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Motley Crew: Overview of the Currently Available Phage Diversity.

ABSTRACT: The first complete genome that was sequenced at the beginning of the sequencing era was that of a phage, since then researchers throughout the world have been steadily describing and publishing genomes from a wide array of phages, uncovering the secrets of the most abundant and diverse biological entities known to man. Currently, we are experiencing an unprecedented rate of novel bacteriophage discovery, which can be seen from the fact that the amount of complete bacteriophage genome entries in public sequence repositories has more than doubled in the past 3 years and is steadily growing without showing any sign of slowing down. The amount of publicly available phage genome-related data can be overwhelming and has been summarized in literature before but quickly becomes out of date. Thus, the aim of this paper is to briefly outline currently available phage diversity data for public acknowledgment that could possibly encourage and stimulate future "depth" studies of particular groups of phages or their gene products.

SUBMITTER: Zrelovs N

PROVIDER: S-EPMC7658105 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Motley Crew: Overview of the Currently Available Phage Diversity.

Zrelovs Nikita N Dislers Andris A Kazaks Andris A

Frontiers in microbiology 20201029

The first complete genome that was sequenced at the beginning of the sequencing era was that of a phage, since then researchers throughout the world have been steadily describing and publishing genomes from a wide array of phages, uncovering the secrets of the most abundant and diverse biological entities known to man. Currently, we are experiencing an unprecedented rate of novel bacteriophage discovery, which can be seen from the fact that the amount of complete bacteriophage genome entries in ...[more]

PMID: 33193205

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Project description:BackgroundDifferential diagnosis (DDX) generators are computer programs that generate a DDX based on various clinical data.ObjectiveWe identified evaluation criteria through consensus, applied these criteria to describe the features of DDX generators, and tested performance using cases from the New England Journal of Medicine (NEJM©) and the Medical Knowledge Self Assessment Program (MKSAP©).MethodsWe first identified evaluation criteria by consensus. Then we performed Google® and Pubmed searches to identify DDX generators. To be included, DDX generators had to do the following: generate a list of potential diagnoses rather than text or article references; rank or indicate critical diagnoses that need to be considered or eliminated; accept at least two signs, symptoms or disease characteristics; provide the ability to compare the clinical presentations of diagnoses; and provide diagnoses in general medicine. The evaluation criteria were then applied to the included DDX generators. Lastly, the performance of the DDX generators was tested with findings from 20 test cases. Each case performance was scored one through five, with a score of five indicating presence of the exact diagnosis. Mean scores and confidence intervals were calculated.Key resultsTwenty three programs were initially identified and four met the inclusion criteria. These four programs were evaluated using the consensus criteria, which included the following: input method; mobile access; filtering and refinement; lab values, medications, and geography as diagnostic factors; evidence based medicine (EBM) content; references; and drug information content source. The mean scores (95% Confidence Interval) from performance testing on a five-point scale were Isabel© 3.45 (2.53, 4.37), DxPlain® 3.45 (2.63-4.27), Diagnosis Pro® 2.65 (1.75-3.55) and PEPID™ 1.70 (0.71-2.69). The number of exact matches paralleled the mean score finding.ConclusionsConsensus criteria for DDX generator evaluation were developed. Application of these criteria as well as performance testing supports the use of DxPlain® and Isabel© over the other currently available DDX generators.

Project description:Systemic sclerosis (SSc) is an autoimmune disease initially recognized by hand involvement due to characteristic Raynaud's phenomenon (RP), puffy hands, skin thickening, and contractures resembling claw deformities. SSc contributes to hand impairment through inflammatory arthritis, joint contractures, tendon friction rubs (TFRs), RP, digital ulcers (DU), puffy hands, skin sclerosis, acro-osteolysis, and calcinosis. These manifestations, which often co-exist, can contribute to difficulty with occupational activities and activities of daily living (ADL), which can result in impaired quality of life. However, despite this knowledge, most diagnostic and treatment principles in SSc are focused on visceral manifestations due to known associations with morbidity and mortality. Treatment of inflammatory arthritis is symptom based and involves corticosteroids ?10mg daily, methotrexate, tumor necrosis factor inhibitors, tocilizumab, and abatacept. Small joint contractures are managed by principles of occupational hand therapy and rarely surgical procedures. TFRs may be treated similar to inflammatory arthritis with corticosteroids. All patients with RP and DU should keep digits covered and warm and avoid vasoconstrictive agents. Pharmacologic management of RP begins with use of calcium channel blockers, but additional agents that may be considered are fluoxetine and phosphodiesterase 5 (PDE5) inhibitors. DU management also involves vasodilators including calcium channel blockers and PDE5 inhibitors; bosentan has also been shown to prevent DU. In patients with severe RP and active DU, intravenous epoprostenol or iloprost can be used and surgical procedures, such as botulinum injections and digital sympathectomies, may be considered. For those with early diffuse cutaneous SSc needing immunosuppression for skin sclerosis, methotrexate or mycophenolate mofetil can be used, but the agent of choice depends on co-existing manifestations, such as inflammatory arthritis and/or lung involvement. Various pharmacologic agents for calcinosis have been considered but are generally ineffective; however, surgical options, including excision of areas of calcinosis, can be considered. Overall management of hand impairment for all patients with SSc should include occupational hand therapy techniques such as range of motion exercises, paraffin wax, and devices to assist in ADL. Thus, treatment options for the various manifestations contributing to hand impairment in SSc are limited and often modestly efficacious at best. Robust studies are needed to address the manifestations of SSc that contribute to hand impairment.

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Dataset Information

Motley Crew: Overview of the Currently Available Phage Diversity.

Publications

Motley Crew: Overview of the Currently Available Phage Diversity.

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