Non-perturbative phenomena enter the theory in a fundamental way at both the classical and quantum level. Over the years a coherent qualitative picture of the interplay between chiral symmetry, quantum mechanical anomalies, and the lattice has emerged and is reviewed here.Comment: 126 pages, 36 figures. Revision corrects additional typos and renumbers equations to be more consistent with the published versio

Greenhouse gas and ammonia emission mitigation priorities for UK policy targets

Publication history: Accepted - 16 March 2023; Published online - 6th May 2023.Agriculture is essential for providing food and maintaining food security while concurrently delivering multiple other ecosystem services. However, agricultural systems are generally a net source of greenhouse gases and ammonia. They, therefore, need to substantively contribute to climate change mitigation and net zero ambitions. It is widely acknowledged that there is a need to further reduce and mitigate emissions across sectors, including agriculture to address the climate emergency and emissions gap. This discussion paper outlines a collation of opinions from a range of experts within agricultural research and advisory roles following a greenhouse gas and ammonia emission mitigation workshop held in the UK in March 2022. The meeting identified the top mitigation priorities within the UK’s agricultural sector to achieve reductions in greenhouse gases and ammonia that are compatible with policy targets. In addition, experts provided an overview of what they believe are the key knowledge gaps, future opportunities and co-benefits to mitigation practices as well as indicating the potential barriers to uptake for mitigation scenarios discussed.This work was supported with funding from the Scottish Government Strategic Research Programme (2022−2027, C2-1 SRUC) and Biotechnology and Biological Sciences Research Council (BBSRC) (BBS/E/C/000I0320 and BBS/E/C/000I0330). We also acknowledge support from UKRI-BBSRC (UK Research and Innovation-Biotechnology and Biological Sciences Research Council) via grants BBS/E/C/000I0320 and BBS/E/C/000I0330, and Rothamsted Research Science Initiative Catalyst Award supported by BBSRC

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.Peer reviewe