Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome ...Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica. TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies.
Bacterial and archaeal viruses are crucial for global biogeochemical cycles and might well be game-changing therapeutic agents in the fight against multi-resistant pathogens. Nevertheless, it is ...still unclear how to best use genome sequence data for a fast, universal and accurate taxonomic classification of such viruses.
We here present a novel in silico framework for phylogeny and classification of prokaryotic viruses, in line with the principles of phylogenetic systematics, and using a large reference dataset of officially classified viruses. The resulting trees revealed a high agreement with the classification. Except for low resolution at the family level, the majority of taxa was well supported as monophyletic. Clusters obtained with distance thresholds chosen for maximizing taxonomic agreement appeared phylogenetically reasonable, too. Analysis of an expanded dataset, containing >4000 genomes from public databases, revealed a large number of novel species, genera, subfamilies and families.
The selected methods are available as the easy-to-use web service 'VICTOR' at https://victor.dsmz.de.
jan.meier-kolthoff@dsmz.de.
Supplementary data are available at Bioinformatics online.
Systemic sclerosis (SSc) is a rare disease requiring multicentre collaboration to reveal comprehensive details of disease-related causes for morbidity and mortality.
The European League Against ...Rheumatism (EULAR) Scleroderma Trials and Research (EUSTAR) group initiated a database to prospectively gather key data of patients with SSc using a minimal essential dataset that was reorganised in 2008 introducing new items. Baseline visit data of patients who were registered between 2004 and 2011 were analysed using descriptive statistics.
In June 2011, 7655 patients (2838 with diffuse cutaneous (dc) and 4481 with limited cutaneous (lc) SSc who fulfilled the American College of Rheumatology diagnostic criteria had been registered in 174 centres, mainly European. The most prominent hallmarks of disease were Raynaud's phenomenon (96.3%), antinuclear antibodies (93.4%) and a typical capillaroscopic pattern (90.9%). Scleroderma was more common on fingers and hands than on any other part of the skin. Proton pump inhibitors (65.2%), calcium channel blockers (52.7%), and corticosteroids (45.3%) were most often prescribed. Among the immunosuppressant agents, cyclophosphamide was used more often in dcSSc than in lcSSc.
The EUSTAR database provides an abundance of information on the true clinical face of SSc that will be helpful in improving the classification of SSc and its subsets and for developing more specific therapeutic recommendations.
Abstract
Microbial systematics is heavily influenced by genome-based methods and challenged by an ever increasing number of taxon names and associated sequences in public data repositories. This ...poses a challenge for database systems, particularly since it is obviously advantageous if such data are based on a globally recognized approach to manage names, such as the International Code of Nomenclature of Prokaryotes. The amount of data can only be handled if accurate and reliable high-throughput platforms are available that are able to both comply with this demand and to keep track of all changes in an efficient and flexible way. The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de. The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de. We here present important updates of these two previously introduced, heavily interconnected platforms for taxonomic nomenclature and classification, including new high-level facilities providing access to bioinformatic algorithms, a considerable expansion of the database content, and new ways to easily access the data.
The largest observed earthquakes occur on subduction interfaces and frequently cause widespread damage and loss of life. Understanding the rupture behavior of megathrust events is crucial for ...earthquake rupture physics, as well as for earthquake early-warning systems. However, the large variability in behavior between individual events seemingly defies a description with a simple unifying model. Here we use three source time function (STF) data sets for subduction zone earthquakes, with moment magnitude M
w ≥ 7, and show that such large ruptures share a typical universal behavior. The median STF is scalable between events with different sizes, grows linearly, and is nearly triangular. The deviations from the median behavior are multiplicative and Gaussian—that is, they are proportionally larger for larger events. Our observations suggest that earthquake magnitudes cannot be predicted from the characteristics of rupture onsets.
The present study examined the relationship between body image and adolescent girls' activity on the social networking site (SNS) Facebook (FB). Research has shown that elevated Internet "appearance ...exposure" is positively correlated with increased body image disturbance among adolescent girls, and there is a particularly strong association with FB use. The present study sought to replicate and extend upon these findings by identifying the specific FB features that correlate with body image disturbance in adolescent girls. A total of 103 middle and high school females completed questionnaire measures of total FB use, specific FB feature use, weight dissatisfaction, drive for thinness, thin ideal internalization, appearance comparison, and self-objectification. An appearance exposure score was calculated based on subjects' use of FB photo applications relative to total FB use. Elevated appearance exposure, but not overall FB usage, was significantly correlated with weight dissatisfaction, drive for thinness, thin ideal internalization, and self-objectification. Implications for eating disorder prevention programs and best practices in researching SNSs are discussed.
The narcissistic personality is characterized by grandiosity, entitlement, and low empathy. This paper describes the development and validation of the Single Item Narcissism Scale (SINS). Although ...the use of longer instruments is superior in most circumstances, we recommend the SINS in some circumstances (e.g. under serious time constraints, online studies).
In 11 independent studies (total N = 2,250), we demonstrate the SINS' psychometric properties.
The SINS is significantly correlated with longer narcissism scales, but uncorrelated with self-esteem. It also has high test-retest reliability. We validate the SINS in a variety of samples (e.g., undergraduates, nationally representative adults), intrapersonal correlates (e.g., positive affect, depression), and interpersonal correlates (e.g., aggression, relationship quality, prosocial behavior). The SINS taps into the more fragile and less desirable components of narcissism.
The SINS can be a useful tool for researchers, especially when it is important to measure narcissism with constraints preventing the use of longer measures.
Gas clouds in present-day galaxies are inefficient at forming stars. Low star-formation efficiency is a critical parameter in galaxy evolution: it is why stars are still forming nearly 14 billion ...years after the Big Bang and why star clusters generally do not survive their births, instead dispersing to form galactic disks or bulges. Yet the existence of ancient massive bound star clusters (globular clusters) in the Milky Way suggests that efficiencies were higher when they formed ten billion years ago. A local dwarf galaxy, NGC 5253, has a young star cluster that provides an example of highly efficient star formation. Here we report the detection of the J = 3→2 rotational transition of CO at the location of the massive cluster. The gas cloud is hot, dense, quiescent and extremely dusty. Its gas-to-dust ratio is lower than the Galactic value, which we attribute to dust enrichment by the embedded star cluster. Its star-formation efficiency exceeds 50 per cent, tenfold that of clouds in the Milky Way. We suggest that high efficiency results from the force-feeding of star formation by a streamer of gas falling into the galaxy.
Despite an increasing number of women in the field of surgery, bias regarding cognitive or technical ability may continue to affect the experience of female trainees differently than their male ...counterparts. This study examines the differences in the degree of operative autonomy given to female compared with male general surgery trainees.
A smartphone app was used to collect evaluations of operative autonomy measured using the 4-point Zwisch scale, which describes defined steps in the progression from novice ("show and tell") to autonomous surgeon ("supervision only"). Differences in autonomy between male and female residents were compared using hierarchical logistic regression analysis.
A total of 412 residents and 524 faculty from 14 general surgery training programs evaluated 8,900 cases over a 9-month period. Female residents received less autonomy from faculty than did male residents overall (P < .001). Resident level of training and case complexity were the strongest predictors of autonomy. Even after controlling for potential confounding factors, including level of training, intrinsic procedural difficulty, patient-related case complexity, faculty sex, and training program environment, female residents still received less operative autonomy than their male counterparts. The greatest discrepancy was in the fourth year of training.
There is a sex-based difference in the autonomy granted to general surgery trainees. This gender gap may affect female residents’ experience in training and possibly their preparation for practice. Strategies need to be developed to help faculty and residents work together to overcome this gender gap.
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