Serial Position Effects in Short-term Visual Memory: A SIMPLE Explanation?

A version of Sternberg’s (1966) short-term, visual memory recognition paradigm with pictures of unfamiliar faces as stimuli was used in three experiments to assess the applicability of the distinctiveness based SIMPLE model proposed by Brown, Neath & Chater (2002). Initial simulations indicated that the amount of recency predicted increased as the parameter measuring the psychological distinctiveness of the stimulus material (c) increased, and that the amount of primacy was dependent on the extent of proactive interference from previously presented stimuli. The data from experiment 1, which used memory lists of four and five faces varying in visual similarity confirmed the predicted, extended recency effect. However, changes in visual similarity were not found to produce changes in c. In Experiments 2 and 3, the conditions that influence the magnitude of c were explored. These revealed that both the familiarity of the stimulus class before testing, and changes in familiarity due to perceptual learning, influenced distinctiveness as indexed by the parameter c. Overall the empirical data from all three experiments were well-fit by SIMPLE

Spherical:an iterative workflow for assembling metagenomic datasets

BACKGROUND: The consensus emerging from the study of microbiomes is that they are far more complex than previously thought, requiring better assemblies and increasingly deeper sequencing. However, current metagenomic assembly techniques regularly fail to incorporate all, or even the majority in some cases, of the sequence information generated for many microbiomes, negating this effort. This can especially bias the information gathered and the perceived importance of the minor taxa in a microbiome. RESULTS: We propose a simple but effective approach, implemented in Python, to address this problem. Based on an iterative methodology, our workflow (called Spherical) carries out successive rounds of assemblies with the sequencing reads not yet utilised. This approach also allows the user to reduce the resources required for very large datasets, by assembling random subsets of the whole in a "divide and conquer" manner. CONCLUSIONS: We demonstrate the accuracy of Spherical using simulated data based on completely sequenced genomes and the effectiveness of the workflow at retrieving lost information for taxa in three published metagenomics studies of varying sizes. Our results show that Spherical increased the amount of reads utilized in the assembly by up to 109% compared to the base assembly. The additional contigs assembled by the Spherical workflow resulted in a significant (P?<?0.05) changes in the predicted taxonomic profile of all datasets analysed. Spherical is implemented in Python 2.7 and freely available for use under the MIT license. Source code and documentation is hosted publically at: https://github.com/thh32/Spherical .publishersversionPeer reviewe

Understanding the lived experiences of healthcare professionals during the COVID-19 pandemic : an interpretative phenomenological analysis

Background: Little research has examined the impact of working within the context of COVID-19 on UK healthcare professionals (HCPs) mental health and well-being, despite previous pandemic findings indicating that HCPs are particularly vulnerable to suffering PTSD and other mental health difficulties due to the nature of healthcare work. Specifically, it appears that no research has employed qualitative methodologies to explore the effects of working amidst COVID-19 on mental health for HCPs in the UK. Objective: To qualitatively examining the lived experiences of HCPs in Northern Ireland, working during the early stages of the pandemic and lockdown period (14.04.20 and 29.04.20). Method: Interpretative phenomenological analysis (IPA) was used to explore the experiences of healthcare professionals, who were working during the COVID-19 outbreak. Ten HCPs were recruited via a social media campaign and snowball sampling. All interviews were conducted via telephone and transcribed verbatim. Results: Three superordinate themes with subordinate themes were elicited through the analysis. Theme one centred on specific challenges of HCPs working during the pandemic, such as redeployment, isolation from loved ones, infection concerns, lack of PPE and impact on patient interpersonal care. Theme two offered insights into the mental health and wellbeing of HCPs, while many experienced feelings of fear, sadness and hypervigilance, all also demonstrated a marked resilience. Finally, many felt undervalued and misunderstood, and wished to press upon the general public seriousness of the disease. Conclusion: To the authors’ knowledge this is the first study to explore in depth, the unique experiences of frontline HCPs in Northern Ireland, offering a detailed account of the challenges confronted in these unprecedented circumstances and highlighting support needs within this cohort

Rumen Virus Populations: Technological Advances Enhancing Current Understanding

The rumen contains a multi-kingdom, commensal microbiome, including protozoa, bacteria, archaea, fungi and viruses, which enables ruminant herbivores to ferment and utilize plant feedstuffs that would be otherwise indigestible. Within the rumen, virus populations are diverse and highly abundant, often out-numbering the microbial populations that they both predate on and co-exist with. To date the research effort devoted to understanding rumen-associated viral populations has been considerably less than that given to the other microbial populations, yet their contribution to maintaining microbial population balance, intra-ruminal microbial lysis, fiber breakdown, nutrient cycling and genetic transfer may be highly significant. This review follows the technological advances which have contributed to our current understanding of rumen viruses and drawing on knowledge from other environmental and animal-associated microbiomes, describes the known and potential roles and impacts viruses have on rumen function and speculates on the future directions of rumen viral research

Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling

16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies

The impacts of environmental warming on Odonata: a review

Climate change brings with it unprecedented rates of increase in environmental temperature, which will have major consequences for the earth's flora and fauna. The Odonata represent a taxon that has many strong links to this abiotic factor due to its tropical evolutionary history and adaptations to temperate climates. Temperature is known to affect odonate physiology including life-history traits such as developmental rate, phenology and seasonal regulation as well as immune function and the production of pigment for thermoregulation. A range of behaviours are likely to be affected which will, in turn, influence other parts of the aquatic ecosystem, primarily through trophic interactions. Temperature may influence changes in geographical distributions, through a shifting of species' fundamental niches, changes in the distribution of suitable habitat and variation in the dispersal ability of species. Finally, such a rapid change in the environment results in a strong selective pressure towards adaptation to cope and the inevitable loss of some populations and, potentially, species. Where data are lacking for odonates, studies on other invertebrate groups will be considered. Finally, directions for research are suggested, particularly laboratory studies that investigate underlying causes of climate-driven macroecological patterns

Microbiome-based interventions to modulate gut ecology and the immune system

The gut microbiome lies at the intersection between the environment and the host, with the ability to modify host responses to disease-relevant exposures and stimuli. This is evident in how enteric microbes interact with the immune system, e.g., supporting immune maturation in early life, affecting drug efficacy via modulation of immune responses, or influencing development of immune cell populations and their mediators. Many factors modulate gut ecosystem dynamics during daily life and we are just beginning to realise the therapeutic and prophylactic potential of microbiome-based interventions. These approaches vary in application, goal, and mechanisms of action. Some modify the entire community, such as nutritional approaches or faecal microbiota transplantation, while others, such as phage therapy, probiotics, and prebiotics, target specific taxa or strains. In this review, we assessed the experimental evidence for microbiome-based interventions, with a particular focus on their clinical relevance, ecological effects, and modulation of the immune system