Reliability of operational data from pig herds and performance ratings by veterinarians and pig farmers collected during telephone interviews for the evaluation of a PCV2 piglet vaccination

BackgroundThe aim of the present study was to evaluate the feasibility of using a telephone survey in gaining an understanding of the possible herd and management factors influencing the performance (i.e. safety and efficacy) of a vaccine against porcine circovirus type 2 (PCV2) in a large number of herds and to estimate customers¿ satisfaction.ResultsDatasets from 227 pig herds that currently applied or have applied a PCV2 vaccine were analysed. Since 1-, 2- and 3-site production systems were surveyed, the herds were allocated in one of two subsets, where only applicable variables out of 180 were analysed. Group 1 was comprised of herds with sows, suckling pigs and nursery pigs, whereas herds in Group 2 in all cases kept fattening pigs. Overall 14 variables evaluating the subjective satisfaction with one particular PCV2 vaccine were comingled to an abstract dependent variable for further models, which was characterized by a binary outcome from a cluster analysis: good/excellent satisfaction (green cluster) and moderate satisfaction (red cluster). The other 166 variables comprised information about diagnostics, vaccination, housing, management, were considered as independent variables. In Group 1, herds using the vaccine due to recognised PCV2 related health problems (wasting, mortality or porcine dermatitis and nephropathy syndrome) had a 2.4-fold increased chance (1/OR) of belonging to the green cluster. In the final model for Group 1, the diagnosis of diseases other than PCV2, the reason for vaccine administration being other than PCV2-associated diseases and using a single injection of iron had significant influence on allocating into the green cluster (P¿<¿0.05). In Group 2, only unchanged time or delay of time of vaccination influenced the satisfaction (P¿<¿0.05).ConclusionThe methodology and statistical approach used in this study were feasible to scientifically assess ¿satisfaction¿, and to determine factors influencing farmers¿ and vets¿ opinion about the safety and efficacy of a new vaccine.

Evolution of methicillin-resistant Staphylococcus aureus (MRSA)

In 2009, a monitoring survey on the prevalence and genetic diversity of methicillin-resistant Staphylococcus aureus (MRSA) in slaughter pigs in Switzerland was started and revealed the presence of an unusual Multi Locus Sequence Type (ST49), which was detected for the first time in slaughter pigs worldwide. In addition to ST49, pigs also harboured ST398 and ST1. The prevalence of MRSA in slaughter pigs in Switzerland increased from 2.0% (95%CI 0.9-3.9) in 2009 to 5.9% (95% CI 3.8-8.7) in 2010, and remained stable in 2011 with 5,6% (95% CI 3.6-8.4). The increase was mainly due to the spread of ST398-t034, whereas ST49 was less frequently detected in 2010 and 2011. The presence of a specific sequence type (ST49) in MRSA from Switzerland suggests that it has been selected in local pig husbandry. However, MRSA of this lineage seems to have a lower potential for dissemination than ST398, which is increasingly detected in Swissslaughter pigs.

8p23 beta-defensin copy number determination by single-locus pseudogene-based paralog ratio tests risk bias due to low-frequency sequence variations.

BACKGROUND The copy number variation (CNV) in beta-defensin genes (DEFB) on human chromosome 8p23 has been proposed to contribute to the phenotypic differences in inflammatory diseases. However, determination of exact DEFB CN is a major challenge in association studies. Quantitative real-time PCR (qPCR), paralog ratio tests (PRT) and multiplex ligation-dependent probe amplification (MLPA) have been extensively used to determine DEFB CN in different laboratories, but inter-method inconsistencies were observed frequently. In this study we asked which one is superior among the three methods for DEFB CN determination. RESULTS We developed a clustering approach for MLPA and PRT to statistically correlate data from a single experiment. Then we compared qPCR, a newly designed PRT and MLPA for DEFB CN determination in 285 DNA samples. We found MLPA had the best convergence and clustering results of the raw data and the highest call rate. In addition, the concordance rates between MLPA or PRT and qPCR (32.12% and 37.99%, respectively) were unacceptably low with underestimated CN by qPCR. Concordance rate between MLPA and PRT (90.52%) was high but PRT systematically underestimated CN by one in a subset of samples. In these samples a sequence variant which caused complete PCR dropout of the respective DEFB cluster copies was found in one primer binding site of one of the targeted paralogous pseudogenes. CONCLUSION MLPA is superior to PRT and even more to qPCR for DEFB CN determination. Although the applied PRT provides in most cases reliable results, such a test is particularly sensitive to low-frequency sequence variations preferably accumulating in loci like pseudogenes which are most likely not under selective pressure. In the light of the superior performance of multiplex assays, the drawbacks of such single PRTs could be overcome by combining more test markers.

Time-lapse pressure tomography for characterizing CO2 plume evolution in a deep saline aquifer

A time-lapse pressure tomography inversion approach is applied to characterize the CO2 plume development in a virtual deep saline aquifer. Deep CO2 injection leads to flow properties of the mixed-phase, which vary depending on the CO2 saturation. Analogous to the crossed ray paths of a seismic tomographic experiment, pressure tomography creates streamline patterns by injecting brine prior to CO2 injection or by injecting small amounts of CO2 into the two-phase (brine and CO2) system at different depths. In a first step, the introduced pressure responses at observation locations are utilized for a computationally rapid and efficient eikonal equation based inversion to reconstruct the heterogeneity of the subsurface with diffusivity (D) tomograms. Information about the plume shape can be derived by comparing D-tomograms of the aquifer at different times. In a second step, the aquifer is subdivided into two zones of constant values of hydraulic conductivity (K) and specific storage (Ss) through a clustering approach. For the CO2 plume, mixed-phase K and Ss values are estimated by minimizing the difference between calculated and “true” pressure responses using a single-phase flow simulator to reduce the computing complexity. Finally, the estimated flow property is converted to gas saturation by a single-phase proxy, which represents an integrated value of the plume. This novel approach is tested first with a doublet well configuration, and it reveals a great potential of pressure tomography based concepts for characterizing and monitoring deep aquifers, as well as the evolution of a CO2 plume. Still, field-testing will be required for better assessing the applicability of this approach.

A New Approach for Automatic Removal of Movement Artifacts in Near-Infrared Spectroscopy Time Series by Means of Acceleration Data

Abstract: Near-infrared spectroscopy (NIRS) enables the non-invasive measurement of changes in hemodynamics and oxygenation in tissue. Changes in light-coupling due to movement of the subject can cause movement artifacts (MAs) in the recorded signals. Several methods have been developed so far that facilitate the detection and reduction of MAs in the data. However, due to fixed parameter values (e.g., global threshold) none of these methods are perfectly suitable for long-term (i.e., hours) recordings or were not time-effective when applied to large datasets. We aimed to overcome these limitations by automation, i.e., data adaptive thresholding specifically designed for long-term measurements, and by introducing a stable long-term signal reconstruction. Our new technique (“acceleration-based movement artifact reduction algorithm”, AMARA) is based on combining two methods: the “movement artifact reduction algorithm” (MARA, Scholkmann et al. Phys. Meas. 2010, 31, 649–662), and the “accelerometer-based motion artifact removal” (ABAMAR, Virtanen et al. J. Biomed. Opt. 2011, 16, 087005). We describe AMARA in detail and report about successful validation of the algorithm using empirical NIRS data, measured over the prefrontal cortex in adolescents during sleep. In addition, we compared the performance of AMARA to that of MARA and ABAMAR based on validation data.

Evolution of the stable carbon isotope composition of atmospheric CO₂ over the last glacial cycle

We present new δ¹³C measurements of atmospheric CO₂ covering the last glacial/interglacial cycle, complementing previous records covering Terminations I and II. Most prominent in the new record is a significant depletion in δ¹³C(atm) of 0.5‰ occurring during marine isotope stage (MIS) 4, followed by an enrichment of the same magnitude at the beginning of MIS 3. Such a significant excursion in the record is otherwise only observed at glacial terminations, suggesting that similar processes were at play, such as changing sea surface temperatures, changes in marine biological export in the Southern Ocean (SO) due to variations in aeolian iron fluxes, changes in the Atlantic meridional overturning circulation, upwelling of deep water in the SO, and long-term trends in terrestrial carbon storage. Based on previous modeling studies, we propose constraints on some of these processes during specific time intervals. The decrease in δ¹³C(atm) at the end of MIS 4 starting approximately 64 kyr B.P. was accompanied by increasing [CO₂]. This period is also marked by a decrease in aeolian iron flux to the SO, followed by an increase in SO upwelling during Heinrich event 6, indicating that it is likely that a large amount of δ¹³C-depleted carbon was transferred to the deep oceans previously, i.e., at the onset of MIS 4. Apart from the upwelling event at the end of MIS 4 (and potentially smaller events during Heinrich events in MIS 3), upwelling of deep water in the SO remained reduced until the last glacial termination, whereupon a second pulse of isotopically light carbon was released into the atmosphere.

Overdeepened glacial basins as archives for the Quaternary landscape evolution of the Alps

The Alps and the Alpine foreland have been shaped by repeated glaciations during Quaternary glacial-interglacial cycles. Extent, timing and impact on landscape evolution of these glaciations are, however, poorly constrained due to the fragmentary character of terrestrial archives. In this context, the sedimentary infills of subglacially eroded, ‘overdeepened’, basins may serve as important archives to complement the Quaternary stratigraphy over several glacial-interglacial cycles. In this thesis, the infills of deep subglacial basins in the Lower Glatt valley (N Switzerland) are explored to better constrain the Middle- to Late Pleistocene environmental change. Five drill cores gave direct insight into to the up to ~200 m thick valley fill at the study site and allowed for detailed analysis of sedimentary facies, age and architecture of the basin fills. A first focus is set on the sedimentology of coarse-grained diamicts with sorted interbeds overlying bedrock in the trough center, which mark the onset of deposition in many glacial bedrock troughs. Evidence from macro- and microsedimentology suggests that these sediments are emplaced subglacially and reflect deposition, reworking and deformation in response to repeated coupling and decoupling of the ice-bed interface promoted by high basal water pressures. Overlying these subglacial sediments, large volumes of sandy glacio-deltaic, fine-grained glacio-lacustrine and lacustrine sediments document sedimentation during glacier retreat from the basins. On these thick valley fill sequences the applicability and reliability of luminescence dating is investigated in a second step on the basis of experiments with several different luminescence signals, protocols and experiments to assess the signal stability. The valley fill of the Lower Glatt valley is then grouped into nine depositional cycles (Formations A-I), which are related to the Birrfeld Glaciation (~MIS2), the Beringen Glaciation (~MIS6), and up to three earlier Middle Pleistocene glaciations, tentatively correlated to the Hagenholz, Habsburg, and Möhlin Glaciations, according to the regional glaciation history. The complex bedrock geometry and valley fill architecture are shown to be the result of multiple erosion and infilling cycles and reflect the interplay of subglacial erosion, glacial to lacustrine infilling of overdeepened basins, and fluvial down-cutting and aggradation in the non-overdeepened valley fill. Evidence suggests that in the study area deep bedrock incision, and/or partial re-excavation, occurred mainly during the Beringen and Hagenholz Glaciation, while older structures may have existed. Together with the observation of minor, ‘inlaid’ glacial basins, dynamic changes in the magnitude and focus of subglacial erosion over time are documented.