The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO2 emissions generated by each Galaxy job.

A Comparative Study of Ex-Vivo Murine Pulmonary Mechanics Under Positive- and Negative-Pressure Ventilation

Increased ventilator use during the COVID-19 pandemic resurrected persistent questions regarding mechanical ventilation including the difference between physiological and artificial breathing induced by ventilators (i.e., positive- versus negative-pressure ventilation, PPV vs NPV). To address this controversy, we compare murine specimens subjected to PPV and NPV in ex vivo quasi-static loading and quantify pulmonary mechanics via measures of quasi-static and dynamic compliances, transpulmonary pressure, and energetics when varying inflation frequency and volume. Each investigated mechanical parameter yields instance(s) of significant variability between ventilation modes. Most notably, inflation compliance, percent relaxation, and peak pressure are found to be consistently dependent on the ventilation mode. Maximum inflation volume and frequency note varied dependencies contingent on the ventilation mode. Contradictory to limited previous clinical investigations of oxygenation and end-inspiratory measures, the mechanics-focused comprehensive findings presented here indicate lung properties are dependent on loading mode, and importantly, these dependencies differ between smaller versus larger mammalian species despite identical custom-designed PPV/NPV ventilator usage. Results indicate that past contradictory findings regarding ventilation mode comparisons in the field may be linked to the chosen animal model. Understanding the differing fundamental mechanics between PPV and NPV may provide insights for improving ventilation strategies and design to prevent associated lung injuries.

Hive Transplantation Has Minimal Impact on the Core Gut Microbiome of the Australian Stingless Bee, Tetragonula carbonaria

Bacteria residing in the guts of pollinating insects play a key role in nutrient acquisition, digestion, and resistance to pests and diseases. Imbalances in microbial flora in response to environmental change and stress can therefore impact insect health and resilience. This study is aimed at defining the core gut microbiome of the Australian native stingless bee, Tetragonula carbonaria, and exploring the impact of colony transplantation on gut health. The gut microbiomes of nine forager bees from natural (log) and manufactured (box) hives were examined via 16S rRNA gene amplicon sequencing. Some differences were observed at the ASV level between the microbiomes of log and box hive bees. However, a core microbiome, dominated by Lactobacillus spp., unclassified Acetobacteraceae spp., and Bombella spp., was maintained. Further, the inferred functional potential of the microbiomes was consistent across all individuals. This study highlights that although hive transplantation has an impact on the overall diversity of stingless bee gut microbiomes, it is unlikely to have a significant negative impact on the overall health and resilience of the colony.

Diseased and healthy murine local lung strains evaluated using digital image correlation

Tissue remodeling in pulmonary disease irreversibly alters lung functionality and impacts quality of life. Mechanical ventilation is amongst the few pulmonary interventions to aid respiration, but can be harmful or fatal, inducing excessive regional (i.e., local) lung strains. Previous studies have advanced understanding of diseased global-level lung response under ventilation, but do not adequately capture the critical local-level response. Here, we pair a custom-designed pressure-volume ventilator with new applications of digital image correlation, to directly assess regional strains in the fibrosis-induced ex-vivo mouse lung, analyzed via regions of interest. We discuss differences between diseased and healthy lung mechanics, such as distensibility, heterogeneity, anisotropy, alveolar recruitment, and rate dependencies. Notably, we compare local and global compliance between diseased and healthy states by assessing the evolution of pressure-strain and pressure-volume curves resulting from various ventilation volumes and rates. We find fibrotic lungs are less-distensible, with altered recruitment behaviors and regional strains, and exhibit disparate behaviors between local and global compliance. Moreover, these diseased characteristics show volume-dependence and rate trends. Ultimately, we demonstrate how fibrotic lungs may be particularly susceptible to damage when contrasted to the strain patterns of healthy counterparts, helping to advance understanding of how ventilator induced lung injury develops.

Climate dictates microbial community composition and diversity in Australian biological soil crusts (biocrusts)

The soil surface of drylands can typically be colonized by cyanobacteria and other microbes, forming biological soil crusts or 'biocrusts'. Biocrusts provide critical benefits to ecosystems and are a common component of the largely arid and semi-arid Australian continent. Yet, their distribution and the parameters that shape their microbial composition have not been investigated. We present here the first detailed description of Australia's biocrust microbiome assessed from 15 sites across the continent using 16S rRNA sequencing. The most abundant bacterial phyla from all sites were Cyanobacteria, Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Cyanobacterial communities from northern regions were more diverse and unclassified cyanobacteria were a noticeable feature of northern biocrusts. Segregation between northern and southern regions was largely due to the differential abundance of Microcoleus spp., with M. paludosus dominating in the north and M. vaginatus dominating in the south. The geographical shifts in bacterial composition and diversity were correlated to seasonal temperatures and summer rainfall. Our findings provide an initial reference for sampling strategies to maximize access to bacterial genetic diversity. As hubs for essential ecosystem services, further investigation into biocrusts in arid and semi-arid regions may yield discoveries of genetic mechanisms that combat increases in warming due to climate change.

Bacterial community structure and metabolic potential in microbialite-forming mats from South Australian saline lakes

Microbialites are sedimentary rocks created in association with benthic microorganisms. While they harbour complex microbial communities, Cyanobacteria perform critical roles in sediment stabilisation and accretion. Microbialites have been described from permanent and ephemeral saline lakes in South Australia; however, the microbial communities that generate and inhabit these biogeological structures have not been studied in detail. To address this knowledge gap, we investigated the composition, diversity and metabolic potential of bacterial communities from different microbialite-forming mats and surrounding sediments in five South Australian saline coastal lakes using 16S rRNA gene sequencing and predictive metagenome analyses. While Proteobacteria and Bacteroidetes were the dominant phyla recovered from the mats and sediments, Cyanobacteria were significantly more abundant in the mat samples. Interestingly, at lower taxonomic levels, the mat communities were vastly different across the five lakes. Comparative analysis of putative mat and sediment metagenomes via PICRUSt2 revealed important metabolic pathways driving the process of carbonate precipitation, including cyanobacterial oxygenic photosynthesis, ureolysis and nitrogen fixation. These pathways were highly conserved across the five examined lakes, although they appeared to be performed by distinct groups of bacterial taxa found in each lake. Stress response, quorum sensing and circadian clock were other important pathways predicted by the in silico metagenome analysis. The enrichment of CRISPR/Cas and phage shock associated genes in these cyanobacteria-rich communities suggests that they may be under selective pressure from viral infection. Together, these results highlight that a very stable ecosystem function is maintained by distinctly different communities in microbialite-forming mats in the five South Australian lakes and reinforce the concept that 'who' is in the community is not as critical as their net metabolic capacity.

Examining lung mechanical strains as influenced by breathing volumes and rates using experimental digital image correlation

BACKGROUND

Mechanical ventilation is often employed to facilitate breathing in patients suffering from respiratory illnesses and disabilities. Despite the benefits, there are risks associated with ventilator-induced lung injuries and death, driving investigations for alternative ventilation techniques to improve mechanical ventilation, such as multi-oscillatory and high-frequency ventilation; however, few studies have evaluated fundamental lung mechanical local deformations under variable loading.

METHODS

Porcine whole lung samples were analyzed using a novel application of digital image correlation interfaced with an electromechanical ventilation system to associate the local behavior to the global volume and pressure loading in response to various inflation volumes and breathing rates. Strains, anisotropy, tissue compliance, and the evolutionary response of the inflating lung were analyzed.

RESULTS

Experiments demonstrated a direct and near one-to-one linear relationship between applied lung volumes and resulting local mean strain, and a nonlinear relationship between lung pressures and strains. As the applied air delivery volume was doubled, the tissue surface mean strains approximately increased from 20 to 40%, and average maximum strains measured 70-110%. The tissue strain anisotropic ratio ranged from 0.81 to 0.86 and decreased with greater inflation volumes. Local tissue compliance during the inflation cycle, associating evolutionary strains in response to inflation pressures, was also quantified.

CONCLUSION

Ventilation frequencies were not found to influence the local stretch response. Strain measures significantly increased and the anisotropic ratio decreased between the smallest and greatest tidal volumes. Tissue compliance did not exhibit a unifying trend. The insights provided by the real-time continuous measures, and the kinetics to kinematics pulmonary linkage established by this study offers valuable characterizations for computational models and establishes a framework for future studies to compare healthy and diseased lung mechanics to further consider alternatives for effective ventilation strategies.

The impacts of faecal subsampling on microbial compositional profiling

Objective

Despite the move to at-home, small-volume collection kits to facilitate large population-based studies of faecal microbial compositional profiling, there remains limited reporting on potential impacts of faecal subsampling approaches on compositional profiles. This study aimed to compare the microbial composition from faecal subsamples (< 5 g) collected from the beginning and end of a single bowel movement in ten otherwise healthy adults (6 female, 4 male; age: 24–55 years). Microbial composition was determined by V3–V4 16s rRNA sequencing and compared between subsamples.

Results

There were no significant differences in OTU count (p = 0.32) or Shannon diversity index (p = 0.29) between the subsamples. Comparison of relative abundance for identified taxa revealed very few differences between subsamples. At the lower levels of taxonomic classification differences in abundance of the Bacillales (p = 0.02) and the Eubacteriaceae family (p = 0.03), and the Eubacterium genera (p = 0.03) were noted. The observation of consistent microbial compositional profiles between faecal subsamples from the beginning and end of a single bowel movement is an important outcome for study designs employing this approach to faecal sample collection. These findings provide assurance that use of a faecal subsample for microbial composition profiling is generally representative of the gut luminal contents more broadly.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-022-05923-6.

Biogenic Amines Increase the Odds of Bacterial Vaginosis and Affect the Growth of and Lactic Acid Production by Vaginal Lactobacillus spp

Bacterial vaginosis (BV) is the most common vaginal disorder of reproductive-aged women, yet its etiology remains enigmatic. One clinical symptom of BV, malodor, is linked to the microbial production of biogenic amines (BA). Using targeted liquid chromatography mass spectrometry, we analyzed 149 longitudinally collected vaginal samples to determine the in vivo concentrations of the most common BAs and then assessed their relationship to BV and effect upon the growth kinetics of axenically cultured vaginal Lactobacillus species. Increases in cadaverine, putrescine, and tyramine were associated with greater odds of women transitioning from L. crispatus-dominated vaginal microbiota to microbiota that have a paucity of Lactobacillus spp. and from Nugent scores of 0 to 3 to Nugent scores of 7 to 10, consistent with BV. Exposure to putrescine lengthened the lag time and/or slowed the growth of all vaginal Lactobacillus spp. except L. jensenii 62G. L. iners AB107's lag time was lengthened by cadaverine but reduced in the presence of spermidine and spermine. The growth rate of L. crispatus VPI 3199 was slowed by cadaverine and tyramine, and strain-specific responses to spermine and spermidine were observed. BAs were associated with reduced production of d- and l-lactic acid by vaginal Lactobacillus spp., and this effect was independent of their effect upon Lactobacillus species growth. The exceptions were higher levels of d- and l-lactic acid by two strains of L. crispatus when grown in the presence of spermine. Results of this study provide evidence of a direct impact of common biogenic amines on vaginal Lactobacillus spp.IMPORTANCELactobacillus spp. are credited with providing the primary defense against gynecological conditions, including BV, most notably through the acidification of the vaginal microenvironment, which results from their production of lactic acid. The microbial production of BAs has been hypothesized to play a mechanistic role in diminishing Lactobacillus species-mediated protection, enabling the colonization and outgrowth of diverse anaerobic bacterial species associated with BV. Here, we demonstrate that in vivo increases in the most commonly observed BAs are associated with a loss of Lactobacillus spp. and the development of BV, measured by Nugent score. Further, we show that BAs formed by amino acid decarboxylase enzymes negatively affect the growth of type strains of the most common vaginal Lactobacillus spp. and separately alter their production of lactic acid. These results suggest that BAs destabilize vaginal Lactobacillus spp. and play an important and direct role in diminishing their protection of the vaginal microenvironment.

Wine Terroir and the Soil Bacteria: An Amplicon Sequencing-Based Assessment of the Barossa Valley and Its Sub-Regions

A wines' terroir, represented as wine traits with regional distinctiveness, is a reflection of both the biophysical and human-driven conditions in which the grapes were grown and wine made. Soil is an important factor contributing to the uniqueness of a wine produced by vines grown in specific conditions. Here, we evaluated the impact of environmental variables on the soil bacteria of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that both dispersal isolation by geographic distance and environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) contribute to microbial community dissimilarity between vineyards. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in soil bacterial community composition were significantly associated with differences in fruit and wine composition. Our results suggest that environmental factors affecting wine terroir, may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil bacteria.

Gut Microbiome Composition Remains Stable in Individuals with Diabetes-Related Early to Late Stage Chronic Kidney Disease

(1) Background: Individuals with diabetes and chronic kidney disease display gut dysbiosis when compared to healthy controls. However, it is unknown whether there is a change in dysbiosis across the stages of diabetic chronic kidney disease. We investigated a cross-sectional study of patients with early and late diabetes associated chronic kidney disease to identify possible microbial differences between these two groups and across each of the stages of diabetic chronic kidney disease. (2) Methods: This cross-sectional study recruited 95 adults. DNA extracted from collected stool samples were used for 16S rRNA sequencing to identify the bacterial community in the gut. (3) Results: The phylum Firmicutes was the most abundant and its mean relative abundance was similar in the early and late chronic kidney disease group, 45.99 ± 0.58% and 49.39 ± 0.55%, respectively. The mean relative abundance for family Bacteroidaceae, was also similar in the early and late group, 29.15 ± 2.02% and 29.16 ± 1.70%, respectively. The lower abundance of Prevotellaceae remained similar across both the early 3.87 ± 1.66% and late 3.36 ± 0.98% diabetic chronic kidney disease groups. (4) Conclusions: The data arising from our cohort of individuals with diabetes associated chronic kidney disease show a predominance of phyla Firmicutes and Bacteroidetes. The families Ruminococcaceae and Bacteroidaceae represent the highest abundance, while the beneficial Prevotellaceae family were reduced in abundance. The most interesting observation is that the relative abundance of these gut microbes does not change across the early and late stages of diabetic chronic kidney disease, suggesting that this is an early event in the development of diabetes associated chronic kidney disease. We hypothesise that the dysbiotic microbiome acquired during the early stages of diabetic chronic kidney disease remains relatively stable and is only one of many risk factors that influence progressive kidney dysfunction.

Cancerbiome: Defining a healthy microbiome for therapeutic targeting

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Background: The gut microbiome has been shown to modify the efficacy of cancer immunotherapy. Currently, there is little understanding of how the microbiome in advanced cancer patients responding to immunotherapy compares to healthy individuals. The aim of this study was to characterise the intestinal microbiome in patients with advanced solid organ tumours that have a durable response to programmed-death-protein-1 inhibitors (PD-1) with healthy individuals. Methods: Ten patients (mean age 69 ± 11; 60% female) with metastatic melanoma, renal cell carcinoma or non-small cell lung cancer and durable response for greater than one year to anti-PD-1 antibodies and ten healthy age and sex matched individuals (mean age 69 ± 9.2; 60% female) were recruited. Clinical data and a three-day diet diary were collected, with faecal sample analysed via shallow shotgun sequencing (CoreBiome, Minneapolis, USA). Results: Duration of response to immunotherapy was 786 ± 282 days. Responders had a significantly higher body mass index (28 ± 5.5 kg/m2 v 23.3 ± 2.65 kg/m2, p = 0.005; mean ± SD) than the healthy group. There was a significantly higher intake of total fat and fibre in the healthy group. The responder group had significantly higher diversity metrics, exhibiting a greater diversity in the number (OTUs) and the richness of species than the healthy group. At the phylum level, the microbiome in the responder group was significantly abundant in proteobacteria and had a significantly lower abundance of Bacteroidetes compared to the healthy group. At the genus level, the microbiome in the responder group was significantly enriched in Desulfovibrio, Acideminococcus, Klebsiella, Enterococcus and Faecalitalea compared to Ruminococcus, Veillonella and Roseburia in the healthy group. Species that were abundantly higher in the cancer group were associated with glycolysis, the TCA cycle, sugar metabolism and amino acid metabolism. Five Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues were significantly enriched in the responder group, mostly relating to transport systems for minerals and nitrogen fixation, but also mismatch repair proteins and cell cycle activity. Conclusions: Our findings suggest that compositional and functional differences in the faecal microbiome exist between advanced cancer patients responding to immunotherapy and healthy individuals, suggesting not only potential mechanisms of durable response but also targets for future therapy.

Cell-mediated and serology-based tests for Mycobacterium ulcerans disease: A systematic review and meta-analysis

Buruli ulcer (BU) is a subcutaneous necrotic infection of the skin caused by Mycobacterium ulcerans. It is the third most common human mycobacterial disease after tuberculosis (TB) and leprosy. The available methods for detection of the bacilli in lesions are microscopic detection, isolation and cultivation of the bacterium, histopathology, and polymerase chain reaction (PCR). These methods, although approved by the World Health Organization (WHO), have infrastructural and resource challenges in medical centres and cell-mediated immunity (CMI) and/or serology-based tests have been suggested as easier and more appropriate for accurate assessment of the disease, especially in remote or underdeveloped areas. This study systematically reviewed and conducted a meta-analysis for all research aimed at developing cell-mediated immunity (CMI) and/or serology-based tests for M. ulcerans disease. Information for this review was searched through PubMed and Web of Science databases and identified up to June 2019. References from relevant articles and reports from the WHO Annual Meeting of the Global Buruli Ulcer Initiative were also used. Twelve studies beginning in 1952, that attempted to develop CMI and/or serology-based tests for the disease were identified. These studies addressed issues of specificity and sensitivity in context of antigen composition as well as study heterogeneity and bias. The two main types of antigenic preparations considered were pathogen-derived and recombinant protein preparations. There was slight difference in test performance when M. ulcerans recombinant proteins [positivity: 67.5%; 32.5%] or pathogen-derived [positivity: 76.0%; 24.0%] preparations were used as test antigens among BU patients. However, pathogen-derived preparations were better at differentiating between patients and control groups [odds ratio (OR) of 27.92, 95%CI: 5.05–154.28]. This was followed by tests with the recombinant proteins [OR = 1.23, 95%CI: 0.27–5.62]. Overall, study heterogeneity index, I² was 92.4% (p = 0.000). It is apparent from this review that standardisation is needed in any future CMI and/or serology-based tests used for M. ulcerans disease.

Buruli ulcer (BU) is a debilitating skin infection caused by M. ulcerans. It is the third most common mycobacterial disease after tuberculosis and leprosy. BU is mainly restricted to the tropical and subtropical countries of the world, though temperate regions report sporadic cases. Polymerase chain reaction targeting IS2404 is the gold standard for M. ulcerans disease diagnosis and other methods such as histopathology, acid fast staining and microscopy are used for validity checks. The currently approved diagnostic tools lack sensitivity and specificity and there are many resource challenges in underdeveloped regions. Isolation and culture of the bacillus from tissue biopsies is the only method that detects viable cells. However, the long incubation period of the pathogen makes it not ideal and rapid enough for point-of-care diagnosis. Cell-mediated immunity and serology-based methods have been suggested as appropriate tools for accurate and rapid testing for the disease within “at-risk-communities”. This study systematically reviewed and conducted a meta-analysis on all research aimed at developing cell-mediated immunity and/or serology-based tests for M. ulcerans disease.

The vaginal metabolome and microbiota of cervical HPV-positive and HPV-negative women: a cross-sectional analysis

OBJECTIVE

Characterise the vaginal metabolome of cervical HPV-infected and uninfected women.

DESIGN

Cross-sectional.

SETTING

The Center for Health Behavior Research at the University of Maryland School of Public Health.

SAMPLE

Thirty-nine participants, 13 categorised as HPV-negative and 26 as HPV-positive (any genotype; HPV⁺ ), 14 of whom were positive with at least one high-risk HPV strain (hrHPV).

METHOD

Self-collected mid-vaginal swabs were profiled for bacterial composition by 16S rRNA gene amplicon sequencing, metabolites by both gas and liquid chromatography mass spectrometry, and 37 types of HPV DNA.

MAIN OUTCOME MEASURES

Metabolite abundances.

RESULTS

Vaginal microbiota clustered into Community State Type (CST) I (Lactobacillus crispatus-dominated), CST III (Lactobacillus iners-dominated), and CST IV (low-Lactobacillus, 'molecular-BV'). HPV⁺ women had higher biogenic amine and phospholipid concentrations compared with HPV^- women after adjustment for CST and cigarette smoking. Metabolomic profiles of HPV⁺ and HPV^- women differed in strata of CST. In CST III, there were higher concentrations of biogenic amines and glycogen-related metabolites in HPV⁺ women than in HPV^- women. In CST IV, there were lower concentrations of glutathione, glycogen, and phospholipid-related metabolites in HPV⁺ participants than in HPV^- participants. Across all CSTs, women with hrHPV strains had lower concentrations of amino acids, lipids, and peptides compared with women who had only low-risk HPV (lrHPV).

CONCLUSIONS

The vaginal metabolome of HPV⁺ women differed from HPV^- women in terms of several metabolites, including biogenic amines, glutathione, and lipid-related metabolites. If the temporal relation between increased levels of reduced glutathione and oxidised glutathione and HPV incidence/persistence is confirmed in future studies, anti-oxidant therapies may be considered as a non-surgical HPV control intervention.

TWEETABLE ABSTRACT

Metabolomics study: Vaginal microenvironment of HPV⁺ women may be informative for non-surgical interventions.

Modulation of high fat diet-induced microbiome changes, but not behaviour, by minocycline

An emerging novel therapeutic agent for major depressive disorder, minocycline, has the potential to influence both gut microbiome and inflammatory status. The present study showed that chronic high fat diet feeding led to changes in both behaviour and the gut microbiome in male mice, without an overt inflammatory response. The diet-induced behavioural changes were characterised as increased immobility in the forced swim test and changes in locomotor activities in the open field test. Minocycline significantly altered the gut microbiome, rendering a community distinctly different to both untreated healthy and diet-affected states. In contrast, minocycline did not reverse high fat diet-induced changes in behaviour.

Experience of Cause in Sighted and Blind Samples

Previous studies of perceptual causality have involved the visual modality directly or indirectly through associative imagery. The question addressed in this paper is whether causal impressions will occur in those never experiencing vision, i.e., in the early blind. A qualified answer of “yes” may be given. Fixed sequences of haptic stimulation “causal” and “non-causal” in type evoked the same reports from early blinded as from late blinded and blindfolded but normally sighted. Also, different semantic structures appear to be applied by the early blind, as contrasted to late blind and sighted persons to phenomena that are primarily (but not solely) visual in nature. It was concluded that the reports of causal interactions given by the early blind do not represent verbal habits based on vision but reflect causal experience unrelated to vision.

Cigarette smoking is associated with an altered vaginal tract metabolomic profile

Cigarette smoking has been associated with both the diagnosis of bacterial vaginosis (BV) and a vaginal microbiota lacking protective Lactobacillus spp. As the mechanism linking smoking with vaginal microbiota and BV is unclear, we sought to compare the vaginal metabolomes of smokers and non-smokers (17 smokers/19 non-smokers). Metabolomic profiles were determined by gas and liquid chromatography mass spectrometry in a cross-sectional study. Analysis of the 16S rRNA gene populations revealed samples clustered into three community state types (CSTs) ---- CST-I (L. crispatus-dominated), CST-III (L. iners-dominated) or CST-IV (low-Lactobacillus). We identified 607 metabolites, including 12 that differed significantly (q-value < 0.05) between smokers and non-smokers. Nicotine, and the breakdown metabolites cotinine and hydroxycotinine were substantially higher in smokers, as expected. Among women categorized to CST-IV, biogenic amines, including agmatine, cadaverine, putrescine, tryptamine and tyramine were substantially higher in smokers, while dipeptides were lower in smokers. These biogenic amines are known to affect the virulence of infective pathogens and contribute to vaginal malodor. Our data suggest that cigarette smoking is associated with differences in important vaginal metabolites, and women who smoke, and particularly women who are also depauperate for Lactobacillus spp., may have increased susceptibilities to urogenital infections and increased malodor.

An outbreak of severe infections among Australian infants caused by a novel recombinant strain of human parechovirus type 3

Human parechovirus types 1–16 (HPeV1–16) are positive strand RNA viruses in the family Picornaviridae. We investigated a 2015 outbreak of HPeV3 causing illness in infants in Victoria, Australia. Virus genome was extracted from clinical material and isolates and sequenced using a combination of next generation and Sanger sequencing. The HPeV3 outbreak genome was 98.7% similar to the HPeV3 Yamagata 2011 lineage for the region encoding the structural proteins up to nucleotide position 3115, but downstream of that the genome varied from known HPeV sequences with a similarity of 85% or less. Analysis indicated that recombination had occurred, may have involved multiple types of HPeV and that the recombination event/s occurred between March 2012 and November 2013. However the origin of the genome downstream of the recombination site is unknown. Overall, the capsid of this virus is highly conserved, but recombination provided a different non-structural protein coding region that may convey an evolutionary advantage. The indication that the capsid encoding region is highly conserved at the amino acid level may be helpful in directing energy towards the development of a preventive vaccine for expecting mothers or antibody treatment of young infants with severe disease.

Vaginal biogenic amines: biomarkers of bacterial vaginosis or precursors to vaginal dysbiosis?

Bacterial vaginosis (BV) is the most common vaginal disorder among reproductive age women. One clinical indicator of BV is a “fishy” odor. This odor has been associated with increases in several biogenic amines (BAs) that may serve as important biomarkers. Within the vagina, BA production has been linked to various vaginal taxa, yet their genetic capability to synthesize BAs is unknown. Using a bioinformatics approach, we show that relatively few vaginal taxa are predicted to be capable of producing BAs. Many of these taxa (Dialister, Prevotella, Parvimonas, Megasphaera, Peptostreptococcus, and Veillonella spp.) are more abundant in the vaginal microbial community state type (CST) IV, which is depleted in lactobacilli. Several of the major Lactobacillus species (L. crispatus, L. jensenii, and L. gasseri) were identified as possessing gene sequences for proteins predicted to be capable of putrescine production. Finally, we show in a small cross sectional study of 37 women that the BAs putrescine, cadaverine and tyramine are significantly higher in CST IV over CSTs I and III. These data support the hypothesis that BA production is conducted by few vaginal taxa and may be important to the outgrowth of BV-associated (vaginal dysbiosis) vaginal bacteria.

Saltwater intrusion history shapes the response of bacterial communities upon rehydration

Saltwater intrusion (SWI) can result in the loss of dominant vegetation from freshwater habitats. In northern Australia, sea level is predicted to rise 17-50 cm by 2030-2070. This will exacerbate the impact of SWI, threatening Ramsar-listed habitats. Soil bacteria in these habitats play a significant role in biogeochemical cycling, regulating availability of essential nutrients such as nitrogen to vegetation. However, there is limited understanding as to how SWI will impact these soil bacteria. Floodplain soil samples were collected from the South Alligator River floodplain in Northern Australia from sites with contrasting histories of SWI. A SWI event was simulated over 7 days with treatments of saltwater and freshwater. Bacterial community composition before and after treatment were measured using next generation sequencing of bacterial DNA. Sites with no history of SWI showed no significant changes in community taxonomic composition following treatments, suggesting the community at these sites have broad functional capacity which may be due to their historic conditioning over many years. Sites with a history of SWI showed a significant response to both treatments. Following saltwater treatment, there was an increase in sulfate-reducing bacteria, which are known to have an impact on carbon and nitrogen cycling. We suggest that the impact of SWI causes a shift in the soil bacteria which alters the community to one which is more specialised, with implications for the cycling of essential elements and nutrients.

Parent-reported distress in children under 3 years old during preventive medical and dental care

PURPOSE

This study examined factors related to young children's distress during preventive oral health visits. Additionally, associations between parent-reported child behaviour during the dental visit and during previous medical visits were tested.

METHODS

One hundred twenty-two children under 3 years of age enrolled in a government insurance programme for low-income children were seen for examination, prophylaxis, and fluoride application at a university-based dental clinic. Child distress was rated by parents on a numerical rating scale.

RESULTS

The average age of children enrolled was 23.5 ± 7.3 months. The majority (55.7 %) were judged to have little or no distress pre-examination. Mild or no distress during the examination was reported for 42.6 % of the children and severe distress was reported for 39.4 %. Intensity of distress during the examination was not associated with the child's age, gender, dental health, or previous experience with dental care. Distress was also unrelated to the caregiver's education level or own dental health. Intensity of distress was associated with the child's pre-dental examination distress and distress during prior medical examinations and injections.

CONCLUSIONS

Dental professionals can better anticipate child distress by assessing children before a dental examination and enquiring about previous medical experiences. Strategies to prepare parents and alleviate distress may help children cope with the preventive dental visit.

The gut bacterial community of mammals from marine and terrestrial habitats

After birth, mammals acquire a community of bacteria in their gastro-intestinal tract, which harvests energy and provides nutrients for the host. Comparative studies of numerous terrestrial mammal hosts have identified host phylogeny, diet and gut morphology as primary drivers of the gut bacterial community composition. To date, marine mammals have been excluded from these comparative studies, yet they represent distinct examples of evolutionary history, diet and lifestyle traits. To provide an updated understanding of the gut bacterial community of mammals, we compared bacterial 16S rRNA gene sequence data generated from faecal material of 151 marine and terrestrial mammal hosts. This included 42 hosts from a marine habitat. When compared to terrestrial mammals, marine mammals clustered separately and displayed a significantly greater average relative abundance of the phylum Fusobacteria. The marine carnivores (Antarctic and Arctic seals) and the marine herbivore (dugong) possessed significantly richer gut bacterial community than terrestrial carnivores and terrestrial herbivores, respectively. This suggests that evolutionary history and dietary items specific to the marine environment may have resulted in a gut bacterial community distinct to that identified in terrestrial mammals. Finally we hypothesize that reduced marine trophic webs, whereby marine carnivores (and herbivores) feed directly on lower trophic levels, may expose this group to high levels of secondary metabolites and influence gut microbial community richness.

Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals

The gut microbiota of mammals underpins the metabolic capacity and health of the host. Our understanding of what influences the composition of this community has been limited primarily to evidence from captive and terrestrial mammals. Therefore, the gut microbiota of southern elephant seals, Mirounga leonina, and leopard seals, Hydrurga leptonyx, inhabiting Antarctica were compared with captive leopard seals. Each seal exhibited a gut microbiota dominated by four phyla: Firmicutes (41.5 ± 4.0%), Fusobacteria (25.6 ± 3.9%), Proteobacteria (17.0 ± 3.2%) and Bacteroidetes (14.1 ± 1.7%). Species, age, sex and captivity were strong drivers of the composition of the gut microbiota, which can be attributed to differences in diet, gut length and physiology and social interactions. Differences in particular prey items consumed by seal species could contribute to the observed differences in the gut microbiota. The longer gut of the southern elephant seal provides a habitat reduced in available oxygen and more suitable to members of the phyla Bacteroidetes compared with other hosts. Among wild seals, 16 'core' bacterial community members were present in the gut of at least 50% of individuals. As identified between southern elephant seal mother-pup pairs, 'core' members are passed on via vertical transmission from a young age and persist through to adulthood. Our study suggests that these hosts have co-evolved with their gut microbiota and core members may provide some benefit to the host, such as developing the immune system. Further evidence of their strong evolutionary history is provided with the presence of 18 shared 'core' members in the gut microbiota of related seals living in the Arctic. The influence of diet and other factors, particularly in captivity, influences the composition of the community considerably. This study suggests that the gut microbiota has co-evolved with wild mammals as is evident in the shared presence of 'core' members.

Improving perception of letters and visual structure of language

Information about letters and the physical structure of language printed in Roman characters was given to children beginning to read. Experimental investigations coupled three alternative graphic modes of printing upper- and lower-case letters with an instructional intervention termed "Alpha-Beta" which provides practice in letter sorting, matching of letters, associative matching, and memory matching. In respect to graphics, Mode A letters were in standard alphabet form. Mode B provided standard letters with each backed by a unique half-tone (Visually Stippled Alphabet); Mode C provided standard letters with each backed by a unique visual texture (Visually Patterned Alphabet). Pre-posttest change in reading readiness was measured using the Metropolitan Readiness Test. In the first study 224 English-speaking 5- to 6-yr.-old children were tested. In the second there were 158 Spanish-speaking girls and boys 6 to 7 years old. It was predicted that Alpha-Beta intervention involving visually patterned alphabet would lead to the greatest increases in readiness scores. This is confirmed in both studies for children low in reading readiness preexperiment. Children high in reading readiness are less affected. The second experiment involved Spanish-speaking children and investigated intervention by Alpha-Beta against a no-intervention control. This confirms the value of Alpha-Beta per se. Possible explanations for the improvements are identified.

Development of fatigue symptoms during simulated driving

Why do people sometimes allow themselves to be overcome by fatigue? Ancient human survival may have depended on ignoring fatigue. Its modern occurrence in the absence of strain may further render us insensitive to its warning value. To test whether deliberate monitoring of certain symptoms may help drivers and other workers realize when they need to rest to avoid hazard, the development of fatigue while driving a simulator was objectively measured in terms of how many persons quit driving as a function of time. Some subjects asked to stop after 90 minutes; others lasted 240 minutes. Grouping data from an adapted Pearson [(1957) Journal of Applied Psychology, 44, 186-191] fatigue checklist revealed a curious phenomenon. No matter how long subjects drove before wanting to quit, they still developed much the same subjective level of fatigue at the end. This suggests that people do not differ greatly in how much fatigue they can tolerate but rather how quickly they reach a certain critical level of fatigue. Averaging fatigue scores backwards from the time subjects quit produced a function similar to the quitting function. Similar treatment of the other data revealed certain clusters of symptoms whose development also paralleled the development of fatigue.

Fatigue, mindset and ecology in the hazard dominant environment

Ratings made by 47 experienced drivers to 18 items of a Fatigue Advisory are highly consistent. Every item is rated 'very' or 'extremely important' to the safety of inexperienced drivers. In contrast, 'adequacy of knowledge' about fatigue is rated consistently lower. This inconsistency may reflect a culturally based confusion about fatigue. Education and public awareness campaigns need to emphasize that 'immoderate indulgence of driving' is as dangerous to safety as 'immoderate indulgence of alcohol'. A basic challenge is to improve understanding of the manner in which the experience of fatigue emerges during driving. Study of perceptual/cognitive manifestations aided by operational definition of fatigue as a 'declarative state' renders driving fatigue a definite observable subjective condition arising from continuous operation of a vehicle. Specific cognitive symptoms of fatigue such as boredom, tiredness, inattention, etc. emerging with driving fatigue, are circumscribed within the activity of driving itself and also reflect the particular conditions in which driving fatigue occurs. This approach reveals ecological dimensions to the problem. The specific experiences of driving fatigue are seen to emerge as a function of the driver environment relationship in a particular driving environment. It is suggested that the concept of the 'hazard dominant environment' and the compensating landscape perceptions of 'prospect' and 'refuge' proposed by Appleton [(1995) The Experience of Landscape. Wiley, London] in concert with the concept of environmental 'affordances' provided by Gibson [(1979) An Ecological Approach to Visual Perception. Houghton Mifflin, Boston] open promising possibilities for improving environmental education about driving fatigue.

The effect of dietary selenium deficiency on acute colorectal mucosal nucleotoxicity induced by several carcinogens in the rodent

BACKGROUND

Selenium (SE) has been inversely associated with colon cancer risk. Two potential mechanisms of this effect were examined in a rodent short-term carcinogenesis assay: whether dietary SE deficiency altered the initiation aspect of carcinogenesis in the colon, and whether SE altered carcinogen metabolism.

SETTING

Animal laboratory.

SUBJECTS

52 Sprague-Dawley rats, divided into a SE diet deficient group (0.002 parts per million; ppm) and a SE sufficient (0.2 ppm) group.

ENDPOINTS

Weight, serum SE concentration, and karryorhectic index (KI), which is a measure of acute carcinogen induced nuclear toxicity in the colonic mucosa.

METHODS

After three weeks of acclimation to the diets, eight animals from each dietary group were injected with one of the following: dimethylhydrazine (DMH), a colon specific carcinogen, its metabolite, methylazoxymethanol (MAM), or 0.9% sodium chloride. Twenty-four hours after injection the colons were removed, blood drawn, and the stained colons assayed for nuclear aberrations.

RESULTS

No weight differences were generated by the dietary variations. Low-dietary SE resulted in serum SE declining markedly in the study period to 6 ng/ml versus 33 ng/ml in the SE sufficient group. Diet alone, and variations in weight gain, did not alter the KI. Both carcinogens greatly increased the KI in both the left and right colon. A SE-deficient diet was associated with a higher KI in both carcinogen groups in the right colon, with statistical significance for both the left and right colon in the MAM injection group.

CONCLUSIONS

Dietary SE deficiency is associated with increased KI of the colon in MAM treated rats. SE, therefore, has a protective effect in the initiation phase of carcinogenesis.

Perineal sigmoidectomy for sigmoid procidentia: report of a case

Although rectal procidentia is not an uncommon disease, presentation of more proximal segments of the large bowel through the anus is extremely rare. We report a male patient with an acute sigmoid prolapse secondary to a large villous adenoma acting as the lead point. Since the prolapsed segment was irreducible and exhibited signs of vascular compromise, an intraoperative colonoscopy and perineal sigmoidectomy with a primary anastomosis was carried out. Postoperatively, the patient did well and was discharged 5 days after his operation. Recognition of the difference between sigmoid and rectal procidentia should influence the surgeon's choice of operation, along with the viability of the prolapsed bowel and overall condition of the patient.

Experimental intercomparisons of younger and older driver perceptions

Drivers over sixty-five years of age and drivers under twenty-one years of age have the highest relative frequency of crashes resulting in injury and death. Attitudes of these two groups were investigated using questionnaires. One hundred twenty-seven (127) younger and one hundred eight (108) older drivers who had voluntarily registered in driving education courses satisfactorily completed questionnaires about attitudes and behaviors pertinent to safe driving. Half of each sample rated the average driver in their age group and the average driver in the opposite age group as regarded thirty-three attitudes promoting safe driving, twenty courteous safe driving behaviors and eleven discourteous, unsafe driving behaviors. Data shows that younger drivers viewed older drivers as overly cautious, too slow to act and apt to cause accidents, and rated their peers as overly aggressive and discourteous. Older drivers characterized younger drivers as deficient in courtesy and safe driving practices, and they rated their peers as cautious, courteous, and aware of age-related limitations. The findings indicate that each group was aware that safety hazards are created by drivers in their age group. It also shows that both groups had a positive impression of some driving practices of their age group, and that the other group was depreciated. The outcome confirms and expands upon conclusions derived from less formal studies about how drivers perceive other roadway users. It also specifies the extent to which particular attitudes and driving practices are attributed to the peer group and to the opposite age group.

Factors affecting perception of outdoor public environments

Comfort and related perceptions are important in respect to use of outdoor public places. In a laboratory, 170 persons viewed four such places on slides and rated them on 10 dimensions, namely, "comfortable," "playful," "serious," "active," "unsafe," "good," "tense," "interesting," "gloomy," and "pleasing." Instructions were used to vary time of day and the number of people present at the location. It was found that women (n = 96) regard outdoor environments as more threatening than do men (n = 74) which suggests that women feel more vulnerable to untoward acts and that public places are rated less desirous at dusk than at dawn, presumably because dusk is followed by night and dawn by day. It was also discovered that such public environments are rated better than deserted places when occupied by two or more persons. Some of these results are consistent with the Prospect-Refuge Theory of Appleton.

Self-perception of the ability to work in the cold

Accumulating evidence of beneficial effects from physical exertion must be balanced against increased risk of cardiac arrest during performance. There is evidence that, by using such cues as heart rate, individuals can monitor their level of exertion perceptually. We undertook experiments to discover whether temperature and heart rate interact to affect self-perception when the effective temperature is moved downard from the comfort zone. In the first pilot study, 36 males practiced a new game, SwedeBall, for a period of 20 minutes. Twelve were randomly assigned to play at a temperature of 22 degrees C, another 12 to play at 0 degrees C, and the remaining 12 to play at -7 degrees C. The players showed tendencies toward an overall improvement in self-evaluations after brief practice, with more favorable responses when the temperatures were lower. In a second experiment on different days, 8 men pedaled a standard bicycle mounted as a wind trainer in a controlled environment chamber where the effective temperature was set at 26 degrees C, 8 degrees C, or -10 degrees C. The first 5-minute ride at each temperature was at a heart rate of 120 beats per minute (bpm), the second at 140 bpm, and a third at 160 bpm. We measured ratings of perceived effort (RPE), thermal impression, discomfort, perceived rate of speed, and projected endurance. The result confirmed that RPE was lowered by temperature when heart rate was constant. The data also showed that the lowered temperatures uniformly produced more favorable self-perceptions on the other four scales. The outcome is related to physiological problems that might arise when temperature depresses heart rate and reduces the experience of effort.

Application of automated human voice delivery to warning devices in an intensive care unit: a laboratory study

Environmental concerns about the delivery of warning messages in intensive care units exist in the belief that conventional non-verbal alarm signals are perceived to be threatening by some patients. There is also a significant opportunity for error in interpretation by fatigued or anxious personnel. A laboratory study was undertaken to determine whether human subjects made fewer errors when messages regarding ICU related tasks were delivered by tape recorded human voice than by the non-verbal signals derived from devices in the ICU. Results demonstrated a statistically significant superiority of human voice messages over non-verbal signals. It is concluded that taped human voice messages merit field trials in intensive care units.

Contributions to the history of psychology: LX. Remarks about S. Howard Bartley, as a scholar, scientist, and human being

The scholarly record of S. Howard Bartley (1902-1988) evokes respect because it shows quality, diversity, and quantity. Bartley's publications are well known and have been frequently cited in the literature of psychology, physiology, and optometry. His contributions to encyclopedias, handbooks, and other summative records of knowledge are legion. Notwithstanding his acknowledged eminence, unusual factors in his early upbringing worked to limit ability to gain full recognition for his work. Acting as a person, Bartley exhibited major talent in artistic areas and created endless delights for friends and colleagues in work and social settings.

Development of maize plants from cultured shoot apices

Excised shoot apices of maize (Zea mays L.), comprising the apical meristem and one or two leaf primordia, have been cultured and can form rooted plantlets. The plantlets, derived from meristems that had previously formed 7-10 nodes, develop into mature, morphologically normal plants with as many nodes as seed-grown plants. These culture-derived plants exhibited the normal pattern of development, with regard to the progression of leaf lengths along the plant and position of axillary buds and aar shoots. Isolation of the meristem from previously formed nodes reinitiates the pattern and number of nodes formed in the new plant. Thus, cells of the meristem of a maize plant at the seedling stage are not determined to form a limited number of nodes.

Affective responses to commercial and experimental auditory alarm signals for anaesthesia delivery and physiological monitoring equipment

The affective response of subjects to the sounds of commercial and experimental auditory alarm signals was tested using a standard experimental protocol for measuring mood states and changes. Both types of signal evoked affective response. The commercial signals, however, evoked more response than the experimental signals, and that response was more negative in affect. A subset of the experimental signals, distinguished by specific acoustic characteristics, evoked particularly low levels of affect. The implications of low-affect alarms for the operating room are discussed.

Delayed monochromatic hue matches indicate characteristics of visual memory

Short-term memory for 16 monochromatic hues from 425 to 640 nm was measured after six delays from .1 to 24.3 sec by means of an iterative, momentary stimulus-matching technique. Small shifts were revealed in the remembered hue produced by certain wavelengths at some delays. These shifts did not follow trends consistent with a storage dependent on sensory pathway characteristics, perceptually unique hues, or semantic encoding but may reflect entropic effects in a storage that is remarkably unbiased. By indicating the discriminability of hues in memory, standard deviations of the delayed matches reveal other characteristics of what is stored: Their smooth, exponential growth questions the existence of "levels" and permits estimating the half-life of hue memory; their continued resemblance to the discrimination function for simultaneously perceived hues suggests that the stored activity; closely resembled the sensory response of color. The results also indicate how successive comparisons may be corrected in applied color work.

Delayed monochromatic hue matches indicate characteristics of visual memory

Short-term memory for 16 monochromatic hues from 425 to 640 nm was measured after six delays from .1 to 24.3 sec by means of an iterative, momentary stimulus-matching technique. Small shifts were revealed in the remembered hue produced by certain wavelengths at some delays. These shifts did not follow trends consistent with a storage dependent on sensory pathway characteristics, perceptually unique hues, or semantic encoding but may reflect entropic effects in a storage that is remarkably unbiased. By indicating the discriminability of hues in memory, standard deviations of the delayed matches reveal other characteristics of what is stored: Their smooth, exponential growth questions the existence of "levels" and permits estimating the half-life of hue memory; their continued resemblance to the discrimination function for simultaneously perceived hues suggests that the stored activity; closely resembled the sensory response of color. The results also indicate how successive comparisons may be corrected in applied color work.

Using Angels and Devils: a board game developed for play in nursing homes

The incidence of perceptual deprivation and social isolation effects, possible correlates of such effects, and the potential for remediation of effects was studied for thirty-two nursing home residents through playing a discussion-stimulating board game called Angels and Devils. Results indicate a high incidence of sensory deprivation and social isolation effects in the population, as measured by resident response to questionnaire items. These do not correlate with length of institutionalization, amount of social contact, or degree of medical restriction, and may be reduced by stimulating resident-staff discussion. Findings are interpreted as indicating the need for more research in application of board games to ameliorate negative effects emerging in institutional environments.

Perceptions of fatigue as related to alcohol ingestion

An experiment is reported in which the role of alcohol in the emergence of fatigue was studied. Eleven (11) participants were requested to operate a driver trainer until they found the task too adverse to continue under conditions of high blood alcohol (BACL greater than 0.08%), low blood alcohol (BACL less than 0.08%), and no blood alcohol. Skill and heart rate were monitored and any personal distresses or observations made about performance were reported to an experimenter who acted in the role of 'passenger'. Results show decline in endurance as blood alcohol increases, but that a higher level of personal distress is endured by drivers who have imbibed, as compared to those who have not. Systematic discrepancies occur between the impressions gained by the experimenter (passenger) from verbal reports made by the driver, and the kinds of self-ratings drivers provide. Features of fatigue are analyzed theoretically as perceptual phenomena as related to alcohol and accidents.

A signal-detection evaluation of flat vs curved marker performance

Driving decisions based on traffic markers placed at acute-angled intersections are considered within the framework of the theory of signal detectability. The implied task requires a binary decision based on sensory information having some uncertainty and thus is amenable to analysis within this framework. The ability to separate the psychological and sensory components of performance can extend analyses from previous research with curved and flat markers. Data from prior laboratory studies rendered d' values of 1.08 and 2.25 for the flat and curved targets respectively, thus lending strong support to the hypothesis that slant is more accurately discriminated when a curved marker is viewed.

Surface colouration, lettering and referential dimension of traffic marker perception

5 experimental traffic markers differentiated with respect to colouration and lettering were each presented at 7 angles of orientation randomly repeated 5 times. 5 groups comprising 15 drivers per group gave judgments of shape and slant. It was found that signalling aspects of the marker (form, colouration and lettering) produced significant differences upon apparent shape. Differences in slant perception were not dependent upon the three signalling characteristics. Consistent with prior research, the reference aspect of the marker (angle of orientation) produced large errors of underestimation particularly at the most acute angles. The perceptual functions suggest that systematic differences separate physical and psychological spaces.