MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.

With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.

Regorafenib in patients with metastatic colorectal cancer in Spain: from clinical trials to real-world evidence.

Aim: To describe the evolution of regorafenib use, since its approval, in patients with previously treated metastatic colorectal cancer (mCRC) in routine clinical practice in Spain. Methods: We extracted patient characteristics, dosing, safety and efficacy data for the Spanish cohorts of the CORRECT and CONSIGN trials, and the real-world CORRELATE study. Results: The Spanish cohorts represented 10.7-13.8% of the global cohorts. Efficacy and safety in the Spanish cohorts reflected findings from the global cohorts, with evidence of a flexible dosing approach being adopted in routine clinical practice. Conclusion: Regorafenib use in patients with mCRC has evolved in the real-world setting, emphasizing the need for further research evaluating dosing patterns that can optimize clinical outcomes in these patients.Clinical trial registration: The CORRECT trial is registered at ClinicalTrials.gov, number NCT01103323; the CONSIGN trial is registered at ClinicalTrials.gov, number NCT01538680; the CORRELATE study is registered at ClinicalTrials.gov, number NCT02042144.

Bowel cancer (also called colorectal cancer) affects the large bowel, including the colon and rectum. Approximately one in ten patients with advanced bowel cancer that has spread to other areas of the body (metastatic bowel cancer) survive 5 years after diagnosis or the start of treatment.Regorafenib is a treatment for patients with advanced bowel cancer that has continued to spread after receiving other treatments. It can slow down cancer growth, as shown in three international studies (CORRECT, CONSIGN and CORRELATE). In Spain, bowel cancer is the most common type of cancer and the cancer that causes the second most deaths. This study describes how the use of regorafenib in Spain has changed since it was approved in 2012, by looking at the patients from Spain who made up 11­14% of the participants in the three international studies.The CORRECT trial that compared regorafenib with a non-therapeutic placebo and the CONSIGN trial of regorafenib alone showed that treatment with regorafenib prolonged life and was well tolerated in patients with metastatic bowel cancer who had previously received or were not suitable to receive other treatments. The CORRELATE study showed that in the real world (i.e., outside of a controlled clinical trial), patients are sometimes prescribed regorafenib at lower starting doses than the recommended dose, without an apparent overall effect on how well regorafenib works or side effects. In the future, it will be important to continue researching how doctors prescribe regorafenib in daily clinical practice in Spain.

A Novel Experimental Apparatus for Characterizing Flow Regime in Mechanically Stirred Tanks through Force Sensors.

Pressure fluctuations in a mixing tank can provide valuable information about the existing flow regime within the tank, which in turn influences the degree of mixing that can be achieved. In the present work, we propose a prototype for identifying the flow regime in mechanically stirred tanks equipped with four vertical baffles through the characterization of pressure fluctuations. Our innovative proposal is based on force sensors strategically placed in the baffles of the mixing tank. The signals coming from the sensors are transmitted to an electronic module based on an Arduino UNO development board. In the electronic module, the pressure signals are conditioned, amplified and sent via Bluetooth to a computer. In the computer, the signals can be plotted or stored in an Excel file. In addition, the proposed system includes a moving average filtering and a hierarchical bottom-up clustering analysis that can determine the real-time flow regime (i.e., the Reynolds number, Re) in which the tank was operated during the mixing process. Finally, to demonstrate the versatility of the proposed prototype, experiments were conducted to identify the Reynolds number for different flow regimes (static, laminar, transition and turbulent), i.e., 0≤Re≤ 42,955. Obtained results were in agreement with the prevailing consensus on the onset and developed from different flow regimes in mechanically stirred tanks.

Recurrences of ventricular tachycardia after stereotactic arrhythmia radioablation arise outside the treated volume: analysis of the Swiss cohort.

AIMS: Stereotactic arrhythmia radioablation (STAR) has been recently introduced for the management of therapy-refractory ventricular tachycardia (VT). VT recurrences have been reported after STAR but the mechanisms remain largely unknown. We analysed recurrences in our patients after STAR. METHODS AND RESULTS: From 09.2017 to 01.2020, 20 patients (68 ± 8 y, LVEF 37 ± 15%) suffering from refractory VT were enrolled, 16/20 with a history of at least one electrical storm. Before STAR, an invasive electroanatomical mapping (Carto3) of the VT substrate was performed. A mean dose of 23 ± 2 Gy was delivered to the planning target volume (PTV). The median ablation volume was 26 mL (range 14-115) and involved the interventricular septum in 75% of patients. During the first 6 months after STAR, VT burden decreased by 92% (median value, from 108 to 10 VT/semester). After a median follow-up of 25 months, 12/20 (60%) developed a recurrence and underwent a redo ablation. VT recurrence was located in the proximity of the treated substrate in nine cases, remote from the PTV in three cases and involved a larger substrate over ≥3 LV segments in two cases. No recurrences occurred inside the PTV. Voltage measurements showed a significant decrease in both bipolar and unipolar signal amplitude after STAR. CONCLUSION: STAR is a new tool available for the treatment of VT, allowing for a significant reduction of VT burden. VT recurrences are common during follow-up, but no recurrences were observed inside the PTV. Local efficacy was supported by a significant decrease in both bipolar and unipolar signal amplitude.

Evolutionary relationships of adenylation domains in fungi.

Non-ribosomal peptide synthetases (NRPSs) and NRPS-like enzymes are abundant in microbes as they are involved in the production of primary and secondary metabolites. In contrast to the well-studied NRPSs, known to produce non-ribosomal peptides, NRPS-like enzymes exhibit more diverse activities and their evolutionary relationships are unclear. Here, we present the first in-depth phylogenetic analysis of fungal NRPS-like A domains from functionally characterized pathways, and their relationships to characterized A domains found in fungal NRPSs. This study clearly differentiated amino acid reductases, including NRPSs, from CoA/AMP ligases, which could be divided into 10 distinct phylogenetic clades that reflect their conserved domain organization, substrate specificity and enzymatic activity. In particular, evolutionary relationships of adenylate forming reductases could be refined and explained the substrate specificity difference. Consistent with their phylogeny, the deduced amino acid code of A domains differentiated amino acid reductases from other enzymes. However, a diagnostic code was found for α-keto acid reductases and clade 7 CoA/AMP ligases only. Comparative genomics of loci containing these enzymes revealed that they can be independently recruited as tailoring genes in diverse secondary metabolite pathways. Based on these results, we propose a refined and clear phylogeny-based classification of A domain-containing enzymes, which will provide a robust framework for future functional analyses and engineering of these enzymes to produce new bioactive molecules.

Predicting microbiomes through a deep latent space.

MOTIVATION: Microbial communities influence their environment by modifying the availability of compounds, such as nutrients or chemical elicitors. Knowing the microbial composition of a site is therefore relevant to improve productivity or health. However, sequencing facilities are not always available, or may be prohibitively expensive in some cases. Thus, it would be desirable to computationally predict the microbial composition from more accessible, easily-measured features. RESULTS: Integrating deep learning techniques with microbiome data, we propose an artificial neural network architecture based on heterogeneous autoencoders to condense the long vector of microbial abundance values into a deep latent space representation. Then, we design a model to predict the deep latent space and, consequently, to predict the complete microbial composition using environmental features as input. The performance of our system is examined using the rhizosphere microbiome of Maize. We reconstruct the microbial composition (717 taxa) from the deep latent space (10 values) with high fidelity (>0.9 Pearson correlation). We then successfully predict microbial composition from environmental variables, such as plant age, temperature or precipitation (0.73 Pearson correlation, 0.42 Bray-Curtis). We extend this to predict microbiome composition under hypothetical scenarios, such as future climate change conditions. Finally, via transfer learning, we predict microbial composition in a distinct scenario with only 100 sequences, and distinct environmental features. We propose that our deep latent space may assist microbiome-engineering strategies when technical or financial resources are limited, through predicting current or future microbiome compositions. AVAILABILITY AND IMPLEMENTATION: Software, results and data are available at https://github.com/jorgemf/DeepLatentMicrobiome. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The surfactant Dioctyl Sodium Sulfosuccinate (DOSS) exposure causes adverse effects in embryos and adults of zebrafish (Danio rerio).

Dioctyl Sodium Sulfosuccinate (DOSS, CAS 577-11-7) is a chemical emulsifying surfactant that is widely used in the food and the cosmetic industry, and it is also the major component of the crude oil chemical dispersant Corexit™. Despite of its wide use, the studies related to its negative effect have been evaluated mainly in marine environments showing that DOSS is highly bioactive, extremely low volatile, and potential to persist in the environment longer than other dispersant components. Up to date, there is no available information of DOSS concentration in freshwater environments, little is known about its downstream fate after excretion and its effect on freshwater organisms. The objective of this study was to evaluate the effect of DOSS at different concentrations in embryos and adults of zebrafish Danio rerio in an acute-static bioassays of 96 h. The median lethal concentration in embryos was 33.3 mg/L. Malformations started to be observed at 10 mg/L. In adults, the gene expression analysis in gill tissues showed a deregulation in genes associated with the antioxidant system and the nucleotide excision repair mechanism. Additionally, Micronuclei (DNA damage) in erythrocytes, and fat degeneration in liver, hypertrophy and hyperplasia in gills, and hyaline drops in kidney tissues were also observed. In conclusion, the concentrations of DOSS evaluated here would be of health relevance to fish based on morphological alterations in embryos and changes in the gene expression profile, DNA damage and tissue impairment in adults.

A computational framework to explore large-scale biosynthetic diversity.

Genome mining has become a key technology to exploit natural product diversity. Although initially performed on a single-genome basis, the process is now being scaled up to mine entire genera, strain collections and microbiomes. However, no bioinformatic framework is currently available for effectively analyzing datasets of this size and complexity. In the present study, a streamlined computational workflow is provided, consisting of two new software tools: the 'biosynthetic gene similarity clustering and prospecting engine' (BiG-SCAPE), which facilitates fast and interactive sequence similarity network analysis of biosynthetic gene clusters and gene cluster families; and the 'core analysis of syntenic orthologues to prioritize natural product gene clusters' (CORASON), which elucidates phylogenetic relationships within and across these families. BiG-SCAPE is validated by correlating its output to metabolomic data across 363 actinobacterial strains and the discovery potential of CORASON is demonstrated by comprehensively mapping biosynthetic diversity across a range of detoxin/rimosamide-related gene cluster families, culminating in the characterization of seven detoxin analogues.

MIBiG 2.0: a repository for biosynthetic gene clusters of known function.

Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters (BGCs). Thousands of candidate BGCs from microbial genomes have been identified and stored in public databases. Interpreting the function and novelty of these predicted BGCs requires comparison with a well-documented set of BGCs of known function. The MIBiG (Minimum Information about a Biosynthetic Gene Cluster) Data Standard and Repository was established in 2015 to enable curation and storage of known BGCs. Here, we present MIBiG 2.0, which encompasses major updates to the schema, the data, and the online repository itself. Over the past five years, 851 new BGCs have been added. Additionally, we performed extensive manual data curation of all entries to improve the annotation quality of our repository. We also redesigned the data schema to ensure the compliance of future annotations. Finally, we improved the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases. The repository is accessible online at https://mibig.secondarymetabolites.org/.

Anterior cerebral artery trifurcation with infraoptic origin and contralateral A1 segment absence.

PURPOSE: To describe an uncommon anatomical variant of the anterior cerebral artery and the imaging findings. METHODS: A 2-month-old infant with known history of atrial and ventricular septal defects was admitted to our institution for evaluation and management of growth failure. Given the clinical presentation and medical history, magnetic resonance imaging (MRI) of the brain and MR angiography (MRA) were performed to exclude congenital hypopituitarism and any vascular abnormality. RESULTS: Time of flight MRA revealed trifurcation of the anterior cerebral artery with one of the vessels arising from the ophthalmic segment of the right internal carotid artery; thus, the A1 segment of the left anterior cerebral artery (ACA) was absent, and the right posterior cerebral artery (PCA) had a fetal origin. CONCLUSION: Anatomical variants of the cerebral circulation are asymptomatic and found incidentally. Knowledge of these variants and careful examination of CT/MRI angiograms are important for diagnosis and treatment planning.

Morphological Alterations in the Early Developmental Stages of Zebrafish (Danio rerio; Hamilton 1822) Induced by Exposure to Polystyrene Microparticles.

Microplastics (MPs) are emerging pollutants of widespread concern in aquatic environments. The aim of this study was to evaluate the negative impact of pristine MPs of polystyrene of 100 µm on embryo and larvae of Danio rerio exposed to three environmentally relevant concentrations of polystyrene (3.84 × 10- 6, 3.84 × 10- 7, and 3.84 × 10- 8 g/mL). The exposure effect was evaluated through the general morphology score, biometrics, and integrated biomarker response version 2 index. No mortality was observed but the anatomical structure of fishes was affected showing pigmentation deficiency and alterations in the head region as the main affected endpoints. The general morphology score and the integrated biomarker response values were highly sensitive to address the effect of the three concentrations of MPs used here. Our results provide solid evidence of the negative impact of 100 µm pristine polystyrene MPs exposure on early stages of zebrafish.

Chilean salmon farming vulnerability to external stressors: The COVID 19 as a case to test and build resilience.

This study addresses the risk and vulnerability of Chilean salmon production to hazards resulting from the COVID-19 pandemic threat, including limited access to farms, limited processing capacity and reduced market demand. The role of different management approaches in reducing risk and vulnerability is also explored. Results suggest that concession areas having the largest accumulated and current biomass have the highest risk, which is also transferred to the municipal level. The scenarios modelled with better management practices that reduce diseases were able to reduce risks by 30-40%. The largest risk reduction is achieved when production biomass is divided in a more equitable manner among concession areas, suggesting the need for strategic improvements in spatial planning of the activity in the marine environment according to ecosystem carrying capacity and better practices. Improving adaptation capacity can reduce vulnerability between 20% and 30% for municipalities; for example, providing local employment can be a win-win management measure under the COVID-19 threat because it reduces movement of people and facilitates handling and responses to emergencies. A larger footprint in local economies and employment can also improve social perception and acceptance of the sector, thus contributing to improve adaptation changes and governance to face the threats. The framework used here to perform a risk and vulnerability assessment of salmon farming to the pandemic-associated threats can also be useful for other aquaculture systems elsewhere, provided that relevant information is available.

Dissipative Distillation of Supercritical Quantum Gases.

We experimentally realize a method to produce nonequilibrium Bose-Einstein condensates with condensed fraction exceeding those of equilibrium samples with the same parameters. To do this, we immerse an ultracold Bose gas of ^{87}Rb in a cloud of ^{39}K with substantially higher temperatures, providing a controlled source of dissipation. By combining the action of the dissipative environment with evaporative cooling, we are able to progressively distil the nonequilibrium Bose-Einstein condensate from the thermal cloud. We show that by increasing the strength of the dissipation it is even possible to produce condensates above the critical temperature. We finally demonstrate that our out-of-equilibrium samples are long lived and do not reach equilibrium in a time that is accessible for our experiment. Due to its high degree of control, our distillation process is a promising tool for the engineering of open quantum systems.

Toxicity evaluation and microbiota response of the lined sole Achirus lineatus (Chordata: Achiridae) exposed to the light petroleum water-accommodated fraction (WAF).

Exposure to contaminants might directly affect organisms and alter their associated microbiota. The objective of the present study was to determine the impact of the petroleum-water-accommodated fraction (WAF) from a light crude oil (API gravity 35) on a benthic fish species native from the Gulf of Mexico (GoM). Ten adults of Achirus lineatus (Linnaeus, 1758) were exposed to a sublethal WAF/water solution of 50% v/v for 48 hr. Multiple endpoints were measured including tissue damage, presence of polycyclic aromatic hydrocarbons (PAHs) metabolites in bile and gut microbiota analyses. Atrophy and fatty degeneration were observed in livers. Nodules and inflammation were detected in spleen, and structural disintegration and atrophy in the kidney. In gills hyperplasia, aneurysm, and gills lamellar fusion were observed. PAHs metabolites concentrations in bile were significantly higher in exposed organisms. Gut microbiome taxonomic analysis showed significant shifts in bacterial structure and composition following WAF exposure. Data indicate that exposure to WAF produced toxic effects in adults of A. lineatus, as evidenced by histological alterations and dysbiosis, which might represent an impairment to long-term subsistence of exposed aquatic organisms.

Early laparoscopic cholecystectomy reduces hospital stay in mild gallstone pancreatitis. A randomized controlled trial.

BACKGROUND: Two strategies for same-admission cholecystectomy in mild gallstone pancreatitis (MGP) exist: early surgery (within 48-72 h from admission) and delayed surgery until resolution of symptoms and normalization of pancreatic tests. METHODS: This was a single-center, open-label RCT. Patients with MGP according to revised Atlanta classification-2012 and SIRS criteria were randomly assigned to early laparoscopic cholecystectomy (E-LC) within 72 h from admission or delayed laparoscopic cholecystectomy (D-LC). Laparoscopic-endoscopic rendezvous was performed when common bile duct stones were found at systematic intraoperative cholangiography. The primary outcome was length of stay (LOS), and the secondary outcomes were complications at 90 days, need for ERCP/choledocolithiasis, conversion, and re-admission. One year of follow-up was carried-on. RESULTS: At interim analysis, 52 patients were randomized (26 E-LC, 26 D-LC). E-LC versus D-LC was associated with a significantly shorter LOS (median 58 versus 167 h; P = 0.001). There were no differences in ERCP necessity for choledocolithiasis between the two approaches (E-LC 26.9% versus D-LC 23.1%, P = 1.00). No differences in postoperative complications were found. CONCLUSIONS: E-LC approach in patients with MGP significantly reduced LOS and was not associated with clinically relevant postoperative complications. TRIAL REGISTRATION: clinicaltrials.gov (NCT02590978).

Comprehensive Evaluation of Differential Serodiagnosis between Zika and Dengue Viral Infections.

Diagnostic testing for Zika virus (ZIKV) or dengue virus (DENV) infection can be accomplished by a nucleic acid detection method; however, a negative result does not exclude infection due to the low virus titer during infection depending on the timing of sample collection. Therefore, a ZIKV- or DENV-specific serological assay is essential for the accurate diagnosis of patients and to mitigate potential severe health outcomes. A retrospective study design with dual approaches of collecting human serum samples for testing was developed. All serum samples were extensively evaluated by using both noninfectious wild-type (wt) virus-like particles (VLPs) and soluble nonstructural protein 1 (NS1) in the standard immunoglobulin M (IgM) antibody-capture enzyme-linked immunosorbent assay (MAC-ELISA). Both ZIKV-derived wt-VLP- and NS1-MAC-ELISAs were found to have similar sensitivities for detecting anti-premembrane/envelope and NS1 antibodies from ZIKV-infected patient sera, although lower cross-reactivity to DENV2/3-NS1 was observed. Furthermore, group cross-reactive (GR)-antibody-ablated homologous fusion peptide-mutated (FP)-VLPs consistently showed higher positive-to-negative values than homologous wt-VLPs. Therefore, we used DENV-2/3 and ZIKV FP-VLPs to develop a novel, serological algorithm for differentiating ZIKV from DENV infection. Overall, the sensitivity and specificity of the FP-VLP-MAC-ELISA and the NS1-MAC-ELISA were each higher than 80%, with no statistical significance. The accuracy can reach up to 95% with the combination of FP-VLP and NS1 assays. In comparison to current guidelines using neutralization tests to measure ZIKV antibody, this approach can facilitate laboratory screening for ZIKV infection, especially in regions where DENV infection is endemic and capacity for neutralization testing does not exist.

Acute inferior myocardial infarction with right ventricular involvement and several clinical-electrocardiographic markers of poor prognosis.

Right ventricular involvement in inferior myocardial infarction is a marker of poor prognosis. We present a case of a 62-year-old man with very recent onset of acute chest pain and cardiac shock with the triad of elevated jugular venous pressure, distension of the jugular veins on inspiration, and clear lung fields. In addition, the admission electrocardiogram showed a slurring J wave or lambda-like wave and conspicuous ST segment depression in several leads, predominantly in the lateral precordial (V4-V6), all clinical-electrocardiographic features of ominous prognosis.

Reliability of OMERACT ultrasound elementary lesions in gout: results from a multicenter exercise.

The aim of this study was to evaluate the reliability of the outcome measures in rheumatology (OMERACT) definitions for ultrasound (US) elementary lesions in gout through an image reading exercise. Images from patients with gout (static images and videos) were collected. As an initial step, we carried out a image reading exercise within the experts of the Pan-American League of Associations for Rheumatology (PANLAR) US Study Group (n = 16). The following step consisted in a web-based exercise with the participation of larger number of sonographers (n = 63) from different centers. Images were rated evaluating the presence/absence of any US elementary lesion. Inter- and intra-reader reliabilities were analyzed using kappa coefficients. Participants were stratified according to their level of experience. In the first exercise, inter-reader kappa values were 0.45 for aggregates, 0.57 for tophus, 0.69 for erosions, and 0.90 for double contour (DC). Intra-reader kappa values were 0.86, 0.76, 0.80, and 0.90, respectively. The web-based exercise showed inter-reader kappa values for aggregates, tophus, erosions, and DC of 0.42, 0.49, 0.69, and 0.79, respectively. The intra-reader kappa values were 0.62, 0.69, 0.77, and 0.85, respectively. Reliability was not influenced by the sonographer's level of experience. The reliability of the new OMERACT US definitions for elementary lesions in gout ranged from moderate to excellent, depending on the type of lesion.

The High-Quality Complete Genome Sequence of the Opportunistic Fungal Pathogen Candida vulturna CBS 14366T.

Candida vulturna is a new member of the Candida haemulonii species complex that recently received much attention as it includes the emerging multidrug-resistant pathogen Candida auris. Here, we describe the high-quality genome sequence of C. vulturna type strain CBS 14366T to cover all genomes of pathogenic C. haemulonii species complex members.

Post-Operative Localization of Deep Brain Stimulation Electrodes in the Subthalamus Using Transcranial Sonography.

OBJECTIVES: The correct positioning of deep brain stimulation electrodes determines the success of surgery. In this study, we attempt to validate transcranial sonography (TCS) as a method for early postoperative confirmation of electrode location in the subthalamic nucleus (STN). MATERIALS AND METHODS: Nineteen patients diagnosed with Parkinson's disease were enrolled in the study. Postoperative TCS was applied to measure the distance between the implanted electrodes and the third ventricle in the axial plane. Whether the electrodes were positioned within or outside the substantia nigra (SN) was evaluated through measurements in the coronal plane. The obtained metrics through TCS were compared with those from postoperative computed tomography (CT) and magnetic resonance imaging (MRI). RESULTS: A statistically significant correlation between distances from electrode to third ventricle by TCS and CT/MRI (r = 0.75, p < 0.01) was observed. Distances from third ventricle to electrodes tips were different when sonographically they showed to be inside or outside the SN (p < 0.01). A cut-off value of 8.85mm in these distances was the most sensitive (100%) and specific (90.5%) to predict if electrodes were positioned inside the SN (CI 95% 0.81-10.30, p = 0.001). CONCLUSIONS: Transcranial sonography is a useful technique to reliably identify targeted positioning of deep brain stimulation electrodes in or out of the SN.