Exploring the functional composition of the human microbiome using a hand-curated microbial trait database

Even when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insight into the principles governing microbiome assembly. Much work to date analyzing the functional composition of microbial communities, however, relies heavily on inference from genomic features. Unfortunately, output from these methods can be hard to interpret and often suffers from relatively high error rates. We built and analyzed a domain-specific microbial trait database from known microbe-trait pairs recorded in the literature to better understand the functional composition of the human microbiome. Using a combination of phylogentically conscious machine learning tools and a network science approach, we were able to link particular traits to areas of the human body, discover traits that determine the range of body areas a microbe can inhabit, and uncover drivers of metabolic breadth. Domain-specific trait databases are an effective compromise between noisy methods to infer complex traits from genomic data and exhaustive, expensive attempts at database curation from the literature that do not focus on any one subset of taxa. They provide an accurate account of microbial traits and, by limiting the number of taxa considered, are feasible to build within a reasonable time-frame. We present a database specific for the human microbiome, in the hopes that this will prove useful for research into the functional composition of human-associated microbial communities.https://doi.org/10.1186/s12859-021-04216-

Cutaneous cut sign: A clue to self inflicted carving on the body by sharp object

Suicide notes are usually written with pen or marker on a paper, notebook, wall or mirror. However, suicide notes written on one’s own body is very rare, and suicide note engraved with some metallic object on the body has not been reported yet. In the present suicidal death, the victim while carving some letters on the left arm with a razor had an incidental cut on right thumb. This incidental cut on the palm may be referred as “cutaneous cut sign” which gives a clue that the carving on the body with a sharp object was written by the victim himself. It also provides an additional importance of examination of palm for the presence of supportive evidences

What’s Next? A Recommendation System for Industrial Training

Abstract Continuous training is crucial for creating and maintaining the right skill-profile for the industrial organization’s workforce. There is a tremendous variety in the available trainings within an organization: technical, project management, quality, leadership, domain-specific, soft-skills, etc. Hence it is important to assist the employee in choosing the best trainings, which perfectly suits her background, project needs and career goals. In this paper, we focus on algorithms for training recommendation in an industrial setting. We formalize the problem of next training recommendation, taking into account the employee’s training and work history. We present several new unsupervised sequence mining algorithms to mine the past trainings data from the organization for arriving at personalized next training recommendation. Using the real-life data about trainings of 118,587 employees over 5019 distinct trainings from a large multi-national IT organization, we show that these algorithms outperform several standard recommendation engine algorithms as well as those based on standard sequence mining algorithms

Additional file 1 of Exploring the functional composition of the human microbiome using a hand-curated microbial trait database

Additional file 1. Trait Database

Additional file 1 of Exploring the functional composition of the human microbiome using a hand-curated microbial trait database

Additional file 1. Trait Database

Additional file 1 of Exploring the functional composition of the human microbiome using a hand-curated microbial trait database

Additional file 1. Trait Database

Global Survey of Outcomes of Neurocritical Care Patients: Analysis of the PRINCE Study Part 2

BACKGROUND: Neurocritical care is devoted to the care of critically ill patients with acute neurological or neurosurgical emergencies. There is limited information regarding epidemiological data, disease characteristics, variability of clinical care, and in-hospital mortality of neurocritically ill patients worldwide. We addressed these issues in the Point PRevalence In Neurocritical CarE (PRINCE) study, a prospective, cross-sectional, observational study. METHODS: We recruited patients from various intensive care units (ICUs) admitted on a pre-specified date, and the investigators recorded specific clinical care activities they performed on the subjects during their first 7 days of admission or discharge (whichever came first) from their ICUs and at hospital discharge. In this manuscript, we analyzed the final data set of the study that included patient admission characteristics, disease type and severity, ICU resources, ICU and hospital length of stay, and in-hospital mortality. We present descriptive statistics to summarize data from the case report form. We tested differences between geographically grouped data using parametric and nonparametric testing as appropriate. We used a multivariable logistic regression model to evaluate factors associated with in-hospital mortality. RESULTS: We analyzed data from 1545 patients admitted to 147 participating sites from 31 countries of which most were from North America (69%, N = 1063). Globally, there was variability in patient characteristics, admission diagnosis, ICU treatment team and resource allocation, and in-hospital mortality. Seventy-three percent of the participating centers were academic, and the most common admitting diagnosis was subarachnoid hemorrhage (13%). The majority of patients were male (59%), a half of whom had at least two comorbidities, and median Glasgow Coma Scale (GCS) of 13. Factors associated with in-hospital mortality included age (OR 1.03; 95% CI, 1.02 to 1.04); lower GCS (OR 1.20; 95% CI, 1.14 to 1.16 for every point reduction in GCS); pupillary reactivity (OR 1.8; 95% CI, 1.09 to 3.23 for bilateral unreactive pupils); admission source (emergency room versus direct admission [OR 2.2; 95% CI, 1.3 to 3.75]; admission from a general ward versus direct admission [OR 5.85; 95% CI, 2.75 to 12.45; and admission from another ICU versus direct admission [OR 3.34; 95% CI, 1.27 to 8.8]); and the absence of a dedicated neurocritical care unit (NCCU) (OR 1.7; 95% CI, 1.04 to 2.47). CONCLUSION: PRINCE is the first study to evaluate care patterns of neurocritical patients worldwide. The data suggest that there is a wide variability in clinical care resources and patient characteristics. Neurological severity of illness and the absence of a dedicated NCCU are independent predictors of in-patient mortality.status: publishe

The value of open-source clinical science in pandemic response: lessons from ISARIC

International audienc