Automatic classification of experimental models in biomedical literature to support searching for alternative methods to animal experiments.

Current animal protection laws require replacement of animal experiments with alternative methods, whenever such methods are suitable to reach the intended scientific objective. However, searching for alternative methods in the scientific literature is a time-consuming task that requires careful screening of an enormously large number of experimental biomedical publications. The identification of potentially relevant methods, e.g. organ or cell culture models, or computer simulations, can be supported with text mining tools specifically built for this purpose. Such tools are trained (or fine tuned) on relevant data sets labeled by human experts. We developed the GoldHamster corpus, composed of 1,600 PubMed (Medline) articles (titles and abstracts), in which we manually identified the used experimental model according to a set of eight labels, namely: "in vivo", "organs", "primary cells", "immortal cell lines", "invertebrates", "humans", "in silico" and "other" (models). We recruited 13 annotators with expertise in the biomedical domain and assigned each article to two individuals. Four additional rounds of annotation aimed at improving the quality of the annotations with disagreements in the first round. Furthermore, we conducted various machine learning experiments based on supervised learning to evaluate the corpus for our classification task. We obtained more than 7,000 document-level annotations for the above labels. After the first round of annotation, the inter-annotator agreement (kappa coefficient) varied among labels, and ranged from 0.42 (for "others") to 0.82 (for "invertebrates"), with an overall score of 0.62. All disagreements were resolved in the subsequent rounds of annotation. The best-performing machine learning experiment used the PubMedBERT pre-trained model with fine-tuning to our corpus, which gained an overall f-score of 0.83. We obtained a corpus with high agreement for all labels, and our evaluation demonstrated that our corpus is suitable for training reliable predictive models for automatic classification of biomedical literature according to the used experimental models. Our SMAFIRA - "Smart feature-based interactive" - search tool ( https://smafira.bf3r.de ) will employ this classifier for supporting the retrieval of alternative methods to animal experiments. The corpus is available for download ( https://doi.org/10.5281/zenodo.7152295 ), as well as the source code ( https://github.com/mariananeves/goldhamster ) and the model ( https://huggingface.co/SMAFIRA/goldhamster ).

Anchovy powder enrichment in brown rice-based instant cereal: a process optimization study using Response Surface Methodology (RSM).

There is a need for expanding the utilization of small fish as they constitute an undervalued and important source of protein and micronutrients in many developing countries suffering from micronutrient deficiencies. One way to increase consumption and health benefits is to add nutrient-rich fish meal into staple food ingredients. In this study, Response Surface Methodology (RSM) was applied to optimize the processing of an instant rice-based cereal enriched with anchovy powder. The Box-Behnken design was used to study the effect of principal processing variables (drying temperature, drum rotation speed, and slurry solids concentration) on product water activity, color, bulk density, and water solubility index. Viscosity, consistency, and cohesiveness of the reconstitute cereal were also evaluated. Empirical models were developed to describe the relationship between independent and dependent variables and showed regression coefficients (R 2) ranging between 71% and 98%. Higher drying temperatures resulted in reduced water activity, darker product color, and lower consistency. While drum speed influenced (p < .05) product color and water-binding capacity, bulk density, and consistency of the reconstituted product was associated with slurry solids concentration. Optimal processing conditions obtained from the study were temperature of 130°C, drum speed of 9.3 rpm, and solids concentration of 20.5%. These conditions would be useful in the production of brown rice-based instant cereal enriched with anchovy powder with desired quality properties.

Draft Genome Sequences of Pseudomonas sp. Isolates Recovered from Ghanaian Fish Food Samples in 2018.

The genus Pseudomonas represents a broad diversity of opportunistic and pathogenic species that are able to colonize a wide range of ecological niches. Here, we report on draft genome sequences of 35 Pseudomonas sp. isolates that were recovered from small processed Ghanaian fishes offered at food markets in 2018.

Composition of nutrients, heavy metals, polycyclic aromatic hydrocarbons and microbiological quality in processed small indigenous fish species from Ghana: Implications for food security.

The triple burden of malnutrition is an incessant issue in low- and middle-income countries, and fish has the potential to mitigate this burden. In Ghana fish is a central part of the diet, but data on nutrients and contaminants in processed indigenous fish species, that are often eaten whole, are missing. Samples of smoked, dried or salted Engraulis encrasicolus (European anchovy), Brachydeuterus auritus (bigeye grunt), Sardinella aurita (round sardinella), Selene dorsalis (African moonfish), Sierrathrissa leonensis (West African (WA) pygmy herring) and Tilapia spp. (tilapia) were collected from five different regions in Ghana. Samples were analyzed for nutrients (crude protein, fat, fatty acids, several vitamins, minerals, and trace elements), microbiological quality (microbial loads of total colony counts, E. coli, coliforms, and Salmonella), and contaminants (PAH4 and heavy metals). Except for tilapia, the processed small fish species had the potential to significantly contribute to the nutrient intakes of vitamins, minerals, and essential fatty acids. High levels of iron, mercury and lead were detected in certain fish samples, which calls for further research and identification of anthropogenic sources along the value chains. The total cell counts in all samples were acceptable; Salmonella was not detected in any sample and E. coli only in one sample. However, high numbers of coliform bacteria were found. PAH4 in smoked samples reached high concentrations up to 1,300 µg/kg, but in contrast salted tilapia samples had a range of PAH4 concentration of 1 µg/kg to 24 µg/kg. This endpoint oriented study provides data for the nutritional value of small processed fish as food in Ghana and also provides information about potential food safety hazards. Future research is needed to determine potential sources of contamination along the value chains in different regions, identify critical points, and develop applicable mitigation strategies to improve the quality and safety of processed small fish in Ghana.

Aeromonas spp. suggested as the causative agents of red spot disease in northern Vietnamese grass carp Ctenopharyngodon idella.

In northern Vietnam, a disease called 'red spot disease' has been causing high morbidity and mortality in populations of farmed grass carp Ctenopharyngodon idella for about 2 decades. The name 'red spot disease' refers to a condition characterised by haemorrhagic lesions, reddening and ulceration of the skin. Eight different bacterial isolates, namely Aeromonas hydrophila, A. sobria, Staphylococcus epidermidis, Vibrio alginolyticus, Pseudomonas fluorescens, P. luteola, Citrobacter freundii and P. putida, were isolated from diseased grass carp and used for experimental infection of the same species. Fish were challenged with the different bacterial isolates both by immersion and intramuscular injection. Different concentrations of bacteria were tested to evaluate their pathogenicity. Injection with 1 × 105 CFU of A. hydrophila and A. sobria resulted in clinical signs identical to those of red spot-diseased grass carp in Vietnam. None of the other bacterial isolates tested caused any morbidity or mortality in fish challenged either intramuscularly (1 × 106 CFU) or by bath immersion (1 × 106 or 1 × 108 CFU ml-1).

Leaves from banana (Musa nana) and maize (Zea mays) have no phyto-prophylactic effects on the susceptibility of grass carp (Ctenopharyngodon idella) to Aeromonas hydrophila infection.

BACKGROUND: The ubiquitous and opportunistic bacterial pathogen Aeromonas hydrophila has been associated with ulcerative dermatitis in fish, especially under stressful conditions. It can cause severe losses in fresh water aquaculture and is particularly prevalent in tropical and subtropical regions. Fresh leaves from maize and bananas have been used as feed supplement by fish farmers in Vietnam and it has been reported that they may have phyto-prophylactic benefits. In the present study, a feeding trial was conducted to investigate the benefits of providing maize and banana leaves as feed supplement: to determine if they were taken up and digested by grass carp (Ctenopharyngodon idella), if this uptake resulted in improved growth performance, and if leaf supplementation protected fish when challenged with A. hydrophila by intramuscular injection. RESULTS: All fish were fed an identical ratio of commercial pelleted feed relative to biomass. However, in 12/18 tanks, this diet was supplemented with either fresh banana leaves or fresh maize leaves; offered ad libitum. Addition of leaves increased the overall feed conversion ratio (FCR) significantly. However, if only the pellet were taken into account, then no difference was found between treatments. Changes to the isotopic composition of the fish showed leaf nutrient uptake occurred. No prophylactic effects of feeding banana or maize leaves were detected against infection with A. hydrophila, and the diet did not induce changes in the fish haematocrit. However, addition of the maize leaves was associated with significantly reduced severity of the skin lesions, which could improve the market value of the fish. CONCLUSIONS: Addition of the leaf supplement did not result in significantly improved growth performance. Similarly, the effect of the supplement on the fish survival to infection was not significant.

Dietary burden calculations relating to fish metabolism studies.

Fish farming is increasingly dependent on plant commodities as a source of feed leading to an increased risk for pesticide residues in aquaculture diets and consequently their transfer into aquaculture food products. The European pesticide regulation requires fish metabolism and fish feeding studies where residues in fish feed exceed 0.1 mg kg(-1) of the total diet (dry weight basis) to enable the setting of appropriate maximum residue levels in fish commodities. Fish dietary burden calculation is therefore an important prerequisite to decide on further experimental testing as part of the consumer risk assessment. In this review, the different aquaculture production systems are compared with regard to their specific feeding practices and the principles of dietary burden calculation are described.

15N tracer application to evaluate nitrogen dynamics of food webs in two subtropical small-scale aquaculture ponds under different managements.

Small, semi-intensively managed aquaculture ponds contribute significantly to the food security of small-scale farmers around the world. However, little is known about nutrient flows within natural food webs in such ponds in which fish production depends on the productivity of natural food resources. (15)N was applied as ammonium at 1.1 and 0.4 % of total nitrogen in a traditionally managed flow-through pond and a semi-intensively managed stagnant pond belonging to small-scale farmers in Northern Vietnam and traced through the natural food resources over 7 days. Small-sized plankton (1-60 µ m) was the dominant pelagic biomass in both ponds with higher biomass in the stagnant pond. This plankton assimilated major portions of the applied tracer and showed a high sedimentation and turnover rate. High re-activation of settled nutrients into the pelagic food web was observed. The tracer was removed more quickly from the flow-through pond than from the stagnant pond. A steady nutrient supply could increase fish production.