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Biofilms 2003: Emerging Themes and Challenges in Studies of Surface-Associated Microbial Life

2004· article· en· W1974274768 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.

aboutThe title or abstract carries a Canadian signal from the geographic lexicon.
no affNo Canadian affiliation: this work is invisible to an affiliation-only frame.
No Canadian affiliation. An affiliation-only frame, the usual design, would never have seen this work. It is one of the works that make the case for inverting the frame.

Bibliographic record

VenueJournal of Bacteriology · 2004
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicBacterial biofilms and quorum sensing
Canadian institutionsnot available
FundersNational Institute of Dental and Craniofacial Research
KeywordsBiofilmBiologyMultidisciplinary approachPopularityEngineering ethicsEcologyBiochemical engineeringPsychologyEngineeringBacteriaSociologySocial scienceGenetics

Abstract

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For over a century microbiologists have studied liquid cultures of bacteria. In fact, a common criterion for choosing a microorganism to study has been its ability to grow in a suspended, homogeneous culture format, thereby simplifying examination of microbial physiology and genetics. Although these studies have been tremendously informative, they neglect the observation that many bacteria in the natural environment grow aggregated with each other, with solid surfaces, and at gas-liquid interfaces. There is a growing appreciation that, although clearly worthwhile, studies of standard planktonic cultures provide us with a biased view of microbial life. The study of microbial biofilms has received significant attention and achieved significant popularity in the last decade. As the numbers of laboratories and scientists interested in biofilms have rapidly increased, the field has suffered some growing pains. Anyone wishing to conduct biofilm research or to compare their results with those of other laboratories faces the distinct problem of the limited number of standardized systems or protocols for studying biofilms. Another challenging aspect of the field is its multidisciplinary nature. Biofilms are important in environmental, industrial, and clinical contexts (16, 19, 99). The study of biofilm communities benefits from the efforts of investigators from many different disciplines, including environmental and clinical biologists, surface chemists, engineers, and mathematical modelers, who bring their unique questions, perspectives, and technologies to bear on this phenomenon. Unfortunately, it's difficult to keep abreast of the scientific literature in one's own field, let alone others. The rapid growth of biofilm research and the need to bring together people from different disciplines interested in biofilms led the American Society for Microbiology (ASM) to sponsor Biofilms 2003, which was held in Victoria, Canada, on 1 to 6 November 2003. This was the third such meeting in a series, with the previous two being held in Snowbird, Utah, in 1996 and Big Sky, Mont., in 2000. There were 638 participants including 260 international scientists representing 36 countries and 112 graduate and undergraduate students. The meeting was divided into six sessions spread over 4 days. One day was set aside for biofilm workshops and demonstrations. There was a mix of invited speakers and those selected from submitted abstracts. Finally, evening breakout sessions were held on four of the nights. These sessions were organized to provoke a round-table discussion of key research topics. Most conferees agreed that although the days were long, the scientific discourse the meeting generated and the information shared were outstanding. Three keynote lectures were given on different evenings of the conference. These talks each captured critical aspects of the field and helped to set the tone of the meeting. The first was given by J. William Costerton, Director of the Center for Biofilm Engineering in Bozeman, Mont. Costerton reminded us how far we have come in the field and emphasized the point that we continually tend to underestimate the ability of bacteria to coordinate behaviors and processes as a community. David Stahl of the University of Washington gave the second keynote address. He provided us with examples of how studying pure cultures of organisms in the laboratory can mislead us and fail to explain observations of their behavior in the context of environmental communities. In the final keynote address, Soren Molin of the Danish Technical University pointed out that biofilm microbiology is a field that relies heavily on microscopic observation. He described the problems of interpreting such data and cautioned that alternative explanations are possible for what may appear to be a straightforward result. With this as the underpinning theme of his talk, he then proceeded to challenge several points of emerging biofilm dogma that are based primarily on microscopic data. The meeting at Victoria also marked a special occasion to recognize the career of J. William Costerton at an opening-night reception. He took the lead role in organizing the first three ASM-sponsored biofilm conferences and has worked tirelessly to promote and to spread the biofilm concept. A distinct impression taken from this meeting was the great number of laboratories doing high-quality research. Much of the work presented at the previous meeting in 2000 was fairly observational and had a qualitative feel to it. In Victoria, it was clear that many laboratories were conducting reductionist research and asking sophisticated questions. Another impression was how advances in imaging technology have transformed the field. At the 2000 meeting, only a few laboratories were capable of sophisticated microscopy, while at the Victoria meeting reports of confocal and time-lapse microscopy were commonplace. The great breadth of the meeting was reflected by the oral platform, which was organized into six sessions. These sessions were (i) Biofilm Structure/Function and Physiology, (ii) Developmental Patterns in Biofilms, (iii) Biofilms in Natural and Industrial systems, (iv) Cross Kingdom Interactions, (v) Pathogenesis, and (vi) The Biofilm Phenotype. Rather than providing a summary of every talk, this review intends to capture emerging themes and report key interesting new findings presented at the meeting. The following topics were the focus of attention and discussion.

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 categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: Bench or experimental
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.116
Threshold uncertainty score0.430

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 science0.0000.000
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 head0.038
GPT teacher head0.269
Teacher spread0.231 · 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