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RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio., (© The Author(s) 2025. Published by Oxford University Press on behalf of Nucleic Acids Research.)

RNA secondary (2D) structure visualisation is an essential tool for understanding RNA function. R2DT is a software package designed to visualise RNA 2D structures in consistent, recognisable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms (SNPs) or SHAPE reactivities. It also offers a new template-free mode allowing visualisation of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualisations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualisation, accessible at https://r2dt.bio., Competing Interests: CONFLICT OF INTEREST None declared.

The EMBL-EBI Job Dispatcher sequence analysis tools framework (https://www.ebi.ac.uk/jdispatcher) enables the scientific community to perform a diverse range of sequence analyses using popular bioinformatics applications. Free access to the tools and required sequence datasets is provided through user-friendly web applications, as well as via RESTful and SOAP-based APIs. These are integrated into popular EMBL-EBI resources such as UniProt, InterPro, ENA and Ensembl Genomes. This paper overviews recent improvements to Job Dispatcher, including its brand new website and documentation, enhanced visualisations, improved job management, and a rising trend of user reliance on the service from low- and middle-income regions., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Protein evolution is constrained by structure and function, creating patterns in residue conservation that are routinely exploited to predict structure and other features. Similar constraints should affect variation across individuals, but it is only with the growth of human population sequencing that this has been tested at scale. Now, human population constraint has established applications in pathogenicity prediction, but it has not yet been explored for structural inference. Here, we map 2.4 million population variants to 5885 protein families and quantify residue-level constraint with a new Missense Enrichment Score (MES). Analysis of 61,214 structures from the PDB spanning 3661 families shows that missense depleted sites are enriched in buried residues or those involved in small-molecule or protein binding. MES is complementary to evolutionary conservation and a combined analysis allows a new classification of residues according to a conservation plane. This approach finds functional residues that are evolutionarily diverse, which can be related to specificity, as well as family-wide conserved sites that are critical for folding or function. We also find a possible contrast between lethal and non-lethal pathogenic sites, and a surprising clinical variant hot spot at a subset of missense enriched positions., (© 2024. The Author(s).)

Chagas disease (CD) is a typical tropical illness caused by Trypanosoma cruzi . The objective of this study was to assess the prevalence of Chagas disease in communities in two states of the Brazilian Amazon. Data collection occurred in July in the Alto Juruá region of Acre and in December in the communities of Humaitá, Amazonas, in 2019. A total of 477 participants were included in the study. In the communities of Alto Juruá, triatomine collections and analyses of T. cruzi infection were also carried out. All confirmed cases were found in the state of Acre, resulting in a total prevalence of 1.67. Of these eight cases, seven underwent ECG, all of which were concluded as normal by the physician team's cardiologists. Seventeen triatomine bugs, all belonging to the Rhodnius genus, were captured. The natural infection rate by T. cruzi was 25% in the Nova Cintra community and 66.67% in the Boca do Moa community (Alto Juruá). This research found that more than 1% of the studied population exhibited positive serological results for Chagas disease in the riverine communities during the study period, representing a small portion of cases among those who have not yet been diagnosed.

Introduction: Recently, simulation as an educational method has gained increasing importance in Medicine. However, medical education has favored the acquisition of individual knowledge and skills, while overlooking the development of teamwork skills. Since most errors in clinical practice are due to human factors, i.e., non-technical skills, the aim of this study was to assess the impact that training in a simulation environment has on teamwork in an undergraduate setting., Material and Methods: This study took place in a simulation center, with a study population of 23 participants, fifth year undergraduate students, randomly divided into teams of four elements. Twenty simulated scenarios of teamwork in the initial assessment and resuscitation of critically ill trauma patients were recorded. Video recordings were made at three distinct learning moments (before training, end of the semester, and six months after the last training), and a blinded evaluation was performed by two independent observers, who applied the Trauma Team Performance Observation Tool (TPOT). Additionally, the Team STEPPS Teamwork Attitudes Questionnaire (T-TAQ) was applied to the study population before and after the training to assess any change in individual attitudes towards non-technical skills. A 5% (or 0.05) significance level was considered for statistical analysis., Results: With a moderate level of inter-observer agreement (Kappa = 0.52, p = 0.002), there was a statistically significant improvement in the team's overall approach, evidenced by the TPOT scores (median of 4.23, 4.35 and 4.50, in the three time-points assessed, respectively, p = 0.003). In the T-TAQ, there was an improvement in non-technical skills, that was statistically significant for "Mutual Support" (median from 2.50 to 3.00, p = 0.010)., Conclusion: In this study, incorporating non-technical skills education and training in undergraduate medical education was associated with sustained improvement in team performance in the approach to the simulated trauma patient. Consideration should be given to introducing non-technical skills training and teamwork in the emergency setting during undergraduate training.

Competing Interests: The authors have no conflicts of interest to declare.

[(Bn 2 Cyclam)Y(N(SiMe 3 ) 2 )] was prepared by reaction of H 2 Bn 2 Cyclam with Y[N(SiMe 3 ) 2 ] 3 . The protonation of the macrocycle ligand in [(Bn 2 Cyclam)Y(N(SiMe 3 ) 2 )] is observed upon reaction with [HNMe 3 ][BPh 4 ] leading to the formation of [(HBn 2 Cyclam)Y(N(SiMe 3 ) 2 )][BPh 4 ]. DFT analysis of [(Bn 2 Cyclam)Y(N(SiMe 3 ) 2 )] showed that the HOMO is located on the anionic nitrogen atoms of the cyclam ring indicating that protonation follows orbital control. Addition of H 2 Bn 2 Cyclam and H 2 ( 3,5-tBu2 Bn) 2 Cyclam to a 1:3 mixture of YCl 3 and LiCH 2 SiMe 3 in THF resulted in the formation of [((C 6 H 4 CH 2 )BnCyclam)Y(THF)(µ-Cl)Li(THF) 2 ] and [Y{(η 3 - 3,5-tBu2 Bn) 2 Cyclam}Li(THF)], respectively. The reaction of H 2 3,5-tBu2 Bn 2 Cyclam with Y(CH 2 SiMe 3 ) 3 (THF) 2 was studied and monitored by a temperature variation NMR experiment revealing the formation of [( 3,5-tBu2 Bn 2 Cyclam)Y(CH 2 SiMe 3 )]. Preliminary catalytic assays have shown that [Y{(η 3 - 3,5-tBu2 Bn) 2 Cyclam}Li(THF)] is a very efficient catalyst for the intramolecular hydroamination of 2,2-diphenyl-pent-4-enylamine.

Physical issues started to receive more attention due to the sedentary lifestyle prevalent in modern culture. The Ten Meter Walk Test allows measuring the person's capacity to walk along 10 m and analyzing the advancement of various medical procedures for ailments, including stroke. This systematic review is related to the use of mobile or wearable devices to measure physical parameters while administering the Ten Meter Walk Test for the analysis of the performance of the test. We applied the PRISMA methodology for searching the papers related to the Ten Meter Walk Test. Natural Language Processing (NLP) algorithms were used to automate the screening process. Various papers published in two decades from multiple scientific databases, including IEEE Xplore, Elsevier, Springer, EMBASE, SCOPUS, Multidisciplinary Digital Publishing Institute (MDPI), and PubMed Central were analyzed, focusing on various diseases, devices, features, and methods. The study reveals that chronometer and accelerometer sensors measuring spatiotemporal features are the most pertinent in the Gait characterization of most diseases. Likewise, all studies emphasized the close relation between the quality of the sensor's data obtained and the system's ultimate accuracy. In other words, calibration procedures are needed because of the body part where the sensor is worn and the type of sensor. In addition, using ambient sensors providing kinematic and kinetic features in conjunction with wearable sensors and consistently acquiring walking signals can enhance the system's performance. The most common weaknesses in the analyzed studies are the sample size and the unavailability of continuous monitoring devices for measuring the Ten Meter Walk Test., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper, (© 2023 The Authors.)

Purpose: This study aimed to reflect on the challenges of Health Information Systems in Portugal at a time when technologies enable the creation of new approaches and models for care provision, as well as to identify scenarios that may characterize this practice in the future., Design/methodology/approach: A guiding research model was created based on an empirical study that was conducted using a qualitative method that integrated content analysis of strategic documents and semi-structured interviews with a sample of fourteen key actors in the health sector., Findings: Results pointed to the existence of emerging technologies that may promote the development of Health Information Systems oriented to "health and well-being" in a preventive model logic and reinforce the social and management implications., Originality/value: The originality of this work resided in the empirical study carried out, which allowed us to analyze how the various actors look at the present and the future of Health Information Systems. There is also a lack of studies addressing this subject., Research Limitations/implications: The main limitations resulted from a low, although representative, number of interviews and the fact that the interviews took place before the pandemic, so the digital transformation that was promoted was not reflected. Managerial implications and social implications: The study highlighted the need for greater commitment from decision makers, managers, healthcare providers, and citizens toward achieving improved digital literacy and health. Decision makers and managers must also agree on strategies to accelerate existing strategic plans and avoid their implementation at different paces.

The fitness of the endangered green sea turtle (Chelonia mydas) may be strongly affected by its gut microbiome, as microbes play important roles in host nutrition and health. This study aimed at establishing environmental microbial baselines that can be used to assess turtle health under altered future conditions. We characterized the microbiome associated with the gastrointestinal tract of green turtles from Guinea Bissau in different life stages and associated with their food items, using 16S rRNA metabarcoding. We found that the most abundant (% relative abundance) bacterial phyla across the gastrointestinal sections were Proteobacteria (68.1 ± 13.9% “amplicon sequence variants”, ASVs), Bacteroidetes (15.1 ± 10.1%) and Firmicutes (14.7 ± 21.7%). Additionally, we found the presence of two red algae bacterial indicator ASVs (the Alphaproteobacteria Brucella pinnipedialis with 75 ± 0% and a Gammaproteobacteria identified as methanotrophic endosymbiont of Bathymodiolus, with <1%) in cloacal compartments, along with six bacterial ASVs shared only between cloacal and local environmental red algae samples. We corroborate previous results demonstrating that green turtles fed on red algae (but, to a lower extent, also seagrass and brown algae), thus, acquiring microbial components that potentially aid them digest these food items. This study is a foundation for better understanding the microbial composition of sea turtle digestive tracts.

The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

THIS ARTICLE USES WORDS OR LANGUAGE THAT IS CONSIDERED PROFANE, VULGAR, OR OFFENSIVE BY SOME READERS. The new generation of direct-acting antivirals has improved dramatically the rates of cure for chronic hepatitis C. Yet, evidence shows that racial groups are deemed more often ineligible for hepatitis C treatment, despite no clinical evidence supporting differential treatment for Black and White patients. One possible explanation has to do with providers' racial biases. This investigation sought to explore medical students' racial stereotypes (Study 1, N = 171) and the role of stereotypical cues on perceptions of medical adherence of Black and White patients (Study 2, N = 208). In Study 1, we first sought to identify health-related aspects that are consistently associated with Blacks as part of a stereotype. In Study 2, we experimentally manipulated racial stereotypes identified in Study 1 by asking participants to read a clinical vignette depicting a patient (Black vs. White) and their medical history (cause of exposure to hepatitis C: unprotected sex vs. non-injectable drugs use). The results show that the impact of stereotypicality on patient perceived compliance varies as a function of medical students' racial prejudice. Implications for further applied health inequalities research and for medical training are discussed., Competing Interests: The authors have declared that no competing interests exist.

Knowledge of the insect densities during crop development is necessary for adopting appropriate measures for the control of insect pests and minimizing yield losses. Within integrated pest management programs, crop rotation has been carried out in recent years, but this current trend delays the planting period for Bt maize. The small amount of available information regarding the influence of sowing Bt maize early or late on the seasonal abundance of herbivores prompted us to study these aspects in two current common planting periods in northeastern Spain in 52 maize fields over three consecutive years. We sampled the fields planted on different dates with sticky yellow traps. Our results show that only the abundances of herbivore thrips, other than Frankliniella occidentalis , and Syrphidae were significantly different between the two planting periods. Moreover, when we performed yearly analyses, we found significant effects of the planting period on Coccinellidae and Chrysopidae in 2015 and on Aeolothrips sp. in 2016 and 2017. In most of the taxa, the abundance peaks in earlier growth stages, which is related to pollination (before or during). Only the abundances of Stethorus punctillum and Syrphidae peak later in the season. In addition, F. occidentalis , aphids, Syrphidae, and Coccinellidae registered higher abundance in fields sown in the late planting period. These results highlight the effects of sowing in different planting periods on insect dynamics in Bt maize and can be used to identify the abundance of certain pests and natural enemies in specific phenological stages of maize, which may allow producers to adopt better-integrated management and thus avoid reaching the level of economic damage.

The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), maintained at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) provides freely accessible services, both for deposition of, and access to, open nucleotide sequencing data. Open scientific data are of paramount importance to the scientific community and contribute daily to the acceleration of scientific advance. Here, we outline the major updates to ENA's services and infrastructure that have been delivered over the past year., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and recognisable 2D layouts, which makes it challenging for users to construct, compare and analyse structures. Here, we present R2DT, a method for predicting and visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,647 templates representing the majority of known structured RNAs. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world's largest RNA 2D structure dataset. The software is amenable to community expansion, and is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt .

The combined effect of the temperature and relative humidity on the survival and development time of the eggs of Spanish populations of the weevil Hypera postica , a key pest of alfalfa around the world, was evaluated under laboratory conditions. The experimental temperatures ranged from 8 to 36 °C, in 4 °C increments. Three relative humidity ranges were defined: high, medium, and low. Eggs of the alfalfa weevil successfully developed until larval emergence at all of the 24 conditions tested. However, the temperature and relative humidity affected the survival of the eggs. The egg developmental time decreased as the temperature increased from 8 to 32 °C, and the longest time was recorded at a low relative humidity (RH). The relationship between the development rate and temperature fit well to the lineal model for relative humidity. The minimum development threshold (T 0 ) and the thermal requirement for egg development (K) ranged between 3 and 4 °C and 209 and 246 degree-days, respectively. According to these values and the occurrence of eggs and larvae (in winter) and adults (in autumn) in field samplings, the period of oviposition was determined. The results of the study contribute to better understanding the annual cycle and phenology of H. postica in the Iberian Peninsula and southern Europe.

Objective: Warm water immersion therapy (WWIT) has been widely used in the treatment of various clinical conditions, with analgesic and anti-inflammatory effects. However, its mechanism of action has not been fully investigated. The present study analyzed the role of spinal inhibitory neuroreceptors in the antihyperalgesic effect of WWIT in an experimental model of inflammatory pain., Methods: Mice were injected with complete Freund's adjuvant (CFA; intraplantar [i.pl.]). Paw withdrawal frequency to mechanical stimuli (von Frey test) was used to determine: (1) the effect of intrathecal (i.t.) preadministration of naloxone (a non-selective opioid receptor antagonist; 5 µg/5 µl), (2); AM281 (a selective cannabinoid receptor type 1 [CB 1 ] antagonist; 2 µg/5 µl), (3); and 1,3-dipropyl-8-cyclopentylxanthine (DPCPX; a selective adenosine A 1 receptor antagonist; 10 nmol/5 µl), on the antihyperalgesic (pain-relieving) effect of WWIT against CFA-induced hyperalgesia., Results: Intrathecal naloxone, AM281, and DPCPX significantly prevented the antihyperalgesic effect of WWIT. This study suggests the involvement of spinal (central) receptors in the antihyperalgesic effect of WWIT in a model of inflammatory pain., Conclusions: Taken together, these results suggest that opioid, CB 1, and A 1 spinal receptors might contribute to the pain-relieving effect of WWIT., (Copyright © 2020 Associação Brasileira de Pesquisa e Pós-Graduação em Fisioterapia. Publicado por Elsevier España, S.L.U. All rights reserved.)

A patient with a dual chamber pacemaker was admitted to the emergency room after out-of-hospital cardioversion for syncopal sustained monomorphic ventricular tachycardia. Device interrogation revealed an abnormally timed ventricular spike after a ventricular premature beat at the beginning of the event, caused by a pacemaker algorithm designed to avoid atrial fibrillation, non-competitive atrial pacing. Despite the absence of significant coronary lesions, in the setting of a vulnerable substrate - a hypokinetic and hyperechogenic region of ventricular myocardium - an upgrade to a dual-chamber implantable cardioverter-defibrillator was performed, and substrate ablation was planned., (Copyright © 2020 Sociedade Portuguesa de Cardiologia. Publicado por Elsevier España, S.L.U. All rights reserved.)

The Dundee Resource for Sequence Analysis and Structure Prediction (DRSASP; http://www.compbio.dundee.ac.uk/drsasp.html) is a collection of web services provided by the Barton Group at the University of Dundee. DRSASP's flagship services are the JPred4 webserver for secondary structure and solvent accessibility prediction and the JABAWS 2.2 webserver for multiple sequence alignment, disorder prediction, amino acid conservation calculations, and specificity-determining site prediction. DRSASP resources are available through conventional web interfaces and APIs but are also integrated into the Jalview sequence analysis workbench, which enables the composition of multitool interactive workflows. Other existing Barton Group tools are being brought under the banner of DRSASP, including NoD (Nucleolar localization sequence detector) and 14-3-3-Pred. New resources are being developed that enable the analysis of population genetic data in evolutionary and 3D structural contexts. Existing resources are actively developed to exploit new technologies and maintain parity with evolving web standards. DRSASP provides substantial computational resources for public use, and since 2016 DRSASP services have completed over 1.5 million jobs., (© 2019 The Authors. Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.)

The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed with the same core principles that allow them to integrate an ever-increasing volume of biological data, making them an integral part of many popular data resources provided at the EMBL-EBI. Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability., (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)

We report a case of a 43-year-old man with situs inversus and dextrocardia who was admitted with syncope in the setting of complete atrioventricular block. The complex anatomy poses a considerable challenge to transvenous permanent pacemaker implantation. We employed a novel technique using vascular ultrasound and agitated saline solution to assist with lead positioning. This technique could be useful in pediatric populations or younger patients, in whom the use of ionizing radiation is an important issue., Competing Interests: There are no conflicts of interest., (Copyright: © 2019 Journal of Cardiovascular Echography.)

The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities.

The idea that noncrop habitat enhances pest control and represents a win-win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win-win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)