Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.

Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.

Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes.

BACKGROUND: As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance. RESULTS: We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered. CONCLUSIONS: Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.

Henry Ingersoll Bowditch: The Prominent Physician Who Introduced Thorax Examination and Trocar Thoracentesis in the United States of America.

Born in a wealthy family with a tradition in science, Henry Ingersoll Bowditch (1808-1882) with studies at Harvard Medical School and in Europe had succeeded in leaving his mark in the American history of medicine. He had been a pioneer in the stethoscope's use, which was promoted and suggested to all physicians of his era. He had widely used thoracentesis, an ancient procedure, for pleuritic effusions, diagnosed with a stethoscope. Inside his most popular treatise "The Young Stethoscopist," he had given a plethora of data concerning the auscultation of the lungs, heart, and vessels; obstetrics; and veterinary. To help younger physicians, he demonstrated through figures local anatomy and positions for auscultation, providing information for various types of stethoscopes being in use during the mid-19th century. He was a humanist and reformer for public hygiene. This historical vignette aims to present Henry Ingersoll Bowditch and his work concerning the thorax. For his contributions to education and public hygiene, he should be celebrated as one of the most important figures of the eve of American medicine.

Growth rate is a dominant factor predicting the rhizosphere effect.

The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. This influence on the microorganisms and soil chemistry in the immediate vicinity of the roots has been referred to as the rhizosphere effect. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions. In this study, we compared the growth rate potential, a complex trait that can be predicted from bacterial genome sequences, to functional traits encoded by proteins. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA gene amplicon datasets from 18 different plants and soil types, performed differential abundance analysis, and estimated growth rates for each bacterial genus. We found that bacteria with higher growth rate potential consistently dominated the rhizosphere, and this trend was confirmed in different bacterial phyla using genome sequences of 3270 bacterial isolates and 6707 metagenome-assembled genomes (MAGs) from 1121 plant- and soil-associated metagenomes. We then identified which functional traits were enriched in MAGs according to their niche or growth rate status. We found that predicted growth rate potential was the main feature for differentiating rhizosphere and soil bacteria in machine learning models, and we then analyzed the features that were important for achieving faster growth rates, which makes bacteria more competitive in the rhizosphere. As growth rate potential can be predicted from genomic data, this work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.

Anatomical Considerations and Plastic Surgery Reconstruction Options of Sacral Chordoma Resection.

Introduction Chordomas are slow-growing malignant bone tumors arising from remnant embryonic notochord cells with predilection for the sacrum. They rarely metastasize, and early surgical resection with clear margins is the treatment of choice followed by plastic surgery reconstruction supplemented with adjuvant radiotherapy based on the local treatment protocol or in cases with a contaminated surgical field. Aim The aim of the present study is to present our experience in surgical management of sacral chordomas and propose a surgical reconstruction algorithm considering anatomical parameters after partial or total sacrectomy. Materials and methods  Twenty-seven patients with sacral chordomas were treated in our Orthopaedic Surgery Department between January 1997 and September 2022, and 10 of them had plastic surgery reconstruction. Patients were divided into groups based on the type of sacrectomy, sacrum anatomical vascular or neural variations, partial or total, and the type of soft tissue reconstruction. The postoperative complications and the functional outcomes in each patient were assessed. Results  Bilateral gluteal advancement flaps or gluteal perforator flaps are the first choice in patients with partial sacrectomy, intact gluteal vessels, and without preoperative radiotherapy followed by transpelvic vertical rectus abdominis myocutaneous flap or free flaps in those patients with near total sacrectomy and preoperative radiation therapy. Conclusion  There are four reliable options for patients after sacral chordoma resection: direct closure, bilateral gluteal advancement flaps, transpelvic vertical rectus abdominis myocutaneous flaps, and free flaps. Each time, tumor-free margins and a good reconstructive plan according to the defect and patient characteristics are mandatory.

Variations of the Median Nerve and Carpal Tunnel Syndrome: a Systematic Review of the Literature.

Objectives:The purpose of this systematic review is to examine the different variations of the median nerve (MN) and the diagnostic methods used to identify carpal tunnel syndrome (CTS), a common neuropathy resulting from the entrapment of the MN within the carpal tunnel. Understanding the different variations of the MN is crucial in order to prevent injuries during surgical treatment of the syndrome. Materials and methods:Data were extracted from studies published in PubMed. A detailed search in PubMed was performed for studies that reviewed the variations of the MN and CTS. Results:There are two main classifications of the MN, known as the Lanz and Amadio categories. Lanz's classification is the one being mostly used in the surgical literature, with group 3 (Bifid MN) being the main cause of the CTS. Additionally, there are branches and anastomosis of the MN that do not fit into either category, with the third common digital branch being the most injured nerve during carpal tunnel release surgery. Diagnostic techniques for CTS include physical examination combined with NCS tests, magnetic resonance imaging (MRI), ultrasound, or elastography. While NCS has been previously the most commonly used diagnostic method, the recent literature suggests that ultrasound and elastography are the most accurate techniques. Conclusions:In order to minimize injuries during carpal tunnel release surgery, it is crucial to have knowledge on the different variations of the MN that cause CTS. Additionally, this review emphasizes the significance of the current diagnostic methods, which not only make CTS more affordable but also facilitate easier recognition of the condition.

On the Age of Information in a Two-User Multiple Access Setup.

This work considers a two-user multiple access channel in which both users have Age of Information (AoI)-oriented traffic with different characteristics. More specifically, the first user has external traffic and cannot control the generation of status updates, and the second user monitors a sensor and transmits status updates to the receiver according to a generate-at-will policy. The receiver is equipped with multiple antennas and the transmitters have single antennas; the channels are subject to Rayleigh fading and path loss. We analyze the average AoI of the first user for a discrete-time first-come-first-served (FCFS) queue, last-come-first-served (LCFS) queue, and queue with packet replacement. We derive the AoI distribution and the average AoI of the second user for a threshold policy. Then, we formulate an optimization problem to minimize the average AoI of the first user for the FCFS and LCFS with preemption queue discipline to maintain the average AoI of the second user below a given level. The constraints of the optimization problem are shown to be convex. It is also shown that the objective function of the problem for the first-come-first-served queue policy is non-convex, and a suboptimal technique is introduced to effectively solve the problem using the algorithms developed for solving a convex optimization problem. Numerical results illustrate the performance of the considered optimization algorithm versus the different parameters of the system. Finally, we discuss how the analytical results of this work can be extended to capture larger setups with more than two users.

Finding functional associations between prokaryotic virus orthologous groups: a proof of concept.

BACKGROUND: The field of viromics has greatly benefited from recent developments in metagenomics, with significant efforts focusing on viral discovery. However, functional annotation of the increasing number of viral genomes is lagging behind. This is highlighted by the degree of annotation of the protein clusters in the prokaryotic Virus Orthologous Groups (pVOGs) database, with 83% of its current 9518 pVOGs having an unknown function. RESULTS: In this study we describe a machine learning approach to explore potential functional associations between pVOGs. We measure seven genomic features and use them as input to a Random Forest classifier to predict protein-protein interactions between pairs of pVOGs. After systematic evaluation of the model's performance on 10 different datasets, we obtained a predictor with a mean accuracy of 0.77 and Area Under Receiving Operation Characteristic (AUROC) score of 0.83. Its application to a set of 2,133,027 pVOG-pVOG interactions allowed us to predict 267,265 putative interactions with a reported probability greater than 0.65. At an expected false discovery rate of 0.27, we placed 95.6% of the previously unannotated pVOGs in a functional context, by predicting their interaction with a pVOG that is functionally annotated. CONCLUSIONS: We believe that this proof-of-concept methodology, wrapped in a reproducible and automated workflow, can represent a significant step towards obtaining a more complete picture of bacteriophage biology.

COVID19: Holiday intentions during a pandemic.

The travel, tourism and hospitality industries have been the worst affected of the world's major economic sectors during the COVID19 pandemic, which has had a devastating effect on both destinations and organisations. Drawing from a sample (N = 385) of adult permanent residents of Athens, Greece, the study examines the impact of COVID19 upon holiday intention. The chaordic systems are evaluated through the use of fuzzy-set Qualitative Comparative Analysis, whilst the study also used Necessary Condition Analysis for the calculation of the size effects of the examined conditions. The findings reveal two sufficient complex configurations leading to holiday intention: (i) holiday risks, and (ii) impact of COVID19. Based on the results, the article also offers a set of managerial implications. The contribution of the study is to both theoretical and methodological tourism domains.

Accommodation decision-making during the COVID-19 pandemic: Complexity insights from Greece.

With the remaining ambiguity around COVID-19 effective treatment, the decision-making process for 2020 tourists remains fraught with complexity. Drawing from a sample of 385 permanent Athenian residents, the study explores the decision-making attributes driving their accommodation purchasing preferences in times of increased uncertainty. The complex dynamics are investigated using fuzzy-set Qualitative Comparative Analysis. A complementary analysis evaluates the size effect of the examined conditions using Necessary Condition Analysis. In total, four solutions are generated concerning: (i) health and safety; (ii) the price-quality nexus; (iii) risk aspects; and (iv) quality related health and safety. The study contributes towards the initiation of the theoretical discourse on the foundations of the exploration of tourists' accommodation choice triggers and dilemmas in times of pandemics. The results inform market intelligence with regard to accommodation-related customer priorities, perceptions and intentions during the pandemic which lay several important managerial implications for the accommodation industry.

Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants.

BACKGROUND: Asexual reproduction has the potential to enhance deleterious mutation accumulation and to constrain adaptive evolution. One source of mutations that can be especially relevant in recent asexuals is activity of transposable elements (TEs), which may have experienced selection for high transposition rates in sexual ancestor populations. Predictions of genomic divergence under asexual reproduction therefore likely include a large contribution of transposable elements but limited adaptive divergence. For plants empirical insight into genome divergence under asexual reproduction remains limited. Here, we characterize expression divergence between clone members of a single apomictic lineage of the common dandelion (Taraxacum officinale) to contribute to our knowledge of genome evolution under asexuality. RESULTS: Using RNA-Seq, we show that about one third of heritable divergence within the apomictic lineage is driven by TEs and TE-related gene activity. In addition, we identify non-random transcriptional differences in pathways related to acyl-lipid and abscisic acid metabolisms which might reflect functional divergence within the apomictic lineage. We analyze SNPs in the transcriptome to assess genetic divergence between the apomictic clone members and reveal that heritable expression differences between the accessions are not explained simply by genome-wide genetic divergence. CONCLUSION: The present study depicts a first effort towards a more complete understanding of apomictic plant genome evolution. We identify abundant TE activity and ecologically relevant functional genes and pathways affecting heritable within-lineage expression divergence. These findings offer valuable resources for future work looking at epigenetic silencing and Cis-regulation of gene expression with particular emphasis on the effects of TE activity on asexual species' genome.

ERBIN is a new SARA-interacting protein: competition between SARA and SMAD2 and SMAD3 for binding to ERBIN.

SARA, an early endosomal protein, plays a key role in TGFß signalling, as it presents SMAD2 and SMAD3 for phosphorylation by the activated TGFß receptors. Here, we show that ERBIN is a new SARA-interacting protein that can be recruited by SARA to early endosomes. ERBIN was recently shown to bind and segregate phosphorylated SMAD2 and SMAD3 (SMAD2/3) in the cytoplasm, thereby inhibiting SMAD2/3-dependent transcription. SARA binds to ERBIN using a new domain, which we have called the ERBID (ERBIN-binding domain), whereas ERBIN binds to SARA using a domain (amino acids 1208-1265) that also interacts with SMAD2 and SMAD3, which we have called the SSID (SARA- and SMAD-interacting domain). We additionally show that SARA competes with SMAD2/3 for binding to ERBIN. In agreement, overexpression of SARA or the ERBID peptide reverses the inhibitory effect of ERBIN on SMAD2/3-dependent transcription. Taken together, these data suggest that the response of cells to TGFß and activin A can be influenced by the relative concentrations of SARA, ERBIN and SMAD2/3.