Structuring of breeding objectives in the pork supply chain in South Africa

Pig production is a techno-scientific internationalized business that is continuously exposed to change and risk. Changes in the Agri-Business are inter alia caused by changes in globalization, information technology, biotechnology and changes in consumer trends. The consumer, within the framework of the pig supply chain, is fundamental to this study. Hence an in depth review of meat market surveys for the period 1970 – 2000 was undertaken. The central theme of the study is: "How to reconcile meat quality, genetics and the consumer with bio-economic pig production in the South African pig supply chain?" A detailed analysis of the South African pig supply chain was subsequently conducted in order to add value further down the supply chain. The inherent structure of the South African pig industry was researched with the emphasis on production statistics, the pig feed industry, genetic improvement and pig information systems, slaughter houses and also slaughtering statistics. The different industry institutions, industry organisations and computer programmes in support of the South African pork supply chain were also investigated. Genetics is the hidden golden thread running through any livestock supply chain. If a substantial portion of consumer satisfaction and quality assurance can be resolved (guaranteed) at the genetic level (thus conception), these guarantees will be conducive to quality assurance further down the supply chain. Carcass and meat quality have become increasingly important in modern day pig production, despite the fact that the emphasis has been too long on input efficiency and too short on output efficiency in South Africa. This called unambiguously for the accurate estimation of genetic parameters of production and carcass traits through appropriate methodology and the right genetic technology. A high degree of accuracy will further optimize the estimation of breeding values, that of breeding objectives and also enhance the credibility of a national breeding scheme. Genetic parameters for five carcass traits were successfully estimated for the first time in the history of South African pig breeding. In future, breeding values for carcass traits, can now be determined more accurately for the Large White, Landrace and Duroc pig breeds. Extension of the present carcass evaluation analysis (Phase E of the National Pig Performance Testing Scheme) to incorporate the essential meat quality traits such as pHu, marbling, tenderness and colour into future breeding goals should eventually satisfy the consumer. In order to finally progress from an immature to a mature pig supply chain, pig producers must align themselves with value partners on both the input (raw materials) and output (end product and value added products) end of the supply chain. To embrace the concept of quality (a consumer demand principle) all levels in the production chain (at the genetic level through the breeding objectives, at the farm level through the entire production system, in transit and at the slaughterhouse and processing levels) should be integrated.Thesis (DPhil (Agricultural Economics))--University of Pretoria, 2006.Agricultural Economics, Extension and Rural Developmentunrestricte

Resolving Power of Visible to Near-Infrared Hybrid β\beta-Ta/NbTiN Kinetic Inductance Detectors

Kinetic Inductance Detectors (KIDs) are superconducting energy-resolving detectors, sensitive to single photons from the near-infrared to ultraviolet. We study a hybrid KID design consisting of a beta phase tantalum ($\beta$-Ta) inductor and a NbTiN interdigitated capacitor (IDC). The devices show an average intrinsic quality factor $Q_i$ of 4.3$\times10^5$ $\pm$ 1.3 $\times10^5$. To increase the power captured by the light sensitive inductor, we 3D-print an array of 150$\times$150 $\mu$m resin micro lenses on the backside of the sapphire substrate. The shape deviation between design and printed lenses is smaller than 1$\mu$m, and the alignment accuracy of this process is $\delta_x = +5.8 \pm 0.5$ $\mu$m and $\delta_y = +8.3 \pm 3.3$ $\mu$m. We measure a resolving power for 1545-402 nm that is limited to 4.9 by saturation in the KID's phase response. We can model the saturation in the phase response with the evolution of the number of quasiparticles generated by a photon event. An alternative coordinate system that has a linear response raises the resolving power to 5.9 at 402 nm. We verify the measured resolving power with a two-line measurement using a laser source and a monochromator. We discuss several improvements that can be made to the devices on a route towards KID arrays with high resolving powers.Comment: 11 pages, 9 Figues, Journal Pape

Genome-Wide Association Study of Alzheimer's Disease Brain Imaging Biomarkers and Neuropsychological Phenotypes in the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery Dataset

Alzheimer's disease (AD) is the most frequent neurodegenerative disease with an increasing prevalence in industrialized, aging populations. AD susceptibility has an established genetic basis which has been the focus of a large number of genome-wide association studies (GWAS) published over the last decade. Most of these GWAS used dichotomized clinical diagnostic status, i.e., case vs. control classification, as outcome phenotypes, without the use of biomarkers. An alternative and potentially more powerful study design is afforded by using quantitative AD-related phenotypes as GWAS outcome traits, an analysis paradigm that we followed in this work. Specifically, we utilized genotype and phenotype data from n = 931 individuals collected under the auspices of the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery (EMIF-AD MBD) study to perform a total of 19 separate GWAS analyses. As outcomes we used five magnetic resonance imaging (MRI) traits and seven cognitive performance traits. For the latter, longitudinal data from at least two timepoints were available in addition to cross-sectional assessments at baseline. Our GWAS analyses revealed several genome-wide significant associations for the neuropsychological performance measures, in particular those assayed longitudinally. Among the most noteworthy signals were associations in or near EHBP1 (EH domain binding protein 1; on chromosome 2p15) and CEP112 (centrosomal protein 112; 17q24.1) with delayed recall as well as SMOC2 (SPARC related modular calcium binding 2; 6p27) with immediate recall in a memory performance test. On the X chromosome, which is often excluded in other GWAS, we identified a genome-wide significant signal near IL1RAPL1 (interleukin 1 receptor accessory protein like 1; Xp21.3). While polygenic score (PGS) analyses showed the expected strong associations with SNPs highlighted in relevant previous GWAS on hippocampal volume and cognitive function, they did not show noteworthy associations with recent AD risk GWAS findings. In summary, our study highlights the power of using quantitative endophenotypes as outcome traits in AD-related GWAS analyses and nominates several new loci not previously implicated in cognitive decline

Signal contents of combined monthly gravity field models derived from Swarm GPS data

The Swarm satellite constellation?s GPS receivers provide valuable gravimetric data, with which it is possible to observe Earth?s large-scale mass transport process. These data have become increasingly relevant given the on-going GRACE/GRACE-FO gap, and are thus needed to provide continuous observations of the Earth system. In this context, the overall accuracy and maximum resolution of the Swarm temporal gravity field models are parameters with interest to the wider geophysical community. We assess the signal contents of the gravity field model resulting from the combination at the solution level of four individual solutions produced considering different gravity field estimation approaches. The combination considers Variance Component Estimation (VCE) and is a service kindly provided by the European Gravity Service for Improved Emergency Management (EGSIEM) initiative. We assume that past GRACE solutions provide an accurate measure of the signal at the spatial lengths captured by the Swarm solutions. On the basis of this, we derive per-degree correlation coefficients and spatial correlation maps for a selection of monthly solutions that were obtained under diverse conditions of geomagnetic and ionospheric activities, as well as variability of non-gravitational accelerations

Dickkopf-1 Overexpression in vitro Nominates Candidate Blood Biomarkers Relating to Alzheimer's Disease Pathology

Previous studies suggest that Dickkopf-1 (DKK1), an inhibitor of Wnt signaling, plays a role in amyloid-induced toxicity and hence Alzheimer's disease (AD). However, the effect of DKK1 expression on protein expression, and whether such proteins are altered in disease, is unknown. We aim to test whether DKK1 induced protein signature obtained in vitro were associated with markers of AD pathology as used in the amyloid/tau/neurodegeneration (ATN) framework as well as with clinical outcomes. We first overexpressed DKK1 in HEK293A cells and quantified 1,128 proteins in cell lysates using aptamer capture arrays (SomaScan) to obtain a protein signature induced by DKK1. We then used the same assay to measure the DKK1-signature proteins in human plasma in two large cohorts, EMIF (n = 785) and ANM (n = 677). We identified a 100-protein signature induced by DKK1 in vitro. Subsets of proteins, along with age and apolipoprotein E ɛ 4 genotype distinguished amyloid pathology (A + T-N-, A+T+N-, A+T-N+, and A+T+N+) from no AD pathology (A-T-N-) with an area under the curve of 0.72, 0.81, 0.88, and 0.85, respectively. Furthermore, we found that some signature proteins (e.g., Complement C3 and albumin) were associated with cognitive score and AD diagnosis in both cohorts. Our results add further evidence for a role of DKK regulation of Wnt signaling in AD and suggest that DKK1 induced signature proteins obtained in vitro could reflect theATNframework as well as predict disease severity and progression in vivo

A metabolite-based machine learning approach to diagnose Alzheimer’s-type dementia in blood: Results from the European Medical Information Framework for Alzheimer's Disease biomarker discovery cohort

INTRODUCTION: Machine learning (ML) may harbor the potential to capture the metabolic complexity in Alzheimer’s Disease (AD). Here we set out to test the performance of metabolites in blood to categorise AD when compared to CSF biomarkers. METHODS: This study analysed samples from 242 cognitively normal (CN) people and 115 with AD-type dementia utilizing plasma metabolites (n=883). Deep Learning (DL), Extreme Gradient Boosting (XGBoost) and Random Forest (RF) were used to differentiate AD from CN. These models were internally validated using Nested Cross Validation (NCV). RESULTS: On the test data, DL produced the AUC of 0.85 (0.80-0.89), XGBoost produced 0.88 (0.86-0.89) and RF produced 0.85 (0.83-0.87). By comparison, CSF measures of amyloid, p-tau and t-tau (together with age and gender) produced with XGBoost the AUC values of 0.78, 0.83 and 0.87, respectively. DISCUSSION: This study showed that plasma metabolites have the potential to match the AUC of well-established AD CSF biomarkers in a relatively small cohort. Further studies in independent cohorts are needed to validate whether this specific panel of blood metabolites can separate AD from controls, and how specific it is for AD as compared with other neurodegenerative disorders

Genome-wide meta-analysis for Alzheimer's disease cerebrospinal fluid biomarkers

Amyloid-beta 42 (A beta 42) and phosphorylated tau (pTau) levels in cerebrospinal fluid (CSF) reflect core features of the pathogenesis of Alzheimer's disease (AD) more directly than clinical diagnosis. Initiated by the European Alzheimer & Dementia Biobank (EADB), the largest collaborative effort on genetics underlying CSF biomarkers was established, including 31 cohorts with a total of 13,116 individuals (discovery n = 8074; replication n = 5042 individuals). Besides the APOE locus, novel associations with two other well-established AD risk loci were observed; CR1 was shown a locus for A beta 42 and BIN1 for pTau. GMNC and C16orf95 were further identified as loci for pTau, of which the latter is novel. Clustering methods exploring the influence of all known AD risk loci on the CSF protein levels, revealed 4 biological categories suggesting multiple A beta 42 and pTau related biological pathways involved in the etiology of AD. In functional follow-up analyses, GMNC and C16orf95 both associated with lateral ventricular volume, implying an overlap in genetic etiology for tau levels and brain ventricular volume.Peer reviewe

MICROSCOPE mission: first results of a space test of the equivalence principle

According to the weak equivalence principle, all bodies should fall at the same rate in a gravitational field. The MICROSCOPE satellite, launched in April 2016, aims to test its validity at the 10−15 precision level, by measuring the force required to maintain two test masses (of titanium and platinum alloys) exactly in the same orbit. A nonvanishing result would correspond to a violation of the equivalence principle, or to the discovery of a new long-range force. Analysis of the first data gives δ(Ti,Pt)=[−1±9(stat)±9(syst)]×10−15 (1σ statistical uncertainty) for the titanium-platinum Eötvös parameter characterizing the relative difference in their free-fall accelerations

Cerebral small vessel disease genomics and its implications across the lifespan

White matter hyperintensities (WMH) are the most common brain-imaging feature of cerebral small vessel disease (SVD), hypertension being the main known risk factor. Here, we identify 27 genome-wide loci for WMH-volume in a cohort of 50,970 older individuals, accounting for modification/confounding by hypertension. Aggregated WMH risk variants were associated with altered white matter integrity (p = 2.5×10-7) in brain images from 1,738 young healthy adults, providing insight into the lifetime impact of SVD genetic risk. Mendelian randomization suggested causal association of increasing WMH-volume with stroke, Alzheimer-type dementia, and of increasing blood pressure (BP) with larger WMH-volume, notably also in persons without clinical hypertension. Transcriptome-wide colocalization analyses showed association of WMH-volume with expression of 39 genes, of which four encode known drug targets. Finally, we provide insight into BP-independent biological pathways underlying SVD and suggest potential for genetic stratification of high-risk individuals and for genetically-informed prioritization of drug targets for prevention trials.Peer reviewe

Altimetry for the future: Building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the ‘‘Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion