National trends in surgical subspecialisation in ophthalmology in the USA

Background/aimsTo assess surgical patterns in ophthalmology by subspecialty in the USA.MethodsOphthalmic surgeons were categorised as comprehensive/subspecialist based on billed procedures in the 2017–2018 Medicare Provider Utilization and Payment Data. Poisson regression models assessed factors associated with physicians performing surgeries in the core domain (eg, cataract extractions) and subspecialty domain. Models were adjusted for provider gender, time since graduation, geographical region, practice setting and hospital affiliation.ResultsThere were 10 346 ophthalmic surgeons, 74.7% comprehensive and 25.3% subspecialists. Cataract extractions were performed by 6.0%, 9.9%, 21.0%, 88.1% and 95.3% of specialists in surgical retina, neuro-ophthalmology/paediatrics, oculoplastics, glaucoma and cornea, respectively. Retina specialists were more likely to perform cataract surgery if they were 20–30 or>30 years in practice (relative risk: 2.20 (95% CI: 1.17 to 4.12) and 3.74 (95% CI: 1.80 to 7.76), respectively) or in a non-metropolitan setting (3.78 (95% CI: 1.71 to 8.38)). Among oculoplastics specialists, male surgeons (2.71 (95% CI: 1.36 to 5.42)), those in practice 10–20 years or 20–30 years (1.93 (95% CI: 1.15 to 3.26) and 1.91 (95% CI: 1.11 to 3.27), respectively) and in non-metropolitan settings (3.07 (95% CI: 1.88 to 5.02)) were more likely to perform cataract surgery. Only 26 of the 2620 subspecialists performed surgeries in two or more subspecialty domains.ConclusionsThere is a trend towards surgical subspecialisation in ophthalmology in the USA whereby some surgeons focus their surgical practice on subspecialty procedures and rarely perform surgeries in the core domain.

Measuring Brazilian Portuguese Product Titles Similarity using Embeddings

Textual similarity deals with determining how similar two pieces of texts are, considering the lexical (surface forms) or semantic (meaning) closeness. In this paper we applied word embeddings for measuring e-commerce product title similarity in Brazilian Portuguese. We generated some domainspecific word embeddings (using Word2Vec, FastText and GloVe) and compared them with general-domain models (word embeddings and BERT models). We concluded that the cosine similarity calculated using the domain-specific word embeddings was a good approach to distinguish between similar and nonsimilar products, but the multilingual BERT pre-trained model proved to be the best one.

Structural comparative modeling of multi-domain ΔF508 CFTR

Cystic Fibrosis (CF) is a common genetic disease caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), an epithelial anion channel expressed in several vital organs. Absence of functional CFTR results in imbalanced osmotic equilibrium and subsequent mucus build up in the lungs - which increases the risk of infection and eventually causes death. CFTR is an ATP binding cassette (ABC) transporter composed of two transmembrane domains (TMDs), two nucleotide binding domains (NBDs), and an unstructured regulatory domain. The most prevalent patient mutation is the deletion of F508 (ΔF508), making ΔF508 CFTR the primary target for current FDA approved CF therapies. However, no experimental multi-domain ΔF508 CFTR structure has been determined and few studies have modeled ΔF508 using multi-domain WT CFTR structures. Here, we used cryo-EM density data and Rosetta comparative modeling (RosettaCM) to compare a ΔF508 model with published experimental data on CFTR NBD1 thermodynamics. We then apply this modeling method to generate multi-domain WT and ΔF508 CFTR structural models. These models demonstrate the destabilizing effects of ΔF508 on NBD1 and the NBD1/TMD interface in both the closed and open conformation of CFTR. Furthermore, we modeled ΔF508/R1070W and ΔF508 bound to a the CFTR corrector VX-809. Our models reveal the stabilizing effects of R1070W and VX-809 on multi-domain models of ΔF508 CFTR and pave the way for rational design of additional drugs that target ΔF508 CFTR for treatment of CF.

Agents’ ontologies negotiation in cohesive hybrid intelligent multi-agent systems

The paper proposes the model for negotiating intelligent agents’ ontologies in cohesive hybrid intelligent multi-agent systems. Intelligent agent in this study will be called relatively autonomous software entity with developed domain models and goal-setting mechanisms. When such agents have to work together within single hybrid intelligent multi-agent systems to solve some problem, the working process “go wild”, if there are significant differences between the agents’ “points of view” on the domain, goals and rules of joint work. In this regard, in order to reduce labor costs for integrating intelligent agents into a single system, the concept of cohesive hybrid intelligent multi-agent systems was proposed that implement mechanisms for negotiating goals, domain models and building a protocol for solving the problems posed. The presence of these mechanisms is especially important when building intelligent systems from intelligent agents created by various independent development teams.

MPDB: a unified multi-domain protein structure database integrating structural analogue detection

With the development of protein structure prediction methods and biological experimental determination techniques, the structure of single-domain proteins can be relatively easier to be modeled or experimentally solved. However, more than 80% of eukaryotic proteins and 67% of prokaryotic proteins contain multiple domains. Constructing a unified multi-domain protein structure database will promote the research of multi-domain proteins, especially in the modeling of multi-domain protein structures. In this work, we develop a unified multi-domain protein structure database (MPDB). Based on MPDB, we also develop a server with two functional modules: (1) the culling module, which filters the whole MPDB according to input criteria; (2) the detection module, which identifies structural analogues of the full-chain according to the structural similarity between input domain models and the protein in MPDB. The module can discover the potential analogue structures, which will contribute to high-quality multi-domain protein structure modeling.

Building Normalized Systems from Domain Models in Ecore

Normalized Systems (NS) theory describes how to design and develop evolvable systems. It is applied in practice to generate enterprise information systems using NS Expanders from models of NS Elements. As there are various well-established modelling languages, the possibility to (re-)use them to create NS applications is desired. This paper presents a mapping between the NS metamodel and the Ecore metamodel as a representant of essential structural modelling. The mapping is the basis of the transformation execution tool based on Eclipse Modeling Framework and NS Java libraries. Both the mapping and the tool are demonstrated in a concise case study but cover all essential Ecore constructs. During the work, several interesting similarities of the two metamodels were found and are described, e.g., its meta-circularity or ability to specify data types using references to Java classes. Still, there are significant differences between the metamodels that prevent some constructs from being mapped. The issues with information loss upon the transformation are mitigated by incorporating additional options that serve as key-value annotations. The results are ready to be used for any Ecore models to create an NS model that can be expanded into an NS application.

TIAMMAt: Leveraging biodiversity to revise protein domain models, evidence from innate immunity

Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with non-model species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called TIAMMAt ( Taxon-Informed Adjustment of Markov Model Attributes) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and non-model species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on non-model species.

Accounting for Slot Harmonics and Nonsinusoidal Unbalanced Voltage Supply in High-Speed Solid-Rotor Induction Motor Using Complex Multi-Harmonic Finite Element Analysis

Solid rotor induction machines are still used in high-speed systems. A two-dimensional field-circuit model based on the finite element method and the complex magnetic vector potential has been shown as a very time-effective tool in the analysis of their steady states compared to time-domain models. This continuation work presents a validated computational algorithm that enables the inclusion of the nonsinusoidal and/or asymmetrical voltage supply in the multi-harmonic field-circuit model of these machines that was presented in the previous works by the authors. The extended model accounts for both spatial harmonics due to slotting and/or winding distribution and the time-harmonics due to voltage waveform. The applicability range of the model therefore increases to cases when the machine is supplied with a nonsinusoidal three-phase system of voltages with symmetry or asymmetry that can be decomposed into three symmetrical components. Its short execution time characteristic allows for much more insightful design studies of the contribution of voltage supply- and slotting-related harmonics to the overall efficiency of the machine than is possible with the time-consuming time-domain models. The proposed computational framework has never been presented in the literature. The model is verified positively by the comprehensive time-domain model. It is especially useful in design studies on solid rotor induction motors related to the optimisation of the efficiency of induction motor-based drive systems.

Rapid Requirements Elicitation of Enterprise Applications Based on Executable Mockups

Software development begins with the requirements. Misunderstandings with customers in this early phase of development result in wasted development time. This work investigates the possibility of using executable UI mockups in the initial phases of functional requirements elicitation during the development of business applications. Although there has been a lot of research in the field in recent years, we find that there is still a need to improve model-driven tool design in order to enable customer participation from the initial phases of requirement specifications based on working prototypes. These prototypes can directly be reused in the rest of the development process. To meet the goal, we have been developing an open-source solution called Kroki that enables rapid collaborative development. We conducted a series of 10 joint user sessions with domain experts from different domains and backgrounds, resulting in the prototype specifications ranging from 7 to 20 screen mockups accompanied with domain models, developed in two-hour time frames. In this paper, we present our tool design that contributes to rapid joint development, and the results from the user sessions.