Temporal trends in opportunistic citizen science reports across multiple taxa

Opportunistic reporting of species observations to online platforms provide one of the most extensive sources of information about the distribution and status of organisms in the wild. The lack of a clear sampling design, and changes in reporting over time, leads to challenges when analysing these data for temporal change in organisms. To better understand temporal changes in reporting, we use records submitted to an online platform in Sweden (Artportalen), currently containing 80 million records. Focussing on five taxonomic groups, fungi, plants, beetles, butterflies and birds, we decompose change in reporting into long-term and seasonal trends, and effects of weekdays, holidays and weather variables. The large surge in number of records since the launch of the, initially taxa-specific, portals is accompanied by non-trivial long-term and seasonal changes that differ between the taxonomic groups and are likely due to changes in, and differences between, the user communities and observer behaviour.

A Value Sensitive Scenario Planning Method for Adaptation to Uncertain Future Sea Level Rise

Value sensitive design (VSD) aims at creating better technology based on social and ethical values. However, VSD has not been applied to long-term and uncertain future developments, such as societal planning for climate change. This paper describes a new method that combines elements from VSD with scenario planning. The method was developed for and applied to a case study of adaptation to sea level rise (SLR) in southern Sweden in a series of workshops. The participants of the workshops found that the method provided a framework for discussing long-term planning, enabled identification of essential values, challenged established planning practices, helped find creative solutions, and served as a reminder that we do not know what will happen in the future. Finally, we reflect on the limitations of the method and suggest further research on how it can be improved for value sensitive design of adaptation measures to manage uncertain future sea level rise.

International organizations and climate change adaptation: A new dataset for the social scientific study of adaptation, 1990-2017

This article introduces a new dataset on the climate change adaptation activities of international organizations (IOs). While climate change adaptation has been studied at the local level and in the context of major climate organizations, such as the United Nations Framework Convention on Climate Change, we provide a first quantitative dataset on non-environmental IOs that can be linked to different social scientific datasets relevant for adaptation. Our new dataset contains information on the governance activities of 30 IOs from 1990 to 2017. Based on this dataset, we introduce different types of adaptation-related activities and develop a quantitative measure of IOs' climate adaptation engagement. We map the adaptation engagement of the 30 IOs across organizations, across issue areas, and over time. This dataset can be used to compare adaptation activities across and within IOs, but also as an empirical foundation for the emerging research field of global adaptation governance, for which IO climate change adaptation activities are relevant.

Evidence for and localization of proposed causative variants in cattle and pig genomes

BACKGROUND

This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to the identification of causative variants from genetic mapping and genome-wide association studies, researchers in animal genetics have proposed putative causative variants for several traits relevant to livestock breeding.

RESULTS

For this review, we read the literature that supports potential causative variants in 13 genes (ABCG2, DGAT1, GHR, IGF2, MC4R, MSTN, NR6A1, PHGK1, PRKAG3, PLRL, RYR1, SYNGR2 and VRTN) in cattle and pigs, and localized them in contemporary reference genomes. We review the evidence for their causality, by aiming to separate the evidence for the locus, the proposed causative gene and the proposed causative variant, and report the bioinformatic searches and tactics needed to localize the sequence variants in the cattle or pig genome.

CONCLUSIONS

Taken together, there is usually good evidence for the association at the locus level, some evidence for a specific causative gene at eight of the loci, and some experimental evidence for a specific causative variant at six of the loci. We recommend that researchers who report new potential causative variants use referenced coordinate systems, show local sequence context, and submit variants to repositories.

Characterizing natural degradation of tetrachloroethene (PCE) using a multidisciplinary approach

A site in mid-western Sweden contaminated with chlorinated solvents originating from a previous dry cleaning facility, was investigated using conventional groundwater analysis combined with compound-specific isotope data of carbon, microbial DNA analysis, and geoelectrical tomography techniques. We show the value of this multidisciplinary approach, as the different results supported each interpretation, and show where natural degradation occurs at the site. The zone where natural degradation occurred was identified in the transition between two geological units, where the change in hydraulic conductivity may have facilitated biofilm formation and microbial activity. This observation was confirmed by all methods and the examination of the impact of geological conditions on the biotransformation process was facilitated by the unique combination of the applied methods. There is thus significant benefit from deploying an extended array of methods for these investigations, with the potential to reduce costs involved in remediation of contaminated sediment and groundwater.

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)

Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction. However, the integration of two different sequencing modalities makes downstream analyses complex. We, therefore, developed MUFFIN, a complete metagenomic workflow that uses short and long reads to produce high-quality bins and their annotations. The workflow is written by using Nextflow, a workflow orchestration software, to achieve high reproducibility and fast and straightforward use. This workflow also produces the taxonomic classification and KEGG pathways of the bins and can be further used for quantification and annotation by providing RNA-Seq data (optionally). We tested the workflow using twenty biogas reactor samples and assessed the capacity of MUFFIN to process and output relevant files needed to analyze the microbial community and their function. MUFFIN produces functional pathway predictions and, if provided de novo metatranscript annotations across the metagenomic sample and for each bin. MUFFIN is available on github under GNUv3 licence: https://github.com/RVanDamme/MUFFIN.

Ocean acidification decreases grazing pressure but alters morphological structure in a dominant coastal seaweed

Ocean acidification driven by anthropogenic climate change is causing a global decrease in pH, which is projected to be 0.4 units lower in coastal shallow waters by the year 2100. Previous studies have shown that seaweeds grown under such conditions may alter their growth and photosynthetic capacity. It is not clear how such alterations might impact interactions between seaweed and herbivores, e.g. through changes in feeding rates, nutritional value, or defense levels. Changes in seaweeds are particularly important for coastal food webs, as they are key primary producers and often habitat-forming species. We cultured the habitat-forming brown seaweed Fucus vesiculosus for 30 days in projected future pCO2 (1100 μatm) with genetically identical controls in ambient pCO2 (400 μatm). Thereafter the macroalgae were exposed to grazing by Littorina littorea, acclimated to the relevant pCO2-treatment. We found increased growth (measured as surface area increase), decreased tissue strength in a tensile strength test, and decreased chemical defense (phlorotannins) levels in seaweeds exposed to high pCO2-levels. The herbivores exposed to elevated pCO2-levels showed improved condition index, decreased consumption, but no significant change in feeding preference. Fucoid seaweeds such as F. vesiculosus play important ecological roles in coastal habitats and are often foundation species, with a key role for ecosystem structure and function. The change in surface area and associated decrease in breaking force, as demonstrated by our results, indicate that F. vesiculosus grown under elevated levels of pCO2 may acquire an altered morphology and reduced tissue strength. This, together with increased wave energy in coastal ecosystems due to climate change, could have detrimental effects by reducing both habitat and food availability for herbivores.

Past, present and future distributions of Oriental beech (Fagus orientalis) under climate change projections

Species distribution models can help predicting range shifts under climate change. The aim of this study is to investigate the late Quaternary distribution of Oriental beech (Fagus orientalis) and to project future distribution ranges under different climate change scenarios using a combined palaeobotanical, phylogeographic, and modelling approach. Five species distribution modelling algorithms under the R-package `biomod2`were applied to occurrence data of Fagus orientalis to predict distributions under present, past (Last Glacial Maximum, 21 ka, Mid-Holocene, 6 ka), and future climatic conditions with different scenarios obtained from MIROC-ESM and CCSM4 global climate models. Distribution models were compared to palaeobotanical and phylogeographic evidence. Pollen data indicate northern Turkey and the western Caucasus as refugia for Oriental beech during the Last Glacial Maximum. Although pollen records are missing, molecular data point to Last Glacial Maximum refugia in northern Iran. For the mid-Holocene, pollen data support the presence of beech in the study region. Species distribution models predicted present and Last Glacial Maximum distribution of Fagus orientalis moderately well yet underestimated mid-Holocene ranges. Future projections under various climate scenarios indicate northern Iran and the Caucasus region as major refugia for Oriental beech. Combining palaeobotanical, phylogeographic and modelling approaches is useful when making projections about distributions of plants. Palaeobotanical and molecular evidence reject some of the model projections. Nevertheless, the projected range reduction in the Caucasus region and northern Iran highlights their importance as long-term refugia, possibly related to higher humidity, stronger environmental and climatic heterogeneity and strong vertical zonation of the forest vegetation.

Cerebrospinal fluid levels of GFAP and pNF-H are elevated in patients with chronic spinal cord injury and neurological deterioration

BACKGROUND

Years after a traumatic spinal cord injury (SCI), a subset of patients may develop progressive clinical deterioration due to intradural scar formation and spinal cord tethering, with or without an associated syringomyelia. Meningitis, intradural hemorrhages, or intradural tumor surgery may also trigger glial scar formation and spinal cord tethering, leading to neurological worsening. Surgery is the treatment of choice in these chronic SCI patients.

OBJECTIVE

We hypothesized that cerebrospinal fluid (CSF) and plasma biomarkers could track ongoing neuronal loss and scar formation in patients with spinal cord tethering and are associated with clinical symptoms.

METHODS

We prospectively enrolled 12 patients with spinal cord tethering and measured glial fibrillary acidic protein (GFAP), ubiquitin C-terminal hydrolase L1 (UCH-L1), and phosphorylated Neurofilament-heavy (pNF-H) in CSF and blood. Seven patients with benign lumbar intradural tumors and 7 patients with cervical radiculopathy without spinal cord involvement served as controls.

RESULTS

All evaluated biomarker levels were markedly higher in CSF than in plasma, without any correlation between the two compartments. When compared with radiculopathy controls, CSF GFAP and pNF-H levels were higher in patients with spinal cord tethering (p ≤ 0.05). In contrast, CSF UCH-L1 levels were not altered in chronic SCI patients when compared with either control groups.

CONCLUSIONS

The present findings suggest that in patients with spinal cord tethering, CSF GFAP and pNF-H levels might reflect ongoing scar formation and neuronal injury potentially responsible for progressive neurological deterioration.

Streptococcus suis in Swedish grower pigs: occurrence, serotypes, and antimicrobial susceptibility

BACKGROUND

Streptococcus suis is a major cause of meningitis, arthritis, and pneumonia in pigs worldwide, and an emerging pathogen in humans. In Sweden, S. suis has previously received little attention but has in recent years become increasingly recognized as affecting the pig production. The aim of the present study was to investigate the occurrence, serotypes and antimicrobial susceptibility of S. suis in Swedish grower pigs from herds with and without reported S. suis associated disease, as well as possible associations between S. suis associated disease and selected environmental and production factors. Swab samples were taken from the tonsils of clinically healthy 8-13-week-old grower pigs from ten case herds and ten control herds. Isolates were cultured, identified using MALDI-TOF MS, and serotyped using latex agglutination. The antimicrobial susceptibility of 188 isolates was tested using broth microdilution. Production data was gathered and environmental parameters were measured on the farms.

RESULTS

Streptococcus suis was isolated from 95% of the sampled pigs in both the case and the control herds. Serotypes 3, 4, 5, 7, 9, 10, 11, 15, 16, and 17-34 were detected, although a majority of the isolates (81.5%) were non-typeable. There was less diversity among the serotypes isolated from the case herds than among those from the control herds; four and nine different serotypes, respectively. Isolates resistant to penicillin (3.8%) were reported for the first time in Sweden. Tetracycline resistance was common (88.4%). No association was noted between the production and the environmental factors investigated, and the carriership of S. suis.

CONCLUSIONS

The carriership of S. suis was found to be higher in clinically healthy Swedish pigs than previously estimated, and for the first time, the presence of Swedish isolates resistant to penicillin was reported. Many of the most commonly disease-associated serotypes, e.g. serotypes 2, 9, 3, and 7, were detected in healthy grower pigs although further studies are needed to investigate the virulence of these isolates.

The regenerative compatibility: A synergy between healthy ecosystems, environmental attitudes, and restorative experiences

Urban nature is and will be the most common provider of nature interactions for humankind. The restorative benefits of nature exposure are renown and creating human habitats that simultaneously support people’s wellbeing and ecological sustainability is an urgent priority. In this study, we investigate how the relationship between environmental attitudes and healthy ecosystems influences restorative experiences combining a place-based online survey with geographical data on ecosystem health in Stockholm (Sweden). Using spatial regression, we predict the 544 restorative experiences (from 325 respondents), with people’s environmental attitudes, natural land covers, ecosystem health, and the statistical interactions among these variables as predictors. Our results show that restorative experiences can happen anywhere in the urban landscape, but when they occur in natural environments, the combined levels of biodiversity and ecological connectivity are better predicting factor than the mere presence of nature. That is, healthy ecosystems seem to be more important than just any nature for restorative experiences. Moreover, the statistical interaction between one’s environmental attitudes and natural environments predict almost all restorative experiences better than when these variables are independent predictors. This suggests that there is synergistic compatibility between environmental attitudes and healthy ecosystems that triggers restorative processes. We call this synergy regenerative compatibility. Regenerative compatibility is an unexploited potential that emerges when people’s attitudes and ecosystems are aligned in sustainability. We consider regenerative compatibility a valuable leverage point to transform towards ecologically sustainable and healthy urban systems. To this end, we encourage multifaceted policy interventions that regenerate human-nature relationships holistically rather than implement atomistic solutions.

Social determinants of under-5 child health: A qualitative study in Wolkayit Woreda, Tigray Region, Ethiopia

Despite the significant reductions seen in under-5 child mortality in Ethiopia over the last two decades, more than 10,000 children still die each year in Tigray Region alone, of whom 75% die from preventable diseases. Using an equity lens, this study aimed to investigate the social determinants of child health in one particularly vulnerable district as a means of informing the health policy decision-making process. An exploratory qualitative study design was adopted, combining focus group discussions and qualitative interviews. Seven Focus Group Discussions with mothers of young children, and 21 qualitative interviews with health workers were conducted in Wolkayit district in May-June 2015. Data were subjected to thematic analysis. Mothers' knowledge regarding the major causes of child mortality appeared to be good, and they also knew about and trusted the available child health interventions. However, utilization and practice of these interventions was limited by a range of issues, including cultural factors, financial shortages, limited female autonomy on financial resources, seasonal mobility, and inaccessible or unaffordable health services. Our findings pointed to the importance of a multi-sectoral strategy to improve child health equity and reduce under-5 mortality in Wolkayit. Recommendations include further decentralizing child health services to local-level Health Posts, and increasing the number of Health Facilities based on local topography and living conditions.

Shoot shovel and sanction yourself: Self-policing as a response to wolf poaching among Swedish hunters

Self-policing is essential for addressing wildlife-related crime where illegal activity is extremely diffuse, and limited resources are available for monitoring and enforcement. Emerging research on self-policing suggest key drivers including economics, folk traditions, and socio-political resistance. We build on this research with a case study evaluating potential drivers of self-policing illegal wolf killing among Swedish hunting teams. Swedish hunters marginally leaned toward considering illegal hunting of wolves an expression of resistance (10.30 out of a possible 17 on a resistance scale) and strongly believed outsiders had undue influence over hunting (15.79 out of a possible 21 on an influence scale). Most (73%) Swedish hunters stated they would report illegal wolf killing to authorities, but 20% stated they would handle the infractions through internal sanctions. Viewing illegal hunting of wolves as a form of political resistance, viewing wolf management as being controlled locally, and perceived prevalence of illegal wolf killing among hunting acquaintances were positive predictors of preferring internal sanctions to address illegal wolf killing over reporting the crimes. Resistance and perceived prevalence of wolf killing also predicted preferring no action to address illegal wolf killing. These results suggest that a counterpublic of marginalized ruralism may promote forms of self-policing that rely on internal censure for illegal wolf killing rather than using formal legal channels. Similarly, folk traditions within this counterpublic (e.g., perceptions of prevalence of illegal wolf killing) shape if and how internal sanctions are advocated. Re-engaging marginalized hunting groups and emphasizing the rarity of illegal wolf killing may promote wolf conservation, both in Sweden and in other democratic regimes.

Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing

BACKGROUND

Inherent sources of error and bias that affect the quality of sequence data include index hopping and bias towards the reference allele. The impact of these artefacts is likely greater for low-coverage data than for high-coverage data because low-coverage data has scant information and many standard tools for processing sequence data were designed for high-coverage data. With the proliferation of cost-effective low-coverage sequencing, there is a need to understand the impact of these errors and bias on resulting genotype calls from low-coverage sequencing.

RESULTS

We used a dataset of 26 pigs sequenced both at 2× with multiplexing and at 30× without multiplexing to show that index hopping and bias towards the reference allele due to alignment had little impact on genotype calls. However, pruning of alternative haplotypes supported by a number of reads below a predefined threshold, which is a default and desired step of some variant callers for removing potential sequencing errors in high-coverage data, introduced an unexpected bias towards the reference allele when applied to low-coverage sequence data. This bias reduced best-guess genotype concordance of low-coverage sequence data by 19.0 absolute percentage points.

CONCLUSIONS

We propose a simple pipeline to correct the preferential bias towards the reference allele that can occur during variant discovery and we recommend that users of low-coverage sequence data be wary of unexpected biases that may be produced by bioinformatic tools that were designed for high-coverage sequence data.

Mixed blessings: A qualitative exploration of mothers' experience of child care and feeding in the rapidly urbanizing city of Addis Ababa, Ethiopia

Many studies have drawn attention to the vital role mothers have in safeguarding the health and nutritional wellbeing of their children. However, little is known about mothers’ experiences and the challenges they face in fulfilling this role in rapidly urbanizing cities in Africa. This study aims to explore child care and feeding practices of mothers with children under five years of age in Addis Ababa, Ethiopia. This qualitative study was conducted using a semi-structured interview guide. A total of thirty-six interviews were conducted with purposively selected participants. All interviews were audio recorded, transcribed verbatim and translated for analysis. We used a thematic analysis approach, which was guided by a resilience framework. The findings are presented as three major themes. 1) ‘Mixed blessings-balancing motherhood’s expectations’. While mothers identified positively with the social recognition and sense of fulfillment of being a ‘good mother’, they were ambivalent/torn about earning the necessary income from outside work and fulfilling their duties at home. 2) ‘Instabilities due to rampant urban sprawl’. While women expressed a keen desire to balance work and motherhood, the disintegrating social capital, due to large in-migration, market fluctuations and abrupt/forced resettlements to new housing units had left mothers without support for childcare, stressed and exhausted. 3) ‘Anchored by faith: a source of resilience to cope with adversities’. In the face of the multiple adversities, mothers cited their strong faith as their most reliable foundation for their resilience. In summary, the societal and environmental changes accompanying the rapid urbanization in low income settings makes combining child care and working outside the home very challenging for mothers. As a result they suffer from fatigue and feelings of isolation. Efforts to improve child feeding and care in urban low-income settings need to consider context appropriate strategies that support mothers with small children.

Magnetic Hysteresis in Nanostructures with Thermally Controlled RKKY Coupling

Mechanisms of the recently demonstrated ex-situ thermal control of the indirect exchange coupling in magnetic multilayer are discussed for different designs of the spacer layer. Temperature-induced changes in the hysteresis of magnetization are shown to be associated with different types of competing interlayer exchange interactions. Theoretical analysis indicates that the measured step-like shape and hysteresis of the magnetization loops is due to local in-plane magnetic anisotropy of nano-crystallites within the strongly ferromagnetic films. Comparison of the experiment and theory is used to contrast the mechanisms of the magnetization switching based on the competition of (i) indirect (RKKY) and direct (non-RKKY) interlayer exchange interactions as well as (ii) indirect ferromagnetic and indirect antiferromagnetic (both of RKKY type) interlayer exchange. These results, detailing the rich magnetic phase space of the system, should help enable the practical use of RKKY for thermally switching the magnetization in magnetic multilayers.

Selection on the Colombian paso horse's gaits has produced kinematic differences partly explained by the DMRT3 gene

The Colombian paso horse, the most important horse breed in Colombia, performs specific and particular gaits (paso fino, trocha, and Colombian trot), which display different footfall patterns and stride frequencies. The breed has been selected for gait and conformation for more than 50 years and we hypothesize that this selection has led to kinematic differences of the gaits that can be explained by different genetic variants. Hence, the aims of the study were: 1. To identify if there are any differences in the kinematic and genetic variants between the Colombian paso horse’s gaits. 2. To evaluate if and how much the gait differences were explained by the nonsense mutation in the DMRT3 gene and 3. To evaluate these results for selecting and controlling the horses gait performance. To test our hypotheses, kinematic data, microsatellites and DMRT3 genotypes for 187 Colombian paso horses were analyzed. The results indicated that there are significant kinematic and DMRT3 differences between the Colombian paso horse’s gaits, and those parameters can be used partially to select and control the horses gait performance. However, the DMRT3 gene does not play a major role in controlling the trocha and the Colombian trot gaits. Therefore, modifying genes likely influence these gaits. This study may serve as a foundation for implementing a genetic selection program in the Colombian paso horse and future gene discovery studies for locomotion pattern in horses.

Aboveground mechanical stimuli affect belowground plant-plant communication

Plants can detect the presence of their neighbours and modify their growth behaviour accordingly. But the extent to which this neighbour detection is mediated by abiotic stressors is not well known. In this study we tested the acclimation response of Zea mays L. seedlings through belowground interactions to the presence of their siblings exposed to brief mechano stimuli. Maize seedling simultaneously shared the growth solution of touched plants or they were transferred to the growth solution of previously touched plants. We tested the growth preferences of newly germinated seedlings toward the growth solution of touched (T_solution) or untouched plants (C_solution). The primary root of the newly germinated seedlings grew significantly less towards T_solution than to C_solution. Plants transferred to T_solution allocated more biomass to shoots and less to roots. While plants that simultaneously shared their growth solution with the touched plants produced more biomass. Results show that plant responses to neighbours can be modified by aboveground abiotic stress to those neighbours and suggest that these modifications are mediated by belowground interactions.

The perception of aquaculture on the Swedish West Coast

Efforts are on the way on the Swedish West Coast to develop the capacity for cultivation of marine resources, notably of kelps. Given that this is a region of great natural and national heritage, public opposition to marine developments has been identified as a possible risk factor. This survey thus sought to shed light on awareness levels, perceptions of different types of aquaculture and on reactions to a scenario depicting future aquaculture developments on the West Coast. When asked about their general opinions of aquaculture, respondents tended to be favourable though a majority chose neutral responses. On the whole, respondents were favourable to the depicted scenario. Finally, it was found that the high-awareness group tended to be more supportive than the low or medium-awareness groups, hinting at the benefits of increasing awareness to reduce public aversion and to support a sustainable development of aquaculture on the Swedish West Coast.

Need for speed: An optimized gridding approach for spatially explicit disease simulations

Numerical models for simulating outbreaks of infectious diseases are powerful tools for informing surveillance and control strategy decisions. However, large-scale spatially explicit models can be limited by the amount of computational resources they require, which poses a problem when multiple scenarios need to be explored to provide policy recommendations. We introduce an easily implemented method that can reduce computation time in a standard Susceptible-Exposed-Infectious-Removed (SEIR) model without introducing any further approximations or truncations. It is based on a hierarchical infection process that operates on entire groups of spatially related nodes (cells in a grid) in order to efficiently filter out large volumes of susceptible nodes that would otherwise have required expensive calculations. After the filtering of the cells, only a subset of the nodes that were originally at risk are then evaluated for actual infection. The increase in efficiency is sensitive to the exact configuration of the grid, and we describe a simple method to find an estimate of the optimal configuration of a given landscape as well as a method to partition the landscape into a grid configuration. To investigate its efficiency, we compare the introduced methods to other algorithms and evaluate computation time, focusing on simulated outbreaks of foot-and-mouth disease (FMD) on the farm population of the USA, the UK and Sweden, as well as on three randomly generated populations with varying degree of clustering. The introduced method provided up to 500 times faster calculations than pairwise computation, and consistently performed as well or better than other available methods. This enables large scale, spatially explicit simulations such as for the entire continental USA without sacrificing realism or predictive power.

Numerical models for simulating the outbreak of infectious disease are powerful tools that can be used to inform policy decisions by simulating outbreaks and control actions. However, they rely on considerable computational power to explore all outcomes and scenarios of interest. Focusing on model types commonly used for livestock diseases, we here introduce novel algorithms for efficient computation, alongside techniques to optimize them based on simplifying assumptions. Through simulations of FMD outbreak in the US, the UK and Sweden, as well as in computer generated landscapes, we test how these methods perform under realistic conditions. We find that our optimization techniques works well, and when the introduced algorithms are implemented with these optimizations, computation time can be reduced by more than two orders of magnitude compared to pairwise calculations. We propose that the considered algorithms—which are straight forward to implement—will be useful for simulation of a wide range of diseases, and will promote the use of simulation models for policy recommendation.

Toxicity bioassays with concentrated cell culture media-a methodology to overcome the chemical loss by conventional preparation of water samples

The use of in vitro bioassays for studies of toxic activity in environmental water samples is a rapidly expanding field of research. Cell-based bioassays can assess the total toxicity exerted by a water sample, regardless whether the toxicity is caused by a known or unknown agent or by a complex mixture of different agents. When using bioassays for environmental water samples, it is often necessary to concentrate the water samples before applying the sample. Commonly, water samples are concentrated 10-50 times. However, there is always a risk of losing compounds in the sample in such sample preparation. We have developed an alternative experimental design by preparing a concentrated cell culture medium which was then diluted in the environmental water sample to compose the final cell culture media for the in vitro assays. Water samples from five Swedish waste water treatment plants were analyzed for oxidative stress response, estrogen receptor (ER), and aryl hydrocarbon receptor (AhR) activity using this experimental design. We were able to detect responses equivalent to 8.8-11.3 ng/L TCCD for AhR activity and 0.4-0.9 ng/L 17β-estradiol for ER activity. We were unable to detect oxidative stress response in any of the studied water samples. In conclusion, we have developed an experimental design allowing us to examine environmental water samples in toxicity in vitro assays at a concentration factor close to 1, without the risk of losing known or unknown compounds during an extraction procedure.

Food supply and bioenergy production within the global cropland planetary boundary

Supplying food for the anticipated global population of over 9 billion in 2050 under changing climate conditions is one of the major challenges of the 21^st century. Agricultural expansion and intensification contributes to global environmental change and risks the long-term sustainability of the planet. It has been proposed that no more than 15% of the global ice-free land surface should be converted to cropland. Bioenergy production for land-based climate mitigation places additional pressure on limited land resources. Here we test normative targets of food supply and bioenergy production within the cropland planetary boundary using a global land-use model. The results suggest supplying the global population with adequate food is possible without cropland expansion exceeding the planetary boundary. Yet this requires an increase in food production, especially in developing countries, as well as a decrease in global crop yield gaps. However, under current assumptions of future food requirements, it was not possible to also produce significant amounts of first generation bioenergy without cropland expansion. These results suggest that meeting food and bioenergy demands within the planetary boundaries would need a shift away from current trends, for example, requiring major change in the demand-side of the food system or advancing biotechnologies.

Infection of Drosophila suzukii with the obligate insect-pathogenic fungus Entomophthora muscae

Physiological constraints restrict specialist pathogens from infecting new hosts. From an applied perspective, a narrow host range makes specialist pathogens interesting for targeting specific pest insects since they have minimal direct effects on non-target species. Entomopathogenic fungi of the genus Entomophthora are dipteran-specific but have not been investigated for their ability to infect the spotted wing drosophila (SWD; Drosophila suzukii) a fruit-damaging pest invasive to Europe and America. Our main goal was to study whether SWD is in the physiological host range of the entomophthoralean species E. muscae. We investigated pathogenicity and virulence of E. muscae towards its main natural host, the housefly Musca domestica, and towards SWD. We found that E. muscae readily infected and significantly reduced survival of SWD by 27.3% with the majority of flies dying 4-8 days post-exposure. In comparison with SWD, infection of the natural host M. domestica resulted in an even higher mortality of 62.9% and larger conidial spores of E. muscae, reflecting the physiological constraints of the pathogen in the atypical host. We demonstrated that pathogens of the E. muscae species complex that typically have a narrow natural host range of one or few dipteran species are able to infect SWD, and we described a new method for in vivo transmission and infection of an entomophthoralean fungus to SWD.

Modification of the nanostructure of lignocellulose cell walls via a non-enzymatic lignocellulose deconstruction system in brown rot wood-decay fungi

Wood decayed by brown rot fungi and wood treated with the chelator-mediated Fenton (CMF) reaction, either alone or together with a cellulose enzyme cocktail, was analyzed by small angle neutron scattering (SANS), sum frequency generation (SFG) spectroscopy, Fourier transform infrared (FTIR) analysis, X-ray diffraction (XRD), atomic force microscopy (AFM), and transmission electron microscopy (TEM). Results showed that the CMF mechanism mimicked brown rot fungal attack for both holocellulose and lignin components of the wood. Crystalline cellulose and lignin were both depolymerized by the CMF reaction. Porosity of the softwood cell wall did not increase during CMF treatment, enzymes secreted by the fungi did not penetrate the decayed wood. The enzymes in the cellulose cocktail also did not appear to alter the effects of the CMF-treated wood relative to enhancing cell wall deconstruction. This suggests a rethinking of current brown rot decay models and supports a model where monomeric sugars and oligosaccharides diffuse from the softwood cell walls during non-enzymatic action. In this regard, the CMF mechanism should not be thought of as a "pretreatment" used to permit enzymatic penetration into softwood cell walls, but instead it enhances polysaccharide components diffusing to fungal enzymes located in wood cell lumen environments during decay. SANS and other data are consistent with a model for repolymerization and aggregation of at least some portion of the lignin within the cell wall, and this is supported by AFM and TEM data. The data suggest that new approaches for conversion of wood substrates to platform chemicals in biorefineries could be achieved using the CMF mechanism with >75% solubilization of lignocellulose, but that a more selective suite of enzymes and other downstream treatments may be required to work when using CMF deconstruction technology. Strategies to enhance polysaccharide release from lignocellulose substrates for enhanced enzymatic action and fermentation of the released fraction would also aid in the efficient recovery of the more uniform modified lignin fraction that the CMF reaction generates to enhance biorefinery profitability.

Increased lignocellulosic inhibitor tolerance of Saccharomyces cerevisiae cell populations in early stationary phase

BACKGROUND

Production of second-generation bioethanol and other bulk chemicals by yeast fermentation requires cells that tolerate inhibitory lignocellulosic compounds at low pH. Saccharomyces cerevisiae displays high plasticity with regard to inhibitor tolerance, and adaptation of cell populations to process conditions is essential for reaching efficient and robust fermentations.

RESULTS

In this study, we assessed responses of isogenic yeast cell populations in different physiological states to combinations of acetic acid, vanillin and furfural at low pH. We found that cells in early stationary phase (ESP) exhibited significantly increased tolerance compared to cells in logarithmic phase, and had a similar ability to initiate growth in the presence of inhibitors as pre-adapted cells. The ESP cultures consisted of subpopulations with different buoyant cell densities which were isolated with flotation and analysed separately. These so-called quiescent (Q) and non-quiescent (NQ) cells were found to possess similar abilities to initiate growth in the presence of lignocellulosic inhibitors at pH 3.7, and had similar viabilities under static conditions. Therefore, differentiation into Q-cells was not the cause for increased tolerance of ESP cultures. Flow cytometry analysis of cell viability, intracellular pH and reactive oxygen species levels revealed that tolerant cell populations had a characteristic response upon inhibitor perturbations. Growth in the presence of a combination of inhibitors at low pH correlated with pre-cultures having a high frequency of cells with low pH_i and low ROS levels. Furthermore, only a subpopulation of ESP cultures was able to tolerate lignocellulosic inhibitors at low pH, while pre-adapted cell populations displayed an almost uniform high tolerance to the adverse condition. This was in stark contrast to cell populations growing exponentially in non-inhibitory medium that were uniformly sensitive to the inhibitors at low pH.

CONCLUSIONS

ESP cultures of S. cerevisiae were found to have high tolerance to lignocellulosic inhibitors at low pH, and were able to initiate growth to the same degree as cells that were pre-adapted to inhibitors at a slightly acidic pH. Carbon starvation may thus be a potential strategy to prepare cell populations for adjacent stressful environments which may be beneficial from a process perspective for fermentation of non-detoxified lignocellulosic substrates at low pH. Furthermore, flow cytometry analysis of pH_i and ROS level distributions in ESP cultures revealed responses that were characteristic for populations with high tolerance to lignocellulosic inhibitors. Measurement of population distribution responses as described herein may be applied to predict the outcome of environmental perturbations and thus can function as feedback for process control of yeast fitness during lignocellulosic fermentation.

Poor construction, not time, takes its toll on subsidised fences designed to deter large carnivores

Large carnivore conservation may be considered as successful in Sweden, as wolf (Canis lupus), lynx (Lynx lynx), brown bear (Ursus arctos), golden eagles (Aquila chrysaetos), and wolverine (Gulo gulo) populations have recovered from extinction or near extinction to viable populations during the last three decades. Particularly the wolf and lynx populations have returned at the cost of an increasing number of carnivore attacks on domestic livestock. To support coexistence between carnivores and livestock production, the Swedish authorities subsidise interventions to prevent or reduce the number of carnivore attacks. The most commonly used intervention is carnivore deterring fencing, and all livestock owners can apply for subsidies to build a fence. To receive reimbursement the fence must be approved by the authorities according to predefined criteria. An important part of any management aiming to be adaptive is evaluating interventions. In this paper we evaluate to what extent previously subsidised fences still meet the criteria 1–15 years after their approval. Of 296 fences that had received subsidies in the county of Värmland, 100 randomly selected fences were revisited in 2016. From this subsample 14% of the fences still met the initial criteria for subsidies. None of the fences that still fulfilled the criteria were more than 8 years old, whereas fences with identified failures occurred in all age groups. Of the 86 fences that failed to meet the criteria, construction failures were the most commonly occurring problem. Maintenance failures, wear and tear, only explain a minor part of the failures. To improve the quality of fencing, as well as the quality and longevity of the subsidies programme, there is a need for improved communication between authorities, and improved communication and support from the authorities to livestock producers before and during construction of fences, as well as more rigorous inspection when the fences are built.

Mindfulness in sustainability science, practice, and teaching

This paper explores the current role of mindfulness in sustainability science, practice, and teaching. Based on a qualitative literature review that is complemented by an experimental learning lab, we sketch the patterns and core conceptual trajectories of the mindfulness-sustainability relationship. In addition, we assess this relationship within the field of climate change adaptation and risk reduction. The results highlight that notions such as 'sustainability from within', 'ecological mindfulness', 'organizational mindfulness', and 'contemplative practices' have been neglected in sustainability science and teaching. Whilst little sustainability research addresses mindfulness, there is scientific support for its positive influence on: (1) subjective well-being; (2) the activation of (intrinsic/ non-materialistic) core values; (3) consumption and sustainable behavior; (4) the human-nature connection; (5) equity issues; (6) social activism; and (7) deliberate, flexible, and adaptive responses to climate change. Most research relates to post-disaster risk reduction, although it is limited to the analysis of mindfulness-related interventions on psychological resilience. Broader analyses and foci are missing. In contrast, mindfulness is gaining widespread recognition in practice (e.g., by the United Nations, governmental and non-governmental organizations). It is concluded that mindfulness can contribute to understanding and facilitating sustainability, not only at the individual level, but sustainability at all scales, and should, thus, become a core concept in sustainability science, practice, and teaching. More research that acknowledges positive emotional connections, spirituality, and mindfulness in particular is called for, acknowledging that (1) the micro and macro are mirrored and interrelated, and (2) non-material causation is part of sustainability. This paper provides the first comprehensive framework for contemplative scientific inquiry, practice, and education in sustainability.

Effects of dietary yeast inclusion and acute stress on post-prandial whole blood profiles of dorsal aorta-cannulated rainbow trout

Yeast is a potential alternative to fish meal in diets for farmed fish, yet replacing more than 50 % of fish meal results in reduced fish growth. In a 4-week experiment, 15 rainbow trout (Oncorhynchus mykiss) were cannulated and fed three diets each week: 30 % fish meal as a control (FM); 60 % replacement of fish meal protein, on a digestible basis, with Saccharomyces cerevisiae (SC); and 60 % replacement with Wickerhamomyces anomalus and S. cerevisiae mix (WA). Blood was collected at 0, 3, 6, 12 and 24 h after feeding. In the final week, fish were exposed to a 1-min netting stressor to evaluate possible diet-stress interactions. Significant increases in pH, TCO₂, HCO₃ and base excess were found after fish were fed the SC and WA diets compared with FM, which elevated blood alkaline tides. Yeast ingredients had lower buffering capacity and ash content than fish meal, which explained the increase in alkaline tides. In addition, fish fed the WA diet had significantly reduced erythrocyte area and fish fed SC and WA diets had increased mean corpuscular haemoglobin levels, indicating haemolytic anaemia. Higher levels of nucleic acid in yeast-based diets and potentially higher production of reactive oxygen species were suspected of damaging haemoglobin, which require replacement by smaller immature erythrocytes. Acute stress caused the expected rise in cortisol and glucose levels, but no interaction with diet was found. These results show that replacing 60 % of fish meal protein with yeasts can induce haemolytic anaemia in rainbow trout, which may limit yeast inclusion in diets for farmed fish.

Habitat diversity and ecosystem multifunctionality-The importance of direct and indirect effects

Ecosystems worldwide are facing habitat homogenization due to human activities. Although it is commonly proposed that such habitat homogenization can have negative repercussions for ecosystem functioning, this question has yet to receive explicit scientific attention. We expand on the framework for evaluating the functional consequences of biodiversity loss by scaling up from the level of species to the level of the entire habitats. Just as species diversity generally fosters ecosystem functioning through positive interspecies interactions, we hypothesize that different habitats within ecosystems can facilitate each other through structural complementarity and through exchange of material and energy across habitats. We show that experimental ecosystems comprised of a diversity of habitats show higher levels of multiple ecosystem functions than ecosystems with low habitat diversity. Our results demonstrate that the effect of habitat diversity on multifunctionality varies with season; it has direct effects on ecosystem functioning in summer and indirect effects, via changes in species diversity, in autumn, but no effect in spring. We propose that joint consideration of habitat diversity and species diversity will prove valuable for both environmental management and basic research.

PACAP Protects Adult Neural Stem Cells from the Neurotoxic Effect of Ketamine Associated with Decreased Apoptosis, ER Stress and mTOR Pathway Activation

Ketamine administration is a well-established approach to mimic experimentally some aspects of schizophrenia. Adult neurogenesis dysregulation is associated with psychiatric disorders, including schizophrenia. The potential role of neurogenesis in the ketamine-induced phenotype is largely unknown. Recent results from human genetic studies have shown the pituitary adenylate cyclase-activating polypeptide (PACAP) gene is a risk factor for schizophrenia. Its potential role on the regulation of neurogenesis in experimental model of schizophrenia remains to be investigated. We aimed to determine whether ketamine affects the viability of adult neural stem cells (NSC). We also investigated whether the detrimental effect mediated by ketamine could be counteracted by PACAP. NSCs were isolated from the subventricular zone of the mouse and exposed to ketamine with/without PACAP. After 24 hours, cell viability, potential involvement of apoptosis, endoplasmic reticulum (ER) stress, mTOR and AMPA pathway activation were assessed by quantitative RT-PCR and Western blot analysis. We show that ketamine impairs NSC viability in correlation with increased apoptosis, ER stress and mTOR activation. The results also suggest that the effect of ketamine occurs via AMPA receptor activation. Finally, we show that PACAP counteracted the decreased NSC viability induced by ketamine via the specific activation of the PAC-1 receptor subtype. Our study shows that the NSC viability may be negatively affected by ketamine with putative importance for the development of a schizophrenia phenotype in the ketamine induced animal model of schizophrenia. The neuroprotective effect via PAC-1 activation suggests a potentially novel pharmacological target for the treatment of schizophrenia, via neurogenesis normalization.

Conserved gene expression in sperm reservoirs between birds and mammals in response to mating

BACKGROUND

Spermatozoa are stored in the oviductal functional sperm reservoir in animals with internal fertilization, including zoologically distant classes such as pigs or poultry. They are held fertile in the reservoir for times ranging from a couple of days (in pigs), to several weeks (in chickens), before they are gradually released to fertilize the newly ovulated eggs. It is currently unknown whether females from these species share conserved mechanisms to tolerate such a lengthy presence of immunologically-foreign spermatozoa. Therefore, global gene expression was assessed using cDNA microarrays on tissue collected from the avian utero-vaginal junction (UVJ), and the porcine utero-tubal junction (UTJ) to determine expression changes after mating (entire semen deposition) or in vivo cloacal/cervical infusion of sperm-free seminal fluid (SF)/seminal plasma (SP).

RESULTS

In chickens, mating changed the expression of 303 genes and SF-infusion changed the expression of 931 genes, as compared to controls, with 68 genes being common to both treatments. In pigs, mating or SP-infusion changed the expressions of 1,722 and 1,148 genes, respectively, as compared to controls, while 592 genes were common to both treatments. The differentially expressed genes were significantly enriched for GO categories related to immune system functions (35.72-fold enrichment). The top 200 differentially expressed genes of each treatment in each animal class were analysed for gene ontology. In both pig and chicken, an excess of genes affecting local immune defence were activated, though frequently these were down-regulated. Similar genes were found in both the chicken and pig, either involved in pH-regulation (SLC16A2, SLC4A9, SLC13A1, SLC35F1, ATP8B3, ATP13A3) or immune-modulation (IFIT5, IFI16, MMP27, ADAMTS3, MMP3, MMP12).

CONCLUSION

Despite being phylogenetically distant, chicken and pig appear to share some gene functions for the preservation of viable spermatozoa in the female reservoirs.

Effect of Biochar Amendment and Ageing on Adsorption and Degradation of Two Herbicides

Biochar amendment can alter soil properties, for instance, the ability to adsorb and degrade different chemicals. However, ageing of the biochar, due to processes occurring in the soil over time, can influence such biochar-mediated effects. This study examined how biochar affected adsorption and degradation of two herbicides, glyphosate (N-(phosphonomethyl)-glycine) and diuron (3-(3,4-dichlorophenyl)-1,1-dimethylurea) in soil and how these effects were modulated by ageing of the biochar. One sandy and one clayey soil that had been freshly amended with a wood-based biochar (0, 1, 10, 20 and 30% w/w) were studied. An ageing experiment, in which the soil-biochar mixtures were aged for 3.5 months in the laboratory, was also performed. Adsorption and degradation were studied in these soil and soil-biochar mixtures, and compared to results from a soil historically enriched with charcoal. Biochar amendment increased the pH in both soils and increased the water-holding capacity of the sandy soil. Adsorption of diuron was enhanced by biochar amendment in both soils, while glyphosate adsorption was decreased in the sandy soil. Ageing of soil-biochar mixtures decreased adsorption of both herbicides in comparison with freshly biochar-amended soil. Herbicide degradation rates were not consistently affected by biochar amendment or ageing in any of the soils. However, glyphosate half-lives correlated with the Freundlich Kf values in the clayey soil, indicating that degradation was limited by availability there.

Terrestrial discharges mediate trophic shifts and enhance methylmercury accumulation in estuarine biota

The input of mercury (Hg) to ecosystems is estimated to have increased two- to fivefold during the industrial era, and Hg accumulates in aquatic biota as neurotoxic methylmercury (MeHg). Escalating anthropogenic land use and climate change are expected to alter the input rates of terrestrial natural organic matter (NOM) and nutrients to aquatic ecosystems. For example, climate change has been projected to induce 10 to 50% runoff increases for large coastal regions globally. A major knowledge gap is the potential effects on MeHg exposure to biota following these ecosystem changes. We monitored the fate of five enriched Hg isotope tracers added to mesocosm scale estuarine model ecosystems subjected to varying loading rates of nutrients and terrestrial NOM. We demonstrate that increased terrestrial NOM input to the pelagic zone can enhance the MeHg bioaccumulation factor in zooplankton by a factor of 2 to 7 by inducing a shift in the pelagic food web from autotrophic to heterotrophic. The terrestrial NOM input also enhanced the retention of MeHg in the water column by up to a factor of 2, resulting in further increased MeHg exposure to pelagic biota. Using mercury mass balance calculations, we predict that MeHg concentration in zooplankton can increase by a factor of 3 to 6 in coastal areas following scenarios with 15 to 30% increased terrestrial runoff. The results demonstrate the importance of incorporating the impact of climate-induced changes in food web structure on MeHg bioaccumulation in future biogeochemical cycling models and risk assessments of Hg.

Seed Predation by the Shore Crab Carcinus maenas: A Positive Feedback Preventing Eelgrass Recovery?

There is an increasing interest to restore the ecosystem services that eelgrass provides, after their continuous worldwide decline. Most attempts to restore eelgrass using seeds are challenged by very high seed losses and the reasons for these losses are not all clear. We assess the impact of predation on seed loss and eelgrass establishment, and explore methods to decrease seed loss during restoration in the Swedish northwest coast. In a laboratory study we identified three previously undescribed seed predators, the shore crab Carcinus maenas, the hermit crab Pagurus bernhardus and the sea urchin Strongylocentrotus droebachiensis, of which shore crabs consumed 2–7 times more seeds than the other two species. The importance of shore crabs as seed predators was supported in field cage experiments where one enclosed crab caused 73% loss of seeds over a 1-week period on average (~ 21 seeds per day). Seedling establishment was significantly higher (14%) in cages that excluded predators over an 8-month period than in uncaged plots and cages that allowed predators but prevented seed-transport (0.5%), suggesting that seed predation constitutes a major source of seed loss in the study area. Burying the seeds 2 cm below the sediment surface prevented seed predation in the laboratory and decreased predation in the field, constituting a way to decrease seed loss during restoration. Shore crabs may act as a key feedback mechanism that prevent the return of eelgrass both by direct consumption of eelgrass seeds and as a predator of algal mesograzers, allowing algal mats to overgrow eelgrass beds. This shore crab feedback mechanism could become self-generating by promoting the growth of its own nursery habitat (algal mats) and by decreasing the nursery habitat (seagrass meadow) of its dominant predator (cod). This double feedback-loop is supported by a strong increase of shore crab abundance in the last decades and may partly explain the regime shift in vegetation observed along the Swedish west coast.

Lack of recognition of genetic biodiversity: International policy and its implementation in Baltic Sea marine protected areas

Genetic diversity is needed for species' adaptation to changing selective pressures and is particularly important in regions with rapid environmental change such as the Baltic Sea. Conservation measures should consider maintaining large gene pools to maximize species' adaptive potential for long-term survival. In this study, we explored concerns regarding genetic variation in international and national policies that governs biodiversity and evaluated if and how such policy is put into practice in management plans governing Baltic Sea Marine Protected Areas (MPAs) in Sweden, Finland, Estonia, and Germany. We performed qualitative and quantitative textual analysis of 240 documents and found that agreed international and national policies on genetic biodiversity are not reflected in management plans for Baltic Sea MPAs. Management plans in all countries are largely void of goals and strategies for genetic biodiversity, which can partly be explained by a general lack of conservation genetics in policies directed toward aquatic environments.

Pheromones and Other Semiochemicals for Monitoring Rare and Endangered Species

As global biodiversity declines, biodiversity and conservation have become ever more important research topics. Research in chemical ecology for conservation purposes has not adapted to address this need. During the last 10-15 years, only a few insect pheromones have been developed for biodiversity and conservation studies, including the identification and application of pheromones specifically for population monitoring. These investigations, supplemented with our knowledge from decades of studying pest insects, demonstrate that monitoring with pheromones and other semiochemicals can be applied widely for conservation of rare and threatened insects. Here, I summarize ongoing conservation research, and outline potential applications of chemical ecology and pheromone-based monitoring to studies of insect biodiversity and conservation research. Such applications include monitoring of insect population dynamics and distribution changes, including delineation of current ranges, the tracking of range expansions and contractions, and determination of their underlying causes. Sensitive and selective monitoring systems can further elucidate the importance of insect dispersal and landscape movements for conservation. Pheromone-based monitoring of indicator species will also be useful in identifying biodiversity hotspots, and in characterizing general changes in biodiversity in response to landscape, climatic, or other environmental changes.

Consequences for Piglet Performance of Group Housing Lactating Sows at One, Two, or Three Weeks Post-Farrowing

Housing lactating sows with piglets in a multi-suckling pen from around 14 days post-farrowing is common practice in Swedish organic piglet production. However, nursing-suckling interaction is less frequent in multi-suckling pens than in individual farrowing pens, thus affecting piglet performance, e.g., piglet growth. Moreover, piglet mortality is higher in systems using multi-suckling pens. Three management routines whereby lactating sows with piglets were moved from individual farrowing pens to multi-suckling pens at one, two, or three weeks post-farrowing were compared in terms of nursing-suckling interaction and piglet performance. Correlations between nursing-suckling interaction, piglet performance, and piglet mortality were also examined. In total, 43 Yorkshire sows with piglets were included in the study. Nursing-suckling interaction and all piglet performance parameters except piglet mortality did not differ between management routines. Piglet mortality in the individual farrowing pens did not differ between management routines, but piglet mortality in the multi-suckling pen was lower (P<0.05) when piglets were group housed at three weeks compared with one week post-farrowing. Overall piglet mortality was positively correlated with mortality in the multi-suckling pen for piglets group housed at one week (r = 0.61: P<0.05) and at two weeks post-farrowing (r = 0.62: P<0.05) but not for piglets group housed at three weeks post-farrowing. In conclusion, overall piglet mortality could be reduced if sows and piglets are group housed at three weeks post-farrowing and piglet survival the first week post-farrowing is improved.

Automatic segmentation of myocardium at risk from contrast enhanced SSFP CMR: validation against expert readers and SPECT

BACKGROUND

Efficacy of reperfusion therapy can be assessed as myocardial salvage index (MSI) by determining the size of myocardium at risk (MaR) and myocardial infarction (MI), (MSI = 1-MI/MaR). Cardiovascular magnetic resonance (CMR) can be used to assess MI by late gadolinium enhancement (LGE) and MaR by either T2-weighted imaging or contrast enhanced SSFP (CE-SSFP). Automatic segmentation algorithms have been developed and validated for MI by LGE as well as for MaR by T2-weighted imaging. There are, however, no algorithms available for CE-SSFP. Therefore, the aim of this study was to develop and validate automatic segmentation of MaR in CE-SSFP.

METHODS

The automatic algorithm applies surface coil intensity correction and classifies myocardial intensities by Expectation Maximization to define a MaR region based on a priori regional criteria, and infarct region from LGE. Automatic segmentation was validated against manual delineation by expert readers in 183 patients with reperfused acute MI from two multi-center randomized clinical trials (RCT) (CHILL-MI and MITOCARE) and against myocardial perfusion SPECT in an additional set (n = 16). Endocardial and epicardial borders were manually delineated at end-diastole and end-systole. Manual delineation of MaR was used as reference and inter-observer variability was assessed for both manual delineation and automatic segmentation of MaR in a subset of patients (n = 15). MaR was expressed as percent of left ventricular mass (%LVM) and analyzed by bias (mean ± standard deviation). Regional agreement was analyzed by Dice Similarity Coefficient (DSC) (mean ± standard deviation).

RESULTS

MaR assessed by manual and automatic segmentation were 36 ± 10% and 37 ± 11%LVM respectively with bias 1 ± 6%LVM and regional agreement DSC 0.85 ± 0.08 (n = 183). MaR assessed by SPECT and CE-SSFP automatic segmentation were 27 ± 10%LVM and 29 ± 7%LVM respectively with bias 2 ± 7%LVM. Inter-observer variability was 0 ± 3%LVM for manual delineation and -1 ± 2%LVM for automatic segmentation.

CONCLUSIONS

Automatic segmentation of MaR in CE-SSFP was validated against manual delineation in multi-center, multi-vendor studies with low bias and high regional agreement. Bias and variability was similar to inter-observer variability of manual delineation and inter-observer variability was decreased by automatic segmentation. Thus, the proposed automatic segmentation can be used to reduce subjectivity in quantification of MaR in RCT.

CLINICAL TRIAL REGISTRATION

NCT01379261. NCT01374321.