### Recent Submissions

• Journal Article

#### Do infants and preschoolers quantify probabilities based on proportions? ﻿

Royal Society Open Science 2020; 7(9) p.1-8: Art. 191751
Most statistical problems encountered throughout life require the ability to quantify probabilities based on proportions. Recent findings on the early ontogeny of this ability have been mixed: For example, when presented with jars containing preferred and less preferred items, 12-month-olds, but not 3- and 4-years-olds, seem to rely on the proportions of objects in the jars to predict the content of samples randomly drawn out of them. Given these contrasting findings, it remains unclear what the probabilistic reasoning abilities of young children are and how they develop. In our study, we addressed this question and tested, with identical methods across age groups and similar methods to previous studies, whether 12-month-olds and 3- and 4-years-olds rely on proportions of objects to estimate probabilities of random sampling events. Results revealed that neither infants nor preschoolers do. While preschoolers' performance is in line with previous findings, infants' performance is difficult to interpret given their failure in a control condition in which the outcomes happened with certainty rather than a graded probability. More systematic studies are needed to explain why infants succeeded in a previous study but failed in our study.
• Journal Article

#### Cavitation bubble dynamics and sonochemiluminescence activity inside sonicated submerged flow tubes ﻿

Chemical Engineering and Processing - Process Intensification 2020; 150
• Journal Article

#### The development of early pioneer neurons in the annelid Malacoceros fuliginosus ﻿

BMC Evolutionary Biology. 2020 Sep 14;20(1):117
Abstract Background Nervous system development is an interplay of many processes: the formation of individual neurons, which depends on whole-body and local patterning processes, and the coordinated growth of neurites and synapse formation. While knowledge of neural patterning in several animal groups is increasing, data on pioneer neurons that create the early axonal scaffold are scarce. Here we studied the first steps of nervous system development in the annelid Malacoceros fuliginosus. Results We performed a dense expression profiling of a broad set of neural genes. We found that SoxB expression begins at 4 h postfertilization, and shortly later, the neuronal progenitors can be identified at the anterior and the posterior pole by the transient and dynamic expression of proneural genes. At 9 hpf, the first neuronal cells start differentiating, and we provide a detailed description of axonal outgrowth of the pioneer neurons that create the primary neuronal scaffold. Tracing back the clonal origin of the ventral nerve cord pioneer neuron revealed that it is a descendant of the blastomere 2d (2d221), which after 7 cleavages starts expressing Neurogenin, Acheate-Scute and NeuroD. Conclusions We propose that an anterior and posterior origin of the nervous system is ancestral in annelids. We suggest that closer examination of the first pioneer neurons will be valuable in better understanding of nervous system development in spirally cleaving animals, to determine the potential role of cell-intrinsic properties in neuronal specification and to resolve the evolution of nervous systems.
• Journal Article

#### Molecular and Serological Footprints of Mycobacterium avium Subspecies Infections in Zoo Animals ﻿

Veterinary Sciences 2020; 7(3) p.1-14: Art. 117
Background: Mycobacteria of the Mycobacterium avium complex (MAC) pose a significant risk to zoological collections. Mycobacterium avium subspecies paratuberculosis (MAP) is a member of MAC and the causative agent of Johne’s disease. Despite many reports in animals kept in zoological gardens, systemic surveillance has rarely been reported. Methods: In this study, archived serum samples collected from animal species at the Wilhelma Zoological and Botanical Gardens in Stuttgart, Germany, were screened for the presence of antibodies against MAC and MAP. In addition, molecular investigations were performed on necropsy, fecal, and environmental samples. Results: In total, 30/381 serum samples of various mammalian species were positive for MAC antibodies in ELISA, while one sample of a reticulated giraffe (Giraffa camelopardalis reticulata) was positive in MAP-specific ELISA. Samples from many species were positive in pan-Mycobacterium real-time PCR (40/43 fecal samples, 27/43 environmental samples, and 31/90 necropsy samples). Surprisingly, no sample was positive in the MAP-specific molecular assays. However, two environmental samples from primate enclosures were positive in Mycobacterium avium subspecies hominissuis (MAH)-specific real-time PCR. Conclusions: The results reveal serological indications of MAC infections in the zoological collection. However, the presence of a MAP-contaminated environment by a high-shedding individual animal or MAP-infected population is unlikely.
• Journal Article

#### Meat Quality Parameters and Sensory Properties of One High-Performing and Two Local Chicken Breeds Fed with Vicia faba ﻿

Foods 2020; 9(8) p.1-18: Art. 1052
The current practices of the poultry industry have raised concerns among consumers. Among these is the culling of day-old male chicks of laying hybrids; a suitable alternative for this could be the use of dual-purpose breeds where both sexes are used. Another practice that causes concern is the import of large quantities of soybeans for feedstuff production. Substitutes for these soybean-based products are regional protein crops, such as faba beans (Vicia faba L.; FBs). The objective of this study was to test the suitability of FB as a locally produced soybean meal replacement for two local dual-purpose chicken breeds and one high-performing layer line. The breast and leg meat of male Bresse Gauloise (BG), Vorwerkhuhn (VH), and White Rock (WR) animals was evaluated for different meat quality parameters: pH, color, water holding capacity, and tenderness. Sensory properties of the samples were evaluated by a trained panel with a conventional descriptive analysis. Results show different effects of FB diets on meat quality parameters in the different breeds. The attributes mostly affected by the diet are related to aroma, flavor, and texture, particularly in VH and WR. Overall, faba beans appear to be an acceptable dietary protein source for rearing these breeds for meat production.
• Journal Article

#### The Effect of Algae or Insect Supplementation as Alternative Protein Sources on the Volatile Profile of Chicken Meat ﻿

Foods 2020; 9(9) p.1-15: Art. 1235
The aim of this study was to investigate the differences in the volatile profile of meat from chickens fed with alternative protein diets (such as algae or insect) through two different trials. In Trial 1, broiler chicken at one day of age were randomly allocated to three experimental groups: a basal control diet (C) and two groups in which the soybean meal was replaced at 75% (in the starter phase) and 50% (in the grower phase) with partially defatted Hermetia illucens (HI) larvae or Arthrospira platensis (SP). In Trial 2, broiler chickens were housed and reared similar to Trial 1, with the exception that the experimental diets replaced soybean meal with either 100% partially defatted HI or 100% SP. In both trials, chickens were slaughtered at day 35. Per group, 10 chickens were submitted to volatile analysis by using solid-phase microextraction (HS-SPME) and gas chromatography–mass spectrometry (GC-MS) analysis. Results in both trials showed that levels of several lipid-derived compounds were found to be lower in chickens fed an HI diet, which could be linked to a possibly lower level of polyunsaturated fatty acid content in HI-fed chicken. In addition, the dietary treatments could be discriminated based on the volatile profile, i.e., the substitution of soy with HI or SP distinctively affected the levels of flavor compounds.
• Journal Article

#### Studded leather collars are very effective in protecting cattle from leopard (Panthera pardus) attacks ﻿

Ecological Solutions and Evidence 2020; 1(1) p.1-9: Art. e12013
1. Human‐wildlife conflicts are widespread, particularly with big cats which can kill domestic livestock and create a counteraction between conservation and local livelihoods, especially near protected areas. Minimisation of livestock losses caused by big cats and other predators is essential to mitigate conflicts and promote socially acceptable conservation. As big cats usually kill by throat bites, protective collars represent a potentially effective non‐lethal intervention to prevent livestock depredation, yet the application and effectiveness estimation of these tools are very limited. 2. In this study, for the first time we measured the effectiveness of studded leather collars in protecting cattle from leopard (Panthera pardus) attacks. We conducted a randomised controlled experiment during 14 months to collar 202 heads and leave uncollared 258 heads grazing in forests and belonging to 27 owners from eight villages near three protected areas in Mazandaran Province, northern Iran. 3. Our results show that none of collared cattle and nine uncollared cattle were lost to leopard depredation, meaning that collars caused a zero relative risk of damage and a perfect 100% damage reduction. Most losses occurred in summer and autumn due to lush vegetation attracting more cattle, long daytime allowing movements deep into leopard habitats and dense cover favouring leopard hunts from ambush. Losses were recorded in only six owners and four villages, suggesting local rarity and patchy distribution of leopards. 4. We suggest that collars can be successfully applied to cattle freely grazing in habitats of leopards or other felids for a long time and thus remaining persistently exposed to depredation. As grazing cattle are usually not supervised by shepherds or dogs, collars can be the only practical protection tool. Production and sales of collars can become a sustainable small‐scale business for farmers to further boost conservation and rural livelihoods.
• Journal Article

#### A new dataset on plant occurrences on smallislands, including species abundances andfunctional traits across different spatial scales ﻿

Biodiversity Data Journal 2020; 8 p.1-16: Art. e55275
Background We introduce a new dataset of woody plants on 60 small tropical islands located in the Raja Ampat archipelago in Indonesia. The dataset includes incidence, abundance and functional trait data for 57 species. All islands were sampled using a standardised transect and plot design providing detailed information on plant occurrences at different spatial scales ranging from the local (plot and transect scale) to the island scale. In addition, the dataset includes information on key plant functional traits linked to species dispersal, resource acquisition and competitive strategies. The dataset can be used to address ecological questions connected to the species-area relationship and community assembly processes on small islands and in isolated habitats. New information The dataset yields detailed information on plant community structure and links incidence, abundance and functional trait data at different spatial scales. Furthermore, this is the first plant-island dataset for the Raja Ampat archipelago, a remote and poorly studied region, and provides important new information on species occurrences.
• Journal Article

#### On the Leucanthemopsis alpina (L.) Heywood growing in the Illyrian region ﻿

PhytoKeys 2020; 161 p.27-40
Leucanthemopsis alpina (L.) Heywood (Asteraceae, Anthemideae) is a small, caespitose plant growing in high alpine environments in all the main southern European mountain ranges. However, the species status in the Balkan Peninsula (and especially in the Dinaric Alps) is not very well known. Surrounding this area, different L. alpina subspecies are found in the Eastern Alps and in the Carpathians. These subspecies differ from one another, both morphologically and in chromosome number. The present study aims to better characterise the populations of L. alpina in the Illyrian and Balkan regions by undertaking a comprehensive survey of herbarium collections for the species in this area, by applying flow cytometry for ploidy determination and by sequencing of two chloroplast markers. Results from our investigation suggest that the only population of the species in the Dinaric Alps is found in the Vranica Mts (Bosnia and Herzegovina). This population consists of diploid plants (unlike tetraploid populations from the Eastern Alps) that are slightly distinct genetically from those of the subspecies growing in the Eastern Alps and the Tatra Mts. Both the ploidy and their genetic distinction indicate that Vranica Mts most probably served as a refugium for the species during the Pleistocene glaciations. Considering its isolated geographical range and its genetic distinction, the population of L. alpina growing in the Vranica Mts should be considered as a separate subspecies.
• Journal Article

#### Water–rock interactions in the Bruchsal geothermal system by U–Th series radionuclides ﻿

Geothermal Energy. 2020 Sep 08;8(1):24
• Journal Article

#### De novo sequencing, assembly and functional annotation of Armillaria borealis genome ﻿

BMC Genomics. 2020 Sep 10;21(Suppl 7):534
Abstract Background Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm. & Korhonen) is a fungus from the Physalacriaceae family (Basidiomycota) widely distributed in Eurasia, including Siberia and the Far East. Species from this genus cause the root white rot disease that weakens and often kills woody plants. However, little is known about ecological behavior and genetics of A. borealis. According to field research data, A. borealis is less pathogenic than A. ostoyae, and its aggressive behavior is quite rare. Mainly A. borealis behaves as a secondary pathogen killing trees already weakened by other factors. However, changing environment might cause unpredictable effects in fungus behavior. Results The de novo genome assembly and annotation were performed for the A. borealis species for the first time and presented in this study. The A. borealis genome assembly contained ~ 68 Mbp and was comparable with ~ 60 and ~ 79.5 Mbp for the A. ostoyae and A. mellea genomes, respectively. The N50 for contigs equaled 50,544 bp. Functional annotation analysis revealed 21,969 protein coding genes and provided data for further comparative analysis. Repetitive sequences were also identified. The main focus for further study and comparative analysis will be on the enzymes and regulatory factors associated with pathogenicity. Conclusions Pathogenic fungi such as Armillaria are currently one of the main problems in forest conservation. A comprehensive study of these species and their pathogenicity is of great importance and needs good genomic resources. The assembled genome of A. borealis presented in this study is of sufficiently good quality for further detailed comparative study on the composition of enzymes in other Armillaria species. There is also a fundamental problem with the identification and classification of species of the Armillaria genus, where the study of repetitive sequences in the genomes of basidiomycetes and their comparative analysis will help us identify more accurately taxonomy of these species and reveal their evolutionary relationships.
• Journal Article

#### Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data ﻿

BMC Genomics. 2020 Sep 11;21(1):624
• Journal Article

#### Buffalopox Virus: An Emerging Virus in Livestock and Humans ﻿

Pathogens 2020; 9(9) p.1-9: Art. 676
Buffalopox virus (BPXV) is the cause of buffalopox, which was recognized by the FAO/WHO Joint Expert Committee on Zoonosis as an important zoonotic disease. Buffalopox was first described in India, later in other countries, and has become an emerging contagious viral zoonotic disease infecting milkers with high morbidity among affected domestic buffalo and cattle. BPXV is a member of the genus Orthopoxvirus and a close variant of the vaccinia virus (VACV). Recent genome data show that BPXV shares a most recent common ancestor of VACV Lister strain, which had been used for inoculating buffalo calves to produce a Smallpox vaccine. Over time, VACV evolved into BPXV by establishing itself in buffaloes to be increasingly pathogenic to this host and to make infections in cattle and humans. Together with the current pandemic of SARS-COV2/COVID 19, BPXV infections illustrate how vulnerable the human population is to the emergence and re-emergence of viral pathogens from unsuspected sources. In view that majority of the world population are not vaccinated against smallpox and are most vulnerable in the event of its re-emergence, reviewing and understanding the biology of vaccinia-like viruses are necessary for developing a new generation of safer smallpox vaccines in the smallpox-free world.
• Journal Article

#### Plasma Treatment of Polypropylene-Based Wood–Plastic Composites (WPC): Influences of Working Gas ﻿

Polymers 2020; 12(9) p.1-15: Art. 1933
In this study, a polypropylene (PP)-based wood–plastic composite with maleic anhydride-grafted polypropylene (MAPP) as a coupling agent and a wood content of 60% was extruded and specimens were injection molded. The samples were plasma treated utilizing a dielectric barrier discharge (DBD) setup with three different working gases: Ar/O$_2$ (90%/10%), Ar/N$_2$ (90%/10%), and synthetic air. This process aims to improve the coating and gluing properties of the otherwise challenging apolar surface of PP based wood–plastic composites (WPC). Chemical analysis with X-ray photoelectron spectroscopy (XPS) and Fourier-transform infrared spectroscopy (FTIR) showed the formation of oxygen-based functional groups on the surface, independently from the working gas used for the treatment. Laser scanning microscopy (LSM) examined the surface roughness and revealed that the two argon-containing working gases roughened the surface more than synthetic air. However, the contact angle for water was reduced significantly after treatment, revealing measurement artifacts for water and diiodomethane due to the severe changes in surface morphology. The adhesion of acrylic dispersion coating was significantly increased, resulting in a pull-off strength of approximately 4 N/mm$^2$, and cross-cut tests assigned the best adhesion class (0), on a scale from 0 to 5, after plasma treatment with any working gas.
• Journal Article

#### Egg Production and Bone Stability of Local Chicken Breeds and Their Crosses Fed with Faba Beans ﻿

Animals 2020; 10(9) p.1-20: Art. 1480
Poultry production is raising concerns within the public regarding the practice of culling day-old chicks and the importation of soy from overseas for feedstuff. Therefore, an alternative approach to poultry production was tested. In two consecutive experiments, two traditional chicken breeds, Vorwerkhuhn and Bresse Gauloise, and White Rock as a commercial layer genotype as well as crossbreds thereof were fed diets containing either 20% vicin-rich or vicin-poor faba beans, though addressing both subjects of debate. Hen performance traits and bone stability were recorded. All parameters were considerably influenced by the genotype with White Rock showing the significantly highest (p < 0.05) laying performance (99.4% peak production) and mean egg weights (56.6 g) of the purebreds, but the lowest bone breaking strength (tibiotarsus 197.2 N, humerus 230.2 N). Regarding crossbreds, the Bresse Gauloise × White Rock cross performed best (peak production 98.1%, mean egg weight 58.0 g). However, only limited dietary effects were found as only the feeding of 20% vicin-rich faba beans led to a significant reduction of egg weights of at most 1.1 g (p < 0.05) and to a significant reduction of the shell stability in the crossbred genotypes. In terms of dual-purpose usage, crossing of Bresse Gauloise with White Rock seems to be the most promising variant studied here.
• Journal Article

#### Quantitative Modelling and Perspective Taking: Two Competencies of Decision Making for Sustainable Development ﻿

Sustainability 2020; 12(17) p.1-32: Art. 6980
Land use change, natural resource use and climate change are challenging Sustainable Development issues (SDGs 13–15). Fostering the competencies to deal with such issues is one core task for current educational endeavors. Among these competencies, decision-making competencies are central. In detail, we investigate how learners evaluate alternative decision-making options to improve existing competence models. We exemplify our competence modelling approach using the designation of a Marine Protected Area. The cross-sectional sample consists of secondary school students and student teachers (N = 760). Partial Credit modelling shows that quantitative modelling of decision-making options is a different competence dimension than perspective taking if contextualized for Sustainable Development. In quantitative modelling, mathematical modelling is used to evaluate and reflect on decision-making options. Perspective taking covers the ability to consider different normative perspectives on Sustainable Development issues. Both dimensions show plausible (latent) correlations with related constructs within the nomological net, i.e., with qualitative arguing, economic literacy, mathematical competencies, reading competencies and analytical problem solving. Furthermore, person-abilities increase with level of education for both dimensions. The identified competence dimensions quantitative modelling and perspective taking were successfully modelled and shown to be distinct; the resulting measuring instrument is reliable and valid.
• Journal Article

#### Assessing the Effect of Diesel Fuel on the Seed Viability and Germination of Medicago sativa Using the Event-Time Model ﻿

Plants 2020; 9(9) p.1-9: Art. 1062
The remediation of contaminated sites using plant-based techniques has gained increasing attention in recent decades. However, information on the effects of contaminant imbibition on seed viability and germination rates are often lacking in the literature. To this end, our research investigated, by means of an event-time model, the effect of diesel fuel imbibition on the seed viability and germination rate of Medicago sativa, a plant species with great potential for remediation of organic contaminants. The event-time model provided an accurate and biologically relevant method for analysing germination data. Our results reveal that the direct imbibition of diesel fuel by M. sativa seeds for ≤48 h, or their exposure to soil diesel fuel concentrations of 0–10 g/kg diesel fuel, affects their germination rates, as shown by increasing t50 values from 90.6 (±2.78) to 114.2 (±2.67) hours, without significantly affecting seed viability. On the other hand, diesel fuel imbibition of longer duration, or the exposure of M. sativa seeds to ≥20 g/kg diesel fuel-contaminated soils, leads to no further effect on time to seed emergence. Instead, these conditions compromise seed viability, resulting in a decrease in the proportion of germinated seeds from 0.91 (±0.03) in 10 g/kg diesel fuel contaminated soil to 0.84 (±0.04) and 0.70 (±0.05) in 20 and 30 g/kg diesel fuel-contaminated soils, respectively. The fact that low concentrations of diesel fuel and 0–48 h of direct imbibition delayed seed emergence without adversely affecting the percentage of viable seeds suggests that this inhibitory effect on germination at low diesel fuel exposure could be attributed more to physical constraints rather than biological damage on the seeds. The models used in this study provide an accurate and biologically relevant method for the analyses of germination data. This is vital since expensive germination experiments, be it in the field of toxicology or agriculture, deserve to be accurately analysed.
• Journal Article

#### Estimating the Aboveground Biomass of an Evergreen Broadleaf Forest in Xuan Lien Nature Reserve, Thanh Hoa, Vietnam, Using SPOT-6 Data and the Random Forest Algorithm ﻿

International Journal of Forestry Research 2020; 2020 p.1-13: Art. 4216160
Forest biomass is an important ecological indicator for the sustainable management of forests. The aim of this study was to estimate forest aboveground biomass (AGB) by integrating SPOT-6 data with field-based measurements using the random forest (RF) algorithm. In total, 52 remote sensing variables, including spectral bands, vegetation indices, topography data, and textures, were extracted from SPOT-6 images to predict the forest AGB of Xuan Lien Nature Reserve, Vietnam. To determine the optimal predictor variables for AGB estimation, 10 different RF models were built. To evaluate these models, 10-fold cross-validation was applied. We found that a combination of spectral and vegetation indices and topography variables offer the highest prediction results ( R$^2_{\textit{adj}}$ = 0.74 and RMSE = 61.24 Mg ha$^{−1}$). Adding texture features into the predictor variables did not improve the model performance. In addition, the SPOT-6 sensor has the potential to predict forest AGB using the RF algorithm.
• Journal Article

#### Rainforest conversion to smallholder plantations of rubber or oil palm leads to species loss and community shifts in canopy ants (Hymenoptera: Formicidae) ﻿

Myrmecological News 2020; 30 p.175-186
Currently, our understanding of the responses of ant communities under rainforest conversion to cash crops in SE Asia is based on comparisons of primary rainforests to large company-owned oil palm estates in Malaysian Borneo and a few comparisons of natural forests to rubber plantations in Thailand and China. In Indonesia, second largest rubber producer and largest oil palm producer worldwide, the vast majority of its rubber economy and almost half its oil palm acreage relies on smallholder farmers. This study compares canopy ant communities among four land-use systems in Jambi Province, Sumatra, Indonesia: 1) lowland rainforest, 2) jungle rubber (i.e., extensive rubber cultivation), and monoculture plantations of 3) rubber or 4) oil palm. Smallholder plantations of rubber and oil palm support less than 25% of the abundance and less than 50% of the canopy ant species richness in lowland rainforest, with intermediate levels in jungle rubber. Canopy ant communities from rainforest and jungle rubber were similar and differed from those in monoculture rubber and oil palm plantations, which each hosted distinct communities. Nestedness and turnover also differed between rainforest and jungle rubber on the one hand and rubber and oil palm on the other. This pattern was in part due to significantly greater proportions of tramp ants in the monoculture plantations: While virtually absent in forest (< 1%), six tramp ant species accounted for 9.8% of the collected ant individuals in jungle rubber, 26.6% in rubber and 41.1% in oil palm plantations (up to 88.1% in one studied plantation). Overall, this study improves our understanding of the effects of rainforest conversion to cash crop plantations of rubber and oil palm on ant communities by incorporating smallholder systems in one of the most important regions for oil palm and rubber production worldwide.
• Journal Article

#### Analysis of the brain transcriptome in lines of laying hens divergently selected for feather pecking ﻿

BMC Genomics. 2020 Aug 27;21(1):595
Abstract Background Feather pecking (FP) in laying hens reduces animal welfare and leads to economic losses for the layer industry. FP is considered a heritable condition that is influenced by dysregulation of neurotransmitter homeostasis, the gut microbiome, and the immune system. To identify genes and biological pathways responsible for FP behavior we compared the brain transcriptomes of 48 hens divergently selected for FP. In addition, we tested if high feather peckers (HFP) and low feather peckers (LFP) respond differently to light since light has been shown to trigger FP behavior. Results Of approximately 48 million reads/sample an average of 98.4% were mapped to the chicken genome (GRCg6a). We found 13,070 expressed genes in the analyzed brains of which 423 showed differential expression between HFP and LFP. Genes of uncertain function and non-coding RNAs were overrepresented among those transcripts. Functional analyses revealed the involvement of cholinergic signaling, postsynaptic activity, membrane channels, and the immune system. After the light stimulus, 28 genes were found to be differentially expressed. These included an interaction cluster of core components of the circadian clock. However, differences in the response to light between HFP and LFP were not detectable. Conclusions Genes involved in cholinergic signaling, channel activity, synaptic transmission, and immune response were found to be involved in FP behavior. We propose a model in which the gut microbiota modulates the immune system, which in turn affects cholinergic signaling. This might have an influence on monoamine signaling with possible involvement of GABA or glutamate signaling.