Assigning protein function from domain-function associations using DomFun

Background Protein function prediction remains a key challenge. Domain composition affects protein function. Here we present DomFun, a Ruby gem that uses associations between protein domains and functions, calculated using multiple indices based on tripartite network analysis. These domain-function associations are combined at the protein level, to generate protein-function predictions. Results We analysed 16 tripartite networks connecting homologous superfamily and FunFam domains from CATH-Gene3D with functional annotations from the three Gene Ontology (GO) sub-ontologies, KEGG, and Reactome. We validated the results using the CAFA 3 benchmark platform for GO annotation, finding that out of the multiple association metrics and domain datasets tested, Simpson index for FunFam domain-function associations combined with Stouffer’s method leads to the best performance in almost all scenarios. We also found that using FunFams led to better performance than superfamilies, and better results were found for GO molecular function compared to GO biological process terms. DomFun performed as well as the highest-performing method in certain CAFA 3 evaluation procedures in terms of $$F_{max}$$ F max and $$S_{min}$$ S min We also implemented our own benchmark procedure, Pathway Prediction Performance (PPP), which can be used to validate function prediction for additional annotations sources, such as KEGG and Reactome. Using PPP, we found similar results to those found with CAFA 3 for GO, moreover we found good performance for the other annotation sources. As with CAFA 3, Simpson index with Stouffer’s method led to the top performance in almost all scenarios. Conclusions DomFun shows competitive performance with other methods evaluated in CAFA 3 when predicting proteins function with GO, although results vary depending on the evaluation procedure. Through our own benchmark procedure, PPP, we have shown it can also make accurate predictions for KEGG and Reactome. It performs best when using FunFams, combining Simpson index derived domain-function associations using Stouffer’s method. The tool has been implemented so that it can be easily adapted to incorporate other protein features, such as domain data from other sources, amino acid k-mers and motifs. The DomFun Ruby gem is available from https://rubygems.org/gems/DomFun. Code maintained at https://github.com/ElenaRojano/DomFun. Validation procedure scripts can be found at https://github.com/ElenaRojano/DomFun_project.

The Organization of Diagnosis, Care and Funding for Specific Learning and Developmental Disorders (SLDD): A French Regional Experimental Protocol

Introduction: Access in France to early diagnosis and care for the most severe, but infrequent, Neurodevelopmental Disorders (NDD), autism spectrum disorder and global developmental delay, in children aged 0–7 was improved through measures implemented in 2019. However, there are no such measures for specific learning disorders (SLD), attention, motricity and language disorders (SLDD), despite their annual incidence of between 5 and 8%.Method: We describe the design of a new type of organization and financing of care for SLDD including evaluation procedure, as well as other factors, mainly at the prevention level that will contribute to local and national policy for this frequent health problem. This in response to a national call for projects, commonly called Article 51, targeted innovation in healthcare delivery and funding in the context of medium-term national reform. This provides project stakeholders with the opportunity to set up and implement “bottom-up” projects, mainly using local professionals. A joint initiative by the regional Health Authorities of the Occitanie region, the French Social Security system and a non-profit Association (Occitadys) proposed an experimental new structure of NDD care and funding.Discussion: We here discuss the design of this experiment that aims, over two to three years, to alleviate families' financial burden of care and establish a regional three-tier care system with respect to evaluation, re-education and rehabilitation care. Our approach may benefit SLDD health-care planning, and addresses the questions of prevention, early detection and care-design for families, taking local and socioeconomic disparities into account.

Comparison of form measurement results for optical aspheres and freeform surfaces

Comparing form measurement data for aspheres and freeform surfaces is an important tool for ensuring the quality and functionality of the devices used to take such measurements and may also allow the underlying measurement methods to be evaluated. However, comparing the highly accurate form measurements of such complex surfaces is a demanding task. It is difficult to analyze measurement results whose accuracies are in the range of several tens of nanometers root-mean-square, especially when comparing data with different, and anisotropic distributions of the 3D measurement points on the surface under test. In this paper, we investigate eight different 3D measurement point distributions that are typical of highly accurate measurement systems currently in use and demonstrate the effects of these distributions on the comparison results by using virtually generated data and applying different evaluation strategies. The results show that, for the examples investigated, the different 3D measurement point distributions can yield different levels of accuracy for the comparison. Furthermore, an improved evaluation procedure is proposed and recommendations on how to significantly reduce the influence of the different 3D measurement point distributions on the comparison result are given. A method of employing virtually generated test data is presented that may be generalized in order to further improve and validate future comparison methods.

Early pregnancy hyperglycaemia as a significant predictor of large for gestational age neonates

Aims We aimed to determine the effect of early pregnancy hyperglycaemia on having a large for gestational age (LGA) neonate. Methods A prospective cohort study was conducted among pregnant women in their first trimester. One-step plasma glucose (PG) evaluation procedure was performed to assess gestational diabetes mellitus (GDM) and diabetes mellitus (DM) in pregnancy as defined by the World Health Organization (WHO) criteria with International Association of Diabetes in Pregnancy Study Group (IADPSG) thresholds. The main outcome studied was large for gestational age neonates (LGA). Results A total of 2,709 participants were recruited with a mean age of 28 years (SD = 5.4) and a median gestational age (GA) of eight weeks (interquartile range [IQR] = 2). The prevalence of GDM in first trimester (T1) was 15.0% (95% confidence interval [CI] = 13.7–16.4). Previously undiagnosed DM was detected among 2.5% of the participants. Out of 2,285 live births with a median delivery GA of 38 weeks (IQR = 3), 7.0% were LGA neonates. The cumulative incidence of LGA neonates in women with GDM and DM was 11.1 and 15.5 per 100 women, respectively. The relative risk of having an LGA neonate among women with DM and GDM was 2.30 (95% CI = 1.23–4.28) and 1.80 (95% CI = 1.27–2.53), respectively. The attributable risk percentage of a LGA neonate for hyperglycaemia was 15.01%. T1 fasting PG was significantly correlated with both neonatal birth weight and birth weight centile. Conclusions The proposed WHO criteria for hyperglycaemia in pregnancy are valid, even in T1, for predicting LGA neonates. The use of IADPSG threshold for Fasting PG, for risk assessment in early pregnancy in high-risk populations is recommended.

Optimal Behavior of Spectral Line Analysis Through Fine Identification of Heavy Metal Lines in Crude Oil Using LIPS-Technique

Assessment of the quality of minerals, especially heavy ones, in crude oil by identifying spectral lines is very important to determine the quality and specifications of crude oil and the following treatments in production of the lines. In this study heavy metals lines (HMs) found in crude oil extracted from Iraq south field were identified that are unique spectral lines by using the laser-induced plasma spectroscopy (LIPS – mechanism), which were analyzed later by spectrometer based on the principle of finger print. The optimum spectrum (analytical lines) of metals emitted from the crude oil plasma in air were selected and determined. By determining the optimization behavior for evaluation procedure, the important condition was laser spot number (scan area). Comparison was performed between the fundamental wavelength and harmonic generation (HG) used in the laser beam to determine the optimum spectrum and optical insulator to cover the selected sample at atmospheric air pressure and room temperature. The results obtained from the actual raw spectrum were determined to represent the emission lines without the influence of foreign light (no noise) using the optical isolator, and unique new analytical lines were identified when increasing the number of lasers points up to 5 points, and a balanced spectrum was determined with good absorption when using a basic wavelength of 1064 nm. Difficulties were presented due to the characteristics of the crude oil as organic liquid case. The optimum results obtained indicated that the LIPS technique is effective and a control technique to well identify the spectrum lines of the heavy metals (HMs) presented in the crude oil.

The Influence of Budget and Financial Control in Selected Government Parastatals in Nigeria

The study examined budget and financial control in selected government parastatals in Nigeria. The survey research design was adopted in the study. Primary data was obtained using a well-designed questionnaire. Data gathered in the study was analyzed using descriptive, correlation analysis, logit regression analysis and other post estimation tests. Findings obtained in the study indicated that budget preparation exerts insignificant positive impact on financial control in Nigerian government parastatals with coefficient estimate of .034178 (p=0.195> 0.05); budget implementation exerts insignificant positive impact on financial control of Nigerian government parastatals with coefficient estimate of .0082354 (p=0.750> 0.05) and budget monitoring and evacuation exert insignificant positive impact on financial control, with coefficient estimate of .0468773 (p=0.234> 0.05). Premise on these findings, the study concluded that financial control on the average tends to increase as government parastatals experience effectual budget performance, with more budget preparation, implementation and monitoring and evaluation as opposed to the usual neglect of budget after implementation. Hence, it was suggested that government should ensure improvement in budget design; government should ensure adequate budget monitoring procedure and government should ensure viable budget evaluation procedure.

A viscoelastic in-plane damage model for fibrous composite materials

This work presents a viscoelastic in-plane damage model for fibrous composites. The material behavior is modeled as linear viscoelastic, with brittle failure in the fiber-dominated direction, and progressive degradation of the matrix-dominated properties, when the composite is loaded perpendicularly to the fibers or in in-plane shear. An evaluation procedure has been performed by comparing computational stress-strain curves against tensile tests curves under three different displacement rates. In addition, a calibration of the viscoelastic properties, by means of the response surface methodology, is also presented. The proposed material model has shown reasonable performance up to the material reaching an experimentally-verified modulus transition zone. Besides, the viscoelastic calibration procedure has produced a good agreement with the experimental results, concerning maximum stresses. It was observed that the computational stress-strain curve has deviated from the experimental one for higher stress values, indicating that it is necessary to improve the assessment of the nonlinear phenomena, which occur within the material.

Compliance Evaluation and Sustainable Resource Management in the CCAMLR

Regional fisheries organisations globally are feeling the impacts of non-compliant behaviour by both contracting and non-contracting parties. Non-compliance arising from activities such as illegal, unreported and unregulated fishing, or failures by flag states to appropriately report the activities of their vessels, has resulted in damage to the environment and damage to the performance of regional fisheries management organisations themselves. As a result, many of these organisations are adopting and implementing a relatively new mechanism to tackle non-compliance: the compliance evaluation procedure. This article demonstrates that by adopting a compliance evaluation procedure, regional fisheries organisations are better placed to identify and address non-compliance in an effort to improve compliance with their conservation measures. It analyses in detail the procedure adopted by one particular organisation, the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR), to suggest that implementation of their procedure has improved transparency, accountability and enforcement. It is argued that the CCAMLR compliance evaluation procedure represents a model for other polar and high seas areas to promote sustainable, and responsible, fishing practices globally.