Biodiversity Studies for Sustainable Lagoon: Thermophilic and Tropical Fish Species vs. Endemic Commercial Species at Mellah Lagoon (Mediterranean, Algeria)

Lagoons play an important socio-economic role and represent a precious natural heritage at risk from fishing pressure and chemical and biological pollution. Our research focused on better understanding the discrimination of fish biodiversity, the detection of non-indigenous species, and the valorization of commercial indigenous species at Mellah lagoon (Algeria). Taxonomic characterization and barcoding for all fish species and Inkscape schematic drawings for the most common species are provided. A total of 20 families and 37 species were recorded. The thermophilic species Coris julis, Thalassoma pavo, and Aphanius fasciatus and tropical species such as Gambusia holbrooki and Parablennius pilicornis were identified. Numerous Mediterranean species of socio-economic importance are highlighted, and detailed information is summarized for the lagoon’s sustainability. This short-term evaluation goes hand in hand with long-term programs documenting the interaction between indigenous and non-indigenous species in the lagoon and will allow the development of a provisional relationship model for future studies. Thermophilic and tropical species patterns in the Mellah lagoon are presented. Taken together, we provide useful data that can guide future investigations and may become a potential management tool for achieving the Sustainable Development Goals and protecting species with large socio-economic roles from potential thermal stress impact

Climate Change and Reproductive Biocomplexity in Fishes: Innovative Management Approaches towards Sustainability of Fisheries and Aquaculture

The ongoing rapid climate change, combined with the disturbance of fish breeding grounds, may impact reproduction by endangering successful breeding and survival, and thus affect the viable sustainability in aquaculture systems as well as in the sea. In this study we focus on the biocomplexity of fish reproduction in response to climate change. Further, we propose adaptive strategies, including technological advancements, using a noninvasive and non-lethal approach, and we outline an assisted reproduction and nutrigenomics approach to mitigating fish reproductive risks posed by climate change. This was done in an effort to monitor fish aquaculture and ensure that, as a livelihood, it may provide a useful source of nutrition for our society

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

We present an updated and integrated version of our widely used protein–protein docking and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality structures of protein–protein complexes along with the unbound structures of their components. Fifty-five new complexes were added to the docking benchmark, 35 of which have experimentally measured binding affinities. These updated docking and affinity benchmarks now contain 230 and 179 entries, respectively. In particular, the number of antibody–antigen complexes has increased significantly, by 67% and 74% in the docking and affinity benchmarks, respectively. We tested previously developed docking and affinity prediction algorithms on the new cases. Considering only the top 10 docking predictions per benchmark case, a prediction accuracy of 38% is achieved on all 55 cases and up to 50% for the 32 rigid-body cases only. Predicted affinity scores are found to correlate with experimental binding energies up to r = 0.52 overall and r = 0.72 for the rigid complexes.Peer ReviewedPostprint (author's final draft

Rapid tests and urine sampling techniques for the diagnosis of urinary tract infection (UTI) in children under five years: a systematic review

Background: Urinary tract infection (UTI) is one of the most common sources of infection in children under five. Prompt diagnosis and treatment is important to reduce the risk of renal scarring. Rapid, cost-effective, methods of UTI diagnosis are required as an alternative to culture. Methods: We conducted a systematic review to determine the diagnostic accuracy of rapid tests for detecting UTI in children under five years of age. Results: The evidence supports the use of dipstick positive for both leukocyte esterase and nitrite (pooled LR+ = 28.2, 95% CI: 17.3, 46.0) or microscopy positive for both pyuria and bacteriuria (pooled LR+ = 37.0, 95% CI: 11.0, 125.9) to rule in UTI. Similarly dipstick negative for both LE and nitrite (Pooled LR- = 0.20, 95% CI: 0.16, 0.26) or microscopy negative for both pyuria and bacteriuria (Pooled LR- = 0.11, 95% CI: 0.05, 0.23) can be used to rule out UTI. A test for glucose showed promise in potty-trained children. However, all studies were over 30 years old. Further evaluation of this test may be useful. Conclusion: Dipstick negative for both LE and nitrite or microscopic analysis negative for both pyuria and bacteriuria of a clean voided urine, bag, or nappy/pad specimen may reasonably be used to rule out UTI. These patients can then reasonably be excluded from further investigation, without the need for confirmatory culture. Similarly, combinations of positive tests could be used to rule in UTI, and trigger further investigation

Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics

The BITS2011 meeting, held in Pisa on June 20-22, 2011, brought together more than 120 Italian researchers working in the field of Bioinformatics, as well as students in Bioinformatics, Computational Biology, Biology, Computer Sciences, and Engineering, representing a landscape of Italian bioinformatics research

How does study quality affect the results of a diagnostic meta-analysis?

Background: The use of systematic literature review to inform evidence based practice in diagnostics is rapidly expanding. Although the primary diagnostic literature is extensive, studies are often of low methodological quality or poorly reported. There has been no rigorously evaluated, evidence based tool to assess the methodological quality of diagnostic studies. The primary objective of this study was to determine the extent to which variations in the quality of primary studies impact the results of a diagnostic meta-analysis and whether this differs with diagnostic test type. A secondary objective was to contribute to the evaluation of QUADAS, an evidence-based tool for the assessment of quality in diagnostic accuracy studies. Methods: This study was conducted as part of large systematic review of tests used in the diagnosis and further investigation of urinary tract infection (UTI) in children. All studies included in this review were assessed using QUADAS, an evidence-based tool for the assessment of quality in systematic reviews of diagnostic accuracy studies. The impact of individual components of QUADAS on a summary measure of diagnostic accuracy was investigated using regression analysis. The review divided the diagnosis and further investigation of UTI into the following three clinical stages: diagnosis of UTI, localisation of infection, and further investigation of the UTI. Each stage used different types of diagnostic test, which were considered to involve different quality concerns. Results: Many of the studies included in our review were poorly reported. The proportion of QUADAS items fulfilled was similar for studies in different sections of the review. However, as might be expected, the individual items fulfilled differed between the three clinical stages. Regression analysis found that different items showed a strong association with test performance for the different tests evaluated. These differences were observed both within and between the three clinical stages assessed by the review. The results of regression analyses were also affected by whether or not a weighting (by sample size) was applied. Our analysis was severely limited by the completeness of reporting and the differences between the index tests evaluated and the reference standards used to confirm diagnoses in the primary studies. Few tests were evaluated by sufficient studies to allow meaningful use of meta-analytic pooling and investigation of heterogeneity. This meant that further analysis to investigate heterogeneity could only be undertaken using a subset of studies, and that the findings are open to various interpretations. Conclusion: Further work is needed to investigate the influence of methodological quality on the results of diagnostic meta-analyses. Large data sets of well-reported primary studies are needed to address this question. Without significant improvements in the completeness of reporting of primary studies, progress in this area will be limited

Pathological, bacteriological and virological findings in sudden and unexpected deaths in young dogs

In human medicine, “sudden death” has been defined by the World Health Organization (WHO) as a non‐violent, unexpected death occurring less than 24 h from the onset of symptoms. The aims of this study were: (1) to estimate the proportional mortality ratio for “sudden and unexpected death” (SUD) in young dogs; (2) to investigate the pathological and microbiological findings in SUD cases in young dogs. For these purposes, a retrospective study of a total of 145 cases of young dead dogs was performed. For each case, we collected information about the age, medical history and the gross and microbiological findings of the animals. The results of this study found 21 cases of SUD. The most frequently observed clinical symptoms in the cases of sudden death were acute respiratory symptoms, followed by acute gastroenteric symptoms, non‐specific symptoms and neurological symptoms. The evaluation of necropsy reports allowed us to observe enteritis in 18 out of 21 cases and pneumonia in seven out of 21 cases. Viral infection with Canine parvovirus type 2 was the most common cause of SUD observed. These results could provide a valuable tool for the investigation of sudden death in young dogs