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Record W4249865205 · doi:10.1128/9781555818180.ch13

“Stable” Genomes

2014· book-chapter· en· W4249865205 on OpenAlex

Why this work is in the frame

A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.

affAt least one author lists a Canadian institution in the pinned OpenAlex snapshot.

Bibliographic record

VenueASM Press eBooks · 2014
Typebook-chapter
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicEscherichia coli research studies
Canadian institutionsUniversity of Calgary
Fundersnot available
KeywordsGenomePulsed-field gel electrophoresisBiologyHomologous recombinationBacterial genome sizeSalmonellaGeneticsGeneBacteriaEscherichia coliComputational biologyGenotype

Abstract

fetched live from OpenAlex

This chapter evaluates the present knowledge about the degree of stability of the genome of enteric bacteria. It discusses about the forces which have contributed to maintaining stability, and considers the types of rearrangements which can and do occur even in those genomes generally considered to be stable. With the use of methods of physical analysis of DNA, and especially the introduction of the use of pulsed-field gel electrophoresis (PFGE), used first in Escherichia coli by Smith and colleagues, the genomes of many strains were determined and conservation of gene order was shown to be the rule. It talks about two modifications of PFGE methods, which allow the determination of genome structure in many strains, have been used in representative enteric bacteria. It focuses on the forces which would be expected to act in a conservative way to maintain gene order. It is possible that transspecies recombination due to conjugation or transduction followed by homologous recombination, though very rare, is so important that colinearity is an important advantage. The author concludes that the overall conservation of gene order within the enteric bacteria which was reported many years ago in comparisons of E. coli and Salmonella typhimurium has been confirmed by the analysis of the physical maps of many strains of Salmonella and other enteric bacteria determined by PFGE and by the comparison of nucleotide sequences.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesMeta-epidemiology (narrow)
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Other · Consensus signal: Other
Teacher disagreement score0.750
Threshold uncertainty score1.000

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0000.000
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.001
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0000.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.027
GPT teacher head0.264
Teacher spread0.237 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it