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Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy.

In recent decades, the taxonomy of Bacteria and Archaea , and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of Bacteria and Archaea that are identified in this study will help assign genera with higher taxonomic resolution. Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and Archaea . IMPORTANCE In recent decades, the taxonomy of Bacteria and Archaea , and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of Bacteria and Archaea that are identified in this study will help assign genera with higher taxonomic resolution.

Metropolitan areas worldwide have grown rapidly and are usually surrounded by peri-urban zones that are neither urban nor rural. Despite widespread use of the term ‘peri-urban’, physical determination of these spaces is difficult due to their transient nature and multiple definitions. While many have identified peri-urban areas regionally or globally, questions persist on where exactly the peri-urban is located, and what are the most apt methods to delineate its boundaries. The answers are pertinent towards framing targeted policies for governing the dynamic socio-spatial transformations in these zones. This paper reviews peri-urban research over the last 50-plus years to discern the existing methodologies for its identification/demarcation and their applications. For this, a total of 3124 documents on peri-urban studies were identified through keyword searches in Scopus and Google Scholar databases. Thereafter, 56 documents were examined that explicitly dealt with demarcating peri-urban zones. Results reveal that there is no standout/generalized method for peri-urban demarcation. Rather, these approaches are geographically specific and vary across developed and developing countries, due to differences in land-use patterns, socioeconomic drivers, and political systems. Thus, we recommend developing a ‘pluralistic’ framework for determining peri-urban boundaries at the regional–global scale to enable better framing of relevant policies.

In various contexts and for various reasons, writers often define cognitive processes and architectures as those involving representational states and structures. Similarly, cognitive theories are also often delineated as those that invoke representations. In this paper, I present several reasons for rejecting this way of demarcating the cognitive. Some of the reasons against defining cognition in representational terms are that doing so needlessly restricts our theorizing, it undermines the empirical status of the representational theory of mind, and it encourages wildly deflationary and explanatorily vacuous conceptions of representation. After criticizing this outlook, I sketch alternative ways we might try to capture what is distinctive about cognition and cognitive theorizing.

There are some differences between the negligence that attracts criminal consequences and the one that attracts consequences in terms of civil liability. These differences are also reflected in the judicial practice, respectively in the solutions pronounced by the courts in the cases whose object is acts committed as a result of the negligence of the perpetrator. Such a case, in which the two types of negligence were addressed, is presented in this article.

Much has been written about the free energy principle (FEP), and much misunderstood. The principle has traditionally been put forth as a theory of brain function or biological self-organisation. Critiques of the framework have focused on its lack of empirical support and a failure to generate concrete, falsifiable predictions. I take both positive and negative evaluations of the FEP thus far to have been largely in error, and appeal to a robust literature on scientific modelling to rectify the situation. A prominent account of scientific modelling distinguishes between model structure and model construal. I propose that the FEP be reserved to designate a model structure, to which philosophers and scientists add various construals, leading to a plethora of models based on the formal structure of the FEP. An entailment of this position is that demands placed on the FEP that it be falsifiable or that it conform to some degree of biological realism rest on a category error. To this end, I deliver first an account of the phenomenon of model transfer and the breakdown between model structure and model construal. In the second section, I offer an overview of the formal elements of the framework, tracing their history of model transfer and illustrating how the formalism comes apart from any interpretation thereof. Next, I evaluate existing comprehensive critical assessments of the FEP, and hypothesise as to potential sources of existing confusions in the literature. In the final section, I distinguish between what I hold to be the FEP—taken to be a modelling language or modelling framework—and what I term “FEP models.”

Genomics allows accurately pinpointing microbial ancestry for taxonomic purposes, yet there is currently no consensus to genus definition based on genome data. Different metrics and criteria are used, with an increasing trend toward genera over-splitting. Here, we report a method for prokaryotic genus assignment that combines normalized tree clustering and network analysis of several genomic relatedness indices. Objectivity is maximized by linear application of the same partitioning thresholds across an entire middle/high taxonomic rank context (order level), with the classical (“pre-genomic”) genera as demarcation reference, ensuring continuity in taxonomy and nomenclature. We tested the method with the Mycobacteriales , where recent examples of genus fragmentation divided Mycobacterium into five genera, or made Rhodococcus paraphyletic by creating the genus Prescottella for the sublineage containing the animal and human pathogen, Rhodococcus equi . Our approach did not support the mycobacterial five-genus split or the Prescottella nested genus, but identified a basal branch in each of the mycobacterial and rhodococcal radiations warranting genus status ( Mycobacteroides , and novel genus Rhodococcoides for the Rhodococcus fascians clade, respectively). The median average amino acid identity (AAI) between the demarcated genera was 56% to 59%, consistent with the <65% AAI genus boundary standard. Shifting the demarcation threshold to the Prescottella /mycobacterial five-genus level systematically elevated the intrageneric sublineages to genus rank, leading to taxonomic atomization (≈threefold increase in potential Mycobacteriales genera). The proposed approach provides a standardizable methodological framework for non-subjective prokaryotic genus delineation. A robust taxonomy is essential for the organized study of prokaryotes and the effective communication of microbial knowledge. The genus rank is the mainstay of biological classification as it brings together under a common name a group of closely related organisms sharing the same recent ancestry and similar characteristics. Despite the unprecedented resolution afforded by whole-genome sequencing in defining evolutionary relationships, a consensus approach for phylogenomics-based prokaryotic genus delineation remains elusive. Taxonomists use different demarcation criteria, sometimes leading to genus rank over-splitting and the creation of multiple new genera. This work reports a simple, reliable, and standardizable method that seeks to minimize subjectivity in genomics-based demarcation of prokaryotic genera, exemplified through application to the order Mycobacteriales . Formal descriptions of proposed taxonomic changes based on our study are included.

Objective: To compare the corneal stromal demarcation line depth after Epithelium-On and Epithelium-Off corneal crosslinking in patients with keratoconus using anterior segment Optical Coherence Tomography (AS-OCT). Study design: Quasi-experimental study. Place and Duration of Study: Armed Forces Institute of Ophthalmology, Rawalpindi Pakistan from Jun 2018 to Jun 2019. Methodology: This study included patients (60 eyes) with progressive keratoconus treated with procedure CXL (corneal cross linkage). There were 30 eyes in each group. Two different protocols of Corneal cross linkage were performed, and patients were divided into two groups according to protocol: 1) epithelium-on Corneal cross-linkage, 2) epithelium-off Corneal crosslinkage. In the First-Group, epithelium-on Corneal cross-linkage,corneal epithelium was not removed, riboflavin solution was instilled on the cornea for one hour, and the cornea was exposed to Ultraviolet A rays. In Epithelium off Corneal cross-linkage,after epithelium was removed by spatula, riboflavin solution was instilled for 30 minutes, and Ultraviolet-A rays were focused on the cornea. After one month of the procedure, Anterior segment Optical Coherence Tomography was performed.Demarcation line depth was measured in treated corneas in all patients from both groups, and findings were compared. Results: The stromal demarcation line depth was similar in both groups, and there was no statistical difference between the groups. The mean value of demarcation line depth was 277.13±107.09 цm (p>0.05). Conclusion: Corneal stromal demarcation line depth after both procedures was similar in both groups after one month of Corneal cross-linkage, so it was concluded that epithelium-on Corneal cross-linkage was comparable to epithelium-off Corneal cross-linkage.

Identification of lesion demarcation during thoracoscopic anatomical lesion resection is fundamental for treating children with congenital lung malformation. Existing lesion demarcations do not always meet the needs of clinical practice. This study aimed to explore the safety and efficacy of near-infrared fluorescence imaging with nebulized inhalation of indocyanine green for thoracoscopic anatomical lesion resection in children with congenital lung malformation. Under the fluorescence scope, the area of uniform green fluorescence was produced when indocyanine green was distributed into normal lung tissue, and lesions showed little or no green fluorescence, thus delineating a clear fluorescent lesion demarcation. Under the guidance of fluorescent demarcation, all the patients except one case of extralobar sequestration underwent thoracoscopic anatomical lesion resection successfully.