scholarly journals COPLA, a taxonomic classifier of plasmids

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Santiago Redondo-Salvo ◽  
Roger Bartomeus-Peñalver ◽  
Luis Vielva ◽  
Kaitlin A. Tagg ◽  
Hattie E. Webb ◽  
...  
Keyword(s):  
Web Service ◽  
Classification Scheme ◽  
Genomic Sequence ◽  
Large Fraction ◽  
Classification Systems ◽  
Virulence Determinants ◽  
Adaptive Traits ◽  
Bioinformatic Tool ◽  
Automated Pipeline ◽  
Definition Of

Abstract Background Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality. The definition of plasmid taxonomic units (PTUs), based on average nucleotide identity metrics, allows the generation of a universal plasmid classification scheme, applicable to all bacterial taxa. Here we present COPLA, a software able to assign plasmids to known and novel PTUs, based on their genomic sequence. Results We implemented an automated pipeline able to assign a given plasmid DNA sequence to its cognate PTU, and assessed its performance using a sample of 1000 unclassified plasmids. Overall, 41% of the samples could be assigned to a previously defined PTU, a number that reached 63% in well-known taxa such as the Enterobacterales order. The remaining plasmids represent novel PTUs, indicating that a large fraction of plasmid backbones is still uncharacterized. Conclusions COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids.

Contemporary Classifications of Suicidal Behaviors

Crisis ◽  
2020 ◽  
Vol 41 (3) ◽  
pp. 179-186 ◽  
Author(s):  
Benjamin Goodfellow ◽  
Kairi Kõlves ◽  
Diego De Leo
Keyword(s):  
Suicidal Behavior ◽  
Classification Scheme ◽  
Field Work ◽  
Operational Definition ◽  
Research Field ◽  
Classification Systems ◽  
International Level ◽  
English Only ◽  
Comparison Results ◽  
Definition Of

Abstract. Background: The absence of agreed-upon terminology, definitions, and operational classifications has hampered research in the field of suicidology for many decades. Aims and Method: We systematically reviewed contemporary classifications of suicidal behavior using the scope of the classification (comprehensive vs. restricted or single behaviors), and the presence or absence of a classification scheme and an operational definition of intent as features to enable analysis and comparison. Results: A chronological perspective shows that classification systems tend to be more and more precise and operational for clinical and research field work. However, on an international level, the development of classifications appears to precede the establishment of agreed-upon definitions and terms to describe suicidal behavior. Limitations: The review was conducted in English only. Conclusion: Universal agreement on definitions and terms for suicidal behavior should precede the development of classifications.

Introductory paper

1966 ◽  
Vol 24 ◽  
pp. 3-5
Author(s):  
W. W. Morgan
Keyword(s):  
Line Intensity ◽  
Classification Scheme ◽  
Two Dimensional ◽  
Spectral Classification ◽  
Dimensional Array ◽  
Rr Lyrae ◽  
Metallic Line ◽  
Introductory Paper ◽  
Parameter Varying ◽  
Definition Of

1. The definition of “normal” stars in spectral classification changes with time; at the time of the publication of theYerkes Spectral Atlasthe term “normal” was applied to stars whose spectra could be fitted smoothly into a two-dimensional array. Thus, at that time, weak-lined spectra (RR Lyrae and HD 140283) would have been considered peculiar. At the present time we would tend to classify such spectra as “normal”—in a more complicated classification scheme which would have a parameter varying with metallic-line intensity within a specific spectral subdivision.

scholarly journals Myelodysplastic syndrome: classification and prognostic systems

2011 ◽  
pp. 25-33
Author(s):  
Rosangela Invernizzi ◽  
Agnese Filocco
Keyword(s):  
Clinical Information ◽  
Scoring Systems ◽  
Classification Systems ◽  
World Health ◽  
Individual Risk ◽  
Information Classification ◽  
Definition Of ◽  
Health Organization ◽  
The Individual ◽  
Prognostic Scoring Systems

Myelodysplastic syndromes (MDS) are acquired clonal disorders of hematopoiesis, that are characterized most frequently by normocellular or hypercellular bone marrow specimens, and maturation that is morphologically and functionally dysplastic. MDS constitute a complex hematological problem: differences in disease presentation, progression and outcome have made it necessary to use classification systems to improve diagnosis, prognostication and treatment selection. On the basis of new scientific and clinical information, classification and prognostic systems have recently been updated and minimal diagnostic criteria forMDS have been proposed by expert panels. In addition, in the last few years our ability to define the prognosis of the individual patient with MDS has improved. In this paper World Health Organization (WHO) classification refinements and recent prognostic scoring systems for the definition of individual risk are highlighted and current criteria are discussed. The recommendations should facilitate diagnostic and prognostic evaluations in MDS and selection of patients for new effective targeted therapies.

scholarly journals The Banff Working Group Classification of Definitive Polyomavirus Nephropathy: Morphologic Definitions and Clinical Correlations

2017 ◽  
Vol 29 (2) ◽  
pp. 680-693 ◽  
Author(s):  
Volker Nickeleit ◽  
Harsharan K. Singh ◽  
Parmjeet Randhawa ◽  
Cinthia B. Drachenberg ◽  
Ramneesh Bhatnagar ◽  
...  
Keyword(s):  
Repeated Measures ◽  
Working Group ◽  
Classification Scheme ◽  
Clinical Presentation ◽  
Interstitial Fibrosis ◽  
The United States ◽  
Systematic Analysis ◽  
Definition Of ◽  
Morphologic Classification

Polyomavirus nephropathy (PVN) is a common viral infection of renal allografts, with biopsy-proven incidence of approximately 5%. A generally accepted morphologic classification of definitive PVN that groups histologic changes, reflects clinical presentation, and facilitates comparative outcome analyses is lacking. Here, we report a morphologic classification scheme for definitive PVN from the Banff Working Group on Polyomavirus Nephropathy, comprising nine transplant centers in the United States and Europe. This study represents the largest systematic analysis of definitive PVN undertaken thus far. In a retrospective fashion, clinical data were collected from 192 patients and correlated with morphologic findings from index biopsies at the time of initial PVN diagnosis. Histologic features were centrally scored according to Banff guidelines, including additional semiquantitative histologic assessment of intrarenal polyomavirus replication/load levels. In-depth statistical analyses, including mixed effects repeated measures models and logistic regression, revealed two independent histologic variables to be most significantly associated with clinical presentation: intrarenal polyomavirus load levels and Banff interstitial fibrosis ci scores. These two statistically determined histologic variables formed the basis for the definition of three PVN classes that correlated strongest with three clinical parameters: presentation at time of index biopsy, serum creatinine levels/renal function over 24 months of follow-up, and graft failure. The PVN classes 1–3 as described here can easily be recognized in routine renal biopsy specimens. We recommend using this morphologic PVN classification scheme for diagnostic communication, especially at the time of index diagnosis, and in scientific studies to improve comparative data analysis.

Introduction and Overview

2013 ◽  
Author(s):  
Kenneth Prewitt
Keyword(s):  
Eighteenth Century ◽  
Civil Rights ◽  
Classification Scheme ◽  
First Century ◽  
The Political ◽  
Racial Classification ◽  
Civil Rights Era ◽  
Racial Hierarchy ◽  
Definition Of

This introductory chapter discusses how there was a racial classification scheme in America's first census (1790), as there was in the next twenty-two censuses, up until the present. Though the classification was altered in response to the political and intellectual fashions of the day, the underlying definition of America's racial hierarchy never escaped its origins in the eighteenth-century. Even the enormous changing of the racial landscape in the civil rights era failed to challenge a dysfunctional classification, though it did bend it to new purposes. Nor has the demographic upheaval of the present time led to much fresh thinking about how to measure America. The chapter contends that twenty-first-century statistics should not be governed by race thinking that is two and a half centuries out of date.

Personal Storage Grid Architecture

2012 ◽  
pp. 97-109
Author(s):  
Mian-Guan Lim ◽  
Sining Wu ◽  
Tomasz Simon ◽  
Md Rashid ◽  
Na Helian
Keyword(s):  
Web Service ◽  
File System ◽  
File Systems ◽  
System Support ◽  
End User ◽  
Operation System ◽  
Disk Space ◽  
On Demand ◽  
Definition Of ◽  
Cloud Applications

On-demand cloud applications like online email accounts and online virtual disk space are becoming widely available in various forms. In cloud applications, one can see the importance of underlying resources, such as disk space, that is available to the end-user but not easily accessible. In the authors’ study, a modern file system developed in linux is proposed, which enables consuming of cloud applications and making the underlying disk space resource available to the end-user. This system is developed as a web service to support cross operation system support. A free online mail account was used to demonstrate this solution, and an IMAP protocol to communicate with remote data spaces was used so that this method can mount onto any email system that supports IMAP. The authors’ definition of infinite storage as the user is able to mount file systems as a single logical drive.

scholarly journals Proposal of a new classification scheme for periocular injuries

2017 ◽  
Vol 50 (01) ◽  
pp. 021-028 ◽  
Author(s):  
Devi Prasad Mohapatra ◽  
Friji Meethale Thiruvoth ◽  
Ravi Kumar Chittoria ◽  
S. Dinesh Kumar ◽  
Sudhanva Hemant Kumar ◽  
...  
Keyword(s):  
Soft Tissue ◽  
Classification Scheme ◽  
Soft Tissue Injuries ◽  
Classification Systems ◽  
Lateral Canthus ◽  
Aesthetic Appearance ◽  
Adjacent Structures ◽  
Tissue Injuries ◽  
Comprehensive Classification

ABSTRACT Background: Eyelids are important structures and play a role in protecting the globe from trauma, brightness, in maintaining the integrity of tear films and moving the tears towards the lacrimal drainage system and contribute to aesthetic appearance of the face. Ophthalmic trauma is an important cause of morbidity among individuals and has also been responsible for additional cost of healthcare. Periocular trauma involving eyelids and adjacent structures has been found to have increased recently probably due to increased pace of life and increased dependence on machinery. A comprehensive classification of periocular trauma would help in stratifying these injuries as well as study outcomes. Material and Methods: This study was carried out at our institute from June 2015 to Dec 2015. We searched multiple English language databases for existing classification systems for periocular trauma. We designed a system of classification of periocular soft tissue injuries based on clinico-anatomical presentations. This classification was applied prospectively to patients presenting with periocular soft tissue injuries to our department. Results: A comprehensive classification scheme was designed consisting of five types of periocular injuries. A total of 38 eyelid injuries in 34 patients were evaluated in this study. According to the System for Peri-Ocular Trauma (SPOT) classification, Type V injuries were most common. SPOT Type II injuries were more common isolated injuries among all zones. Discussion: Classification systems are necessary in order to provide a framework in which to scientifically study the etiology, pathogenesis, and treatment of diseases in an orderly fashion. The SPOT classification has taken into account the periocular soft tissue injuries i.e., upper eyelid, lower eyelid, medial and lateral canthus injuries., based on observed clinico-anatomical patterns of eyelid injuries. Conclusion: The SPOT classification seems to be a reliable system to address eyelid injuries. This classification scheme would guide the ophthalmic and facial reconstructive surgeons to provide optimal outcomes in eyelid injuries. Based on the classification scheme and review of existing literature, an algorithm is presented to facilitate repair and reconstruction.

A Semantic Web Service Architecture for Learing Object Repositories

2011 ◽  
pp. 141-158 ◽  
Author(s):  
José-Manuel Lopez-Cobo ◽  
Sinuhé Arroyo ◽  
Miguel-Angel Sicilia ◽  
Salvador Sanchez
Keyword(s):  
Semantic Web ◽  
Web Service ◽  
Learning Objects ◽  
Learning Object ◽  
Learning Technology ◽  
Computational Semantics ◽  
Semantic Web Service ◽  
Service Architecture ◽  
Develop Technology ◽  
Definition Of

The evolution of learning technology standards has resulted in a degree of interoperability across systems that enable the interchange of learning contents and activities. Nonetheless, learning resource metadata does not provide formal computational semantics, which hampers the possibilities to develop technology that automates tasks like learning object selection and negotiation. In this paper, the provision of computational semantics to metadata is addressed from the perspective of the concept of Semantic Web service. An architecture based on the specifications of the WSMO project is described, including the definition of an ontology for learning object metadata, and issues of mediation, all under the perspective of the learning object repository as the central entity in learning object reuse scenarios. The resulting framework serves as a foundation for advanced implementations that consider formal metadata semantics as a mechanism for the automation of tasks related to the interchange of learning objects.

scholarly journals Quantitative spectral classification of late WC stars

1997 ◽  
Vol 180 ◽  
pp. 19-19
Author(s):  
Orsola de Marco ◽  
P. A. Crowther ◽  
M. J. Barlow
Keyword(s):  
Classification Scheme ◽  
Natural Extension ◽  
Optical Observations ◽  
Spectral Classification ◽  
High Quality ◽  
Definition Of

We present a revised classification scheme for late WC-type stars based on new high quality optical observations of seven stars. For consistency with the usual WC scheme (Smith, ApJ 358 229 1990), our principal diagnostic is Cvi λ5801/Ciii λ5696, while Ciii λ5696/Cii λ4267, and He II λ4686/He I λ5876 serve as secondary criteria. Our quantitative scheme forms an natural extension to the existing WC scheme and provides an unambiguous definition of subtypes, with natural breaks found between subclasses.

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