The domestication of the probiotic bacterium Lactobacillus acidophilus

Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population

Retinal ganglion cell survival and axon regeneration in WldS transgenic rats after optic nerve crush and lens injury.

BACKGROUND: We have previously shown that the slow Wallerian degeneration mutation, whilst delaying axonal degeneration after optic nerve crush, does not protect retinal ganglion cell (RGC) bodies in adult rats. To test the effects of a combination approach protecting both axons and cell bodies we performed combined optic nerve crush and lens injury, which results in both enhanced RGC survival as well as axon regeneration past the lesion site in wildtype animals. RESULTS: As previously reported we found that the Wld(S) mutation does not protect RGC bodies after optic nerve crush alone. Surprisingly, we found that Wld(S) transgenic rats did not exhibit the enhanced RGC survival response after combined optic nerve crush and lens injury that was observed in wildtype rats. RGC axon regeneration past the optic nerve lesion site was, however, similar in Wld(S) and wildtypes. Furthermore, activation of retinal glia, previously shown to be associated with enhanced RGC survival and axon regeneration after optic nerve crush and lens injury, was unaffected in Wld(S) transgenic rats. CONCLUSIONS: RGC axon regeneration is similar between Wld(S) transgenic and wildtype rats, but Wld(S) transgenic rats do not exhibit enhanced RGC survival after combined optic nerve crush and lens injury suggesting that the neuroprotective effects of lens injury on RGC survival may be limited by the Wld(S) protein.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Getting It on Record: Issues and Strategies for Ethnographic Practice in Recording Studios

The recording studio has been somewhat neglected as a site for ethnographic fieldwork in the field of ethno-musicology and, moreover, the majority of published studies tend to overlook the specific concerns faced by the researcher within these contexts. Music recording studios can be places of creativity, artistry, and collaboration, but they often also involve challenging, intimidating, and fractious relations. Given that recording studios are, first and foremost, concerned with documenting musicians’ performances, we discuss the concerns of getting studio interactions “on record” in terms of access, social relations, and methods of data collection. This article reflects on some of the issues we faced when conducting our fieldwork within British music recording facilities and makes suggestions based on strategies that we employed to address these issues

Multitask feature selection within structural datasets

Population-based structural health monitoring (PBSHM) systems use data from multiple structures to make inferences of health states. An area of PBSHM that has recently been recognized for potential development is the use of multitask learning (MTL) algorithms that differ from traditional single-task learning. This study presents an application of the MTL approach, Joint Feature Selection with LASSO, to provide automatic feature selection. The algorithm is applied to two structural datasets. The first dataset covers a binary classification between the port and starboard side of an aircraft tailplane, for samples from two aircraft of the same model. The second dataset covers normal and damaged conditions for pre- and postrepair of the same aircraft wing. Both case studies demonstrate that the MTL results are interpretable, highlighting features that relate to structural differences by considering the patterns shared between tasks. This is opposed to single-task learning, which improved accuracy at the cost of interpretability and selected features, which failed to generalize in previously unobserved experiments

Birch bark tar in early Medieval England:continuity of tradition or technological revival?

International audienc

The foreground transfer function for HI intensity mapping signal reconstruction: MeerKLASS and precision cosmology applications

Blind cleaning methods are currently the preferred strategy for handling foreground contamination in single-dish HI intensity mapping surveys. Despite the increasing sophistication of blind techniques, some signal loss will be inevitable across all scales. Constructing a corrective transfer function using mock signal injection into the contaminated data has been a practice relied on for HI intensity mapping experiments. However, assessing whether this approach is viable for future intensity mapping surveys where precision cosmology is the aim, remains unexplored. In this work, using simulations, we validate for the first time the use of a foreground transfer function to reconstruct power spectra of foreground-cleaned low-redshift intensity maps and look to expose any limitations. We reveal that even when aggressive foreground cleaning is required, which causes ${>}\,50\%$ negative bias on the largest scales, the power spectrum can be reconstructed using a transfer function to within sub-percent accuracy. We specifically outline the recipe for constructing an unbiased transfer function, highlighting the pitfalls if one deviates from this recipe, and also correctly identify how a transfer function should be applied in an auto-correlation power spectrum. We validate a method that utilises the transfer function variance for error estimation in foreground-cleaned power spectra. Finally, we demonstrate how incorrect fiducial parameter assumptions (up to ${\pm}100\%$ bias) in the generation of mocks, used in the construction of the transfer function, do not significantly bias signal reconstruction or parameter inference (inducing ${<}\,5\%$ bias in recovered values).Comment: 25 pages, 20 figures. See Figure 4 for the main demonstration of the transfer function's performance for reconstructing signal loss from foreground cleaning. Submitted to MNRAS for publicatio

A sampling-based approach for information-theoretic inspection management

A partially supervised approach to Structural Health Monitoring is proposed, to manage the cost associated with expert inspections and maximize the value of monitoring regimes. Unlike conventional data-driven procedures, the monitoring classifier is learnt online while making predictions—negating the requirement for complete data before a system is in operation (which are rarely available). Most critically, periodic inspections are replaced (or enhanced) by an automatic inspection regime, which only queries measurements that appear informative to the evolving model of the damage-sensitive features. The result is a partially supervised Dirichlet process clustering that manages expert inspections online given incremental data. The method is verified on a simulated example and demonstrated on in situ bridge monitoring data