Report of the Sub-Committee on Other Southern Hemisphere Whale Stocks

SC/65b/SH12rev provided an overview of Southern Ocean Research Partnership (IWC-SORP) progress since SC/65a. Progress made by the five on-going research projects is summarised below. SC/65b/SH12rev Annex 1 provided an update on the Antarctic Blue Whale Project. Its objectives are to improve current understanding of the status of the Antarctic blue whales and their role in the Antarctic ecosystem. The project has recently cooperated on five voyages to the Southern Ocean: (1) 2013 Voyage to the Ross Sea, led by the Australian Antarctic Division (SC/65a/SH21); (2) 2013/14 Whale Song Antarctic Voyage for Ecosystem Studies (WAVES) Expedition, led by the Centre for Whale Research, Australia; (3) 2014 voyage to the Antarctic Peninsula, an initiative of the South American Consortium led by Argentina (SC/65b/SH16Rev); (4) South African voyage to the Queen Maud Land coast (SC/65b/SH01); and (5) CETA voyage to the Dumont d’Urville Sea led by France (SC/65b/SH05). Data are also being augmented with information from ships of opportunity that contribute sightings data to the online reporting system

Taking account of sample size in the GLM analyses of the response variable data from the island closure feasibility study

Two approaches are used to examine the impact of taking sample size into account in GLM analyses to estimate the fishing effect parameter λ. In the first the variance of each mean value input to the analyses is disaggregated into separate contributions reflecting process error (taken to be constant) and observation error (taken to be inversely proportional to sample size). The second simpler approach merely omits values for which the sample size was very low. The implications are evaluated for the majority of the scenarios considered and methods applied in earlier analyses which did not account explicitly for sample size. The pattern of results when sample size is taken into account is clear and consistent: broadly speaking results do not change much in the great majority of cases, and in particular the substantial preponderance of positive to negative estimates of the fishing effect parameter λ remains

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

BACKGROUND Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use. FINDINGS Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find that the technical infrastructure is available to support rudimentary archiving, but the frequency of archiving is low. Currently, most phylogenetic knowledge is not easily re-used due to a lack of archiving, lack of awareness of best practices, and lack of community-wide standards for formatting data, naming entities, and annotating data. Most attempts at data re-use seem to end in disappointment. Nevertheless, we find many positive examples of data re-use, particularly those that involve customized species trees generated by grafting to, and pruning from, a much larger tree. CONCLUSIONS The technologies and practices that facilitate data re-use can catalyze synthetic and integrative research. However, success will require engagement from various stakeholders including individual scientists who produce or consume shareable data, publishers, policy-makers, technology developers and resource-providers. The critical challenges for facilitating re-use of phylogenetic trees and associated data, we suggest, include: a broader commitment to public archiving; more extensive use of globally meaningful identifiers; development of user-friendly technology for annotating, submitting, searching, and retrieving data and their metadata; and development of a minimum reporting standard (MIAPA) indicating which kinds of data and metadata are most important for a re-useable phylogenetic record

The interplay of intrinsic and extrinsic bounded noises in genetic networks

After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a genetic network. The influence of intrinsic and extrinsic noises on genetic networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: $(i)$ the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, $(ii)$ a model of enzymatic futile cycle and $(iii)$ a genetic toggle switch. In $(ii)$ and $(iii)$ we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possibile functional role of bounded noises

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

Background Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use. Findings Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find that the technical infrastructure is available to support rudimentary archiving, but the frequency of archiving is low. Currently, most phylogenetic knowledge is not easily re-used due to a lack of archiving, lack of awareness of best practices, and lack of community-wide standards for formatting data, naming entities, and annotating data. Most attempts at data re-use seem to end in disappointment. Nevertheless, we find many positive examples of data re-use, particularly those that involve customized species trees generated by grafting to, and pruning from, a much larger tree. Conclusions The technologies and practices that facilitate data re-use can catalyze synthetic and integrative research. However, success will require engagement from various stakeholders including individual scientists who produce or consume shareable data, publishers, policy-makers, technology developers and resource-providers. The critical challenges for facilitating re-use of phylogenetic trees and associated data, we suggest, include: a broader commitment to public archiving; more extensive use of globally meaningful identifiers; development of user-friendly technology for annotating, submitting, searching, and retrieving data and their metadata; and development of a minimum reporting standard (MIAPA) indicating which kinds of data and metadata are most important for a re-useable phylogenetic record

Long-term evaluation of a course on evidence-based public health in the U.S. and Europe

The evidence-based public health course equips public health professionals with skills and tools for applying evidence-based frameworks and processes in public health practice. To date, training has included participants from all the 50 U.S. states, 2 U.S. territories, and multiple other countries besides the U.S. This study pooled follow-up efforts (5 surveys, with 723 course participants, 2005-2019) to explore the benefits, application, and barriers to applying the evidence-based public health course content. All analyses were completed in 2020. The most common benefits (reported by \u3e80% of all participants) were identifying ways to apply knowledge in their work, acquiring new knowledge, and becoming a better leader who promotes evidence-based approaches. Participants most frequently applied course content to searching the scientific literature (72.9%) and least frequently to writing grants (42.7%). Lack of funds for continued training (35.3%), not having enough time to implement evidence-based public health approaches (33.8%), and not having coworkers trained in evidence-based public health (33.1%) were common barriers to applying the content from the course. Mean scores were calculated for benefits, application, and barriers to explore subgroup differences. European participants generally reported higher benefits from the course (mean difference=0.12, 95% CI=0.00, 0.23) and higher frequency of application of the course content to their job (mean difference=0.17, 95% CI=0.06, 0.28) than U.S. participants. Participants from later cohorts (2012-2019) reported more overall barriers to applying course content in their work (mean difference=0.15, 95% CI=0.05, 0.24). The evidence-based public health course represents an important strategy for increasing the capacity (individual skills) for evidence-based processes within public health practice. Organization-level methods are also needed to scale up and sustain capacity-building efforts

Live to cheat another day: bacterial dormancy facilitates the social exploitation of beta-lactamases

The breakdown of antibiotics by β-lactamases may be cooperative, since resistant cells can detoxify their environment and facilitate the growth of susceptible neighbours. However, previous studies of this phenomenon have used artificial bacterial vectors or engineered bacteria to increase the secretion of β-lactamases from cells. Here, we investigated whether a broad-spectrum β-lactamase gene carried by a naturally occurring plasmid (pCT) is cooperative under a range of conditions. In ordinary batch culture on solid media, there was little or no evidence that resistant bacteria could protect susceptible cells from ampicillin, although resistant colonies could locally detoxify this growth medium. However, when susceptible cells were inoculated at high densities, late-appearing phenotypically susceptible bacteria grew in the vicinity of resistant colonies. We infer that persisters, cells that have survived antibiotics by undergoing a period of dormancy, founded these satellite colonies. The number of persister colonies was positively correlated with the density of resistant colonies and increased as antibiotic concentrations decreased. We argue that detoxification can be cooperative under a limited range of conditions: if the toxins are bacteriostatic rather than bacteridical; or if susceptible cells invade communities after resistant bacteria; or if dormancy allows susceptible cells to avoid bactericides. Resistance and tolerance were previously thought to be independent solutions for surviving antibiotics. Here, we show that these are interacting strategies: the presence of bacteria adopting one solution can have substantial effects on the fitness of their neighbours

Evaluating a train-the-trainer approach for improving capacity for evidence-based decision making in public health

BACKGROUND: Evidence-based public health gives public health practitioners the tools they need to make choices based on the best and most current evidence. An evidence-based public health training course developed in 1997 by the Prevention Research Center in St. Louis has been taught by a transdisciplinary team multiple times with positive results. In order to scale up evidence-based practices, a train-the-trainer initiative was launched in 2010. METHODS: This study examines the outcomes achieved among participants of courses led by trained state-level faculty. Participants from trainee-led courses in four states (Indiana, Colorado, Nebraska, and Kansas) over three years were asked to complete an online survey. Attempts were made to contact 317 past participants. One-hundred forty-four (50.9 %) reachable participants were included in analysis. Outcomes measured include frequency of use of materials, resources, and other skills or tools from the course; reasons for not using the materials and resources; and benefits from attending the course. Survey responses were tabulated and compared using Chi-square tests. RESULTS: Among the most commonly reported benefits, 88 % of respondents agreed that they acquired knowledge about a new subject, 85 % saw applications for the knowledge to their work, and 78 % agreed the course also improved abilities to make scientifically informed decisions at work. The most commonly reported reasons for not using course content as much as intended included not having enough time to implement evidence-based approaches (42 %); other staff/peers lack training (34 %); and not enough funding for continued training (34 %). The study findings suggest that utilization of course materials and teachings remains relatively high across practitioner groups, whether they were taught by the original trainers or by state-based trainers. CONCLUSIONS: The findings of this study suggest that train-the-trainer is an effective method for broadly disseminating evidence-based public health principles. Train-the-trainer is less costly than the traditional method and allows for courses to be tailored to local issues, thus making it a viable approach to dissemination and scale up of new public health practices. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12913-015-1224-2) contains supplementary material, which is available to authorized users

Cooperative secretions facilitate host range expansion in bacteria

The majority of emergent human pathogens are zoonotic in origin, that is, they can transmit to humans from other animals. Understanding the factors underlying the evolution of pathogen host range is therefore of critical importance in protecting human health. There are two main evolutionary routes to generalism: organisms can tolerate multiple environments or they can modify their environments to forms to which they are adapted. Here we use a combination of theory and a phylogenetic comparative analysis of 191 pathogenic bacterial species to show that bacteria use cooperative secretions that modify their environment to extend their host range and infect multiple host species. Our results suggest that cooperative secretions are key determinants of host range in bacteria, and that monitoring for the acquisition of secreted proteins by horizontal gene transfer can help predict emerging zoonoses