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Snow is an important driver of ecosystem processes in cold biomes. Snow accumulation determines ground temperature, light conditions, and moisture availability during winter. It also affects the growing season’s start and end, and plant access to moisture and nutrients. Here, we review the current knowledge of the snow cover’s role for vegetation, plant-animal interactions, permafrost conditions, microbial processes, and biogeochemical cycling. We also compare studies of natural snow gradients with snow experimental manipulation studies to assess time scale difference of these approaches. The number of tundra snow studies has increased considerably in recent years, yet we still lack a comprehensive overview of how altered snow conditions will affect these ecosystems. Specifically, we found a mismatch in the timing of snowmelt when comparing studies of natural snow gradients with snow manipulations. We found that snowmelt timing achieved by snow addition and snow removal manipulations (average 7.9 days advance and 5.5 days delay, respectively) were substantially lower than the temporal variation over natural spatial gradients within a given year (mean range 56 days) or among years (mean range 32 days). Differences between snow study approaches need to be accounted for when projecting snow dynamics and their impact on ecosystems in future climates.

Recombination is critical both for accelerating adaptation and purging deleterious mutations. Chromosomal inversions can act as recombination modifiers that suppress local recombination in heterozygotes and thus, under some conditions, are predicted to accumulate such mutations. In this study, we investigated patterns of recombination, transposable element abundance, and coding sequence evolution across the genomes of 1,445 individuals from three sunflower species, as well as within nine inversions segregating within species. We also analyzed the effects of inversion genotypes on 87 phenotypic traits to test for overdominance. We found significant negative correlations of long terminal repeat retrotransposon abundance and deleterious mutations with recombination rates across the genome in all three species. However, we failed to detect an increase in these features in the inversions, except for a modest increase in the proportion of stop codon mutations in several very large or rare inversions. Consistent with this finding, there was little evidence of overdominance of inversions in phenotypes that may relate to fitness. On the other hand, significantly greater load was observed for inversions in populations polymorphic for a given inversion compared to populations monomorphic for one of the arrangements, suggesting that the local state of inversion polymorphism affects deleterious load. These seemingly contradictory results can be explained by the low frequency of inversion heterozygotes in wild sunflower populations, apparently due to divergent selection and associated geographic structure. Inversions contributing to local adaptation represent ideal recombination modifiers, acting to facilitate adaptive divergence with gene flow, while largely escaping the accumulation of deleterious mutations.

Open top chambers (OTCs) were adopted as the recommended warming mechanism by the International Tundra Experiment network in the early 1990s. Since then, OTCs have been deployed across the globe. Hundreds of papers have reported the impacts of OTCs on the abiotic environment and the biota. Here, we review the impacts of the OTC on the physical environment, with comments on the appropriateness of using OTCs to characterize the response of biota to warming. The purpose of this review is to guide readers to previously published work and to provide recommendations for continued use of OTCs to understand the implications of warming on low stature ecosystems. In short, the OTC is a useful tool to experimentally manipulate temperature; however, the characteristics and magnitude of warming varies greatly in different environments; therefore, it is important to document chamber performance to maximize the interpretation of biotic response. When coupled with long-term monitoring, warming experiments are a valuable means to understand the impacts of climate change on natural ecosystems.

Introduction Children and young people (CYP) presenting with a mental health (MH) crisis are frequently admitted to general acute paediatric wards as a place of safety. Prior to the pandemic, a survey in England showed that CYP occupied 6% of general paediatric inpatient beds due to an MH crisis, and there have been longstanding concerns about the quality of care to support these patients in this setting. Mental Health Admissions to Paediatric Wards Study aims to generate a theory of change (ToC) model to improve the quality of care for CYP admitted to acute paediatric services after presenting in a MH crisis.Methods and analysis We will undertake a national (England), sequential, mixed methods study to inform a ToC framework alongside a stakeholder group consisting of patients, families/carers and healthcare professionals (HCPs). Our study consists of four work packages (WP) undertaken over 30 months. WP1 is limited to using national routine administrative data to identify and characterise trends in MH admissions in acute paediatric wards in England between 2015– 2022.Ethics and dissemination WP1 received ethical approval (Ref 23/NW/0192). We will publish the overall synthesis of data and the final ToC to improve care of CYP with MH crisis admitted to general acute paediatric settings. As coproducers of the ToC, we will work with our stakeholder group to ensure wide dissemination of findings. Potential impacts will be on service development, new models of care, training and workforce planning.

Introduction Children and young people (CYP) presenting with a mental health (MH) crisis are frequently admitted to general acute paediatric wards as a place of safety. Prior to the pandemic, a survey in England showed that CYP occupied 6% of general paediatric inpatient beds due to an MH crisis, and there have been longstanding concerns about the quality of care to support these patients in this setting. MAPS aims to generate a Theory of Change (ToC) model to improve the quality of care for CYP admitted to acute paediatric services after presenting with an MH crisis. Here, we describe work packages (WPs) 2 and 3 of the study, which have been granted ethics approval.Methods and analysis We will undertake a national (England), sequential, mixed-methods study to inform a ToC framework alongside a stakeholder group consisting of patients, families/carers and healthcare professionals (HCPs). Our study consists of four WPs undertaken over 30 months. WP2 is limited to working with stakeholders to develop a data collection instrument and then use this in a prospective study of MH admissions over 6 months in 15 purposively recruited acute paediatric wards across England. WP3 consists of gathering the views of CYP, their families/carers and HCPs during admissions using semistructured interviews.Ethics and dissemination WP2 and WP3 received ethical approval (ref: 23/LO/0349). We will publish the overall synthesis of data and the final ToC to improve care of CYP with MH crisis admitted to general acute paediatric settings. As co-producers of the ToC, we will work with our stakeholder group to ensure wide dissemination of findings. Potential impacts will be upon service development, new models of care, training and workforce planning.PROSPERO registration number CRD42022350655.

BackgroundGender euphoria (i.e., a positive feeling associated with one’s gender identity, expression, or affirmation) is widely discussed among transgender and gender diverse (hereafter referred to as trans) individuals. However, as a construct, gender euphoria has never been formally measured and has rarely been empirically studied. Hence, this protocol paper illustrates our process for developing and validating a new tool to measure gender euphoria, known as the Gender Euphoria Scale (GES), for use with trans populations.MethodsDeductive methods including findings from previous research and a review of existing measures, together with inductive methods such as expert feedback and focus groups with trans individuals, were used to generate a preliminary item pool for the GES. Pilot testing with trans community members and mental health clinicians was then used to refine items and develop a preliminary scale. Trans participants involved in an ongoing longitudinal study (TRANSform) were invited to complete the scale alongside measures of personality and gender factors to assess validity. Participants were then invited to complete the scale two weeks after initial completion to assess the test–retest reliability of the scale. The next stage in the scale development process will be to examine the dimensionality of the GES using exploratory factor analytic techniques. The scale will then be assessed for internal consistency, temporal stability, discriminant validity, and convergent validity.ConclusionThis paper outlines the development and characterization of a novel tool to measure gender euphoria for the first time. The GES will facilitate research opportunities to better understand the nature of gender euphoria and its influences, and may be used clinically to examine relationships between gender euphoria and gender affirming interventions. Hence, we expect the GES to make a significant contribution to both research and clinical practice with trans communities.

Objective The current study explored (1) changes in trust in federal and state governments and scientists across representative Australian national samples from 2003–2020; and (2) the extent to which trust in these sources predicted compliance with COVID-19 prevention measures at the onset of the pandemic. Method Using a nationally representative samples (N = 1000), we asked participants to rate their trust in federal and state government and in scientists, their extent of compliance with COVID-19 prevention measures, and to provide demographic information. Results We found that trust in federal and state governments had significantly increased, while trust in scientists was at a high level matched by only three other time-points. Higher levels of trust in state government and scientists uniquely predicted greater compliance with COVID-19 prevention measures. Women and older respondents also reported greater compliance. Conclusion The current findings reinforce those from Australia and other countries indicating that trust increased during the onset of the COVID-19 pandemic, and those identifying trust in government and in scientists as important predictors of compliance. Importantly, our findings highlight the role of trust in state government, which potentially reflects the role played by Australian state governments in enacting and enforcing COVID-19 prevention measures.

Summary: Background: Malaria in early pregnancy is a risk factor for preterm birth and is associated with sustained inflammation and dysregulated angiogenesis across gestation. This study investigated whether malaria is associated with increased gut leak and whether this contributes to systemic inflammation, altered angiogenesis, and preterm birth. Methods: We quantified plasma concentrations of gut leak markers, soluble CD14 (sCD14) and lipopolysaccharide binding protein (LBP) from 1339 HIV-negative pregnant Malawians at

Abstract Background Ralstonia solanacearum species complex (RSSC) strains are destructive plant pathogenic bacteria and the causative agents of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, their virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e., prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape RSSC virulence, the global diversity, distribution, and wider functional gene content of RSSC prophages are unknown. In this study, prophages were identified in a diverse collection of 192 RSSC draft genome assemblies originating from six continents. Results Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distributions were characterised using metadata on RSSC strain geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 313 intact prophages were identified, forming ten genetically distinct clusters. These included six prophage clusters with similarity to the Inoviridae, Myoviridae, and Siphoviridae phage families, and four uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distributions, being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained many auxiliary genes involved in metabolism and virulence of both phage and bacteria. Conclusions Our results show that while RSSC prophages are highly diverse globally, they make lineage-specific contributions to the RSSC accessory genome, which could have resulted from shared coevolutionary history.

The International Tundra Experiment (ITEX) was founded in 1990 as a network of scientists studying responses of tundra ecosystems to ambient and experimental climate change at Arctic and alpine sites across the globe. Common measurement and experimental design protocols have facilitated synthesis of results across sites to gain biome-wide insights of climate change impacts on tundra. This special issue presents results from more than 30 years of ITEX research. The importance of snow regimes, bryophytes, and herbivory are highlighted, with new protocols and studies proposed. The increasing frequency and magnitude of extreme climate events is shown to have strong effects on plant reproduction. The most consistent plant trait response across sites is an increase in vegetation height, especially for shrubs. This will affect surface energy balance, carbon and nutrient dynamics and trophic level interactions. Common garden studies show adaptation responses in tundra species to climate change but they are species and regionally specific. Recommendations are made including establishing sites near northern communities to increase reciprocal engagement with local knowledge holders and establishing multi-factor experiments. The success of ITEX is based on collegial cooperation among researchers and the network remains focused on documenting and understanding impacts of environmental change on tundra ecosystems.

Snow is an important driver of ecosystem processes in cold biomes. Snow accumulation determines ground temperature, light conditions, and moisture availability during winter. It also affects the growing season’s start and end, and plant access to moisture and nutrients. Here, we review the current knowledge of the snow cover’s role for vegetation, plant-animal interactions, permafrost conditions, microbial processes, and biogeochemical cycling. We also compare studies of natural snow gradients with snow experimental manipulation studies to assess time scale difference of these approaches. The number of tundra snow studies has increased considerably in recent years, yet we still lack a comprehensive overview of how altered snow conditions will affect these ecosystems. Specifically, we found a mismatch in the timing of snowmelt when comparing studies of natural snow gradients with snow manipulations. We found that snowmelt timing achieved by snow addition and snow removal manipulations (average 7.9 days advance and 5.5 days delay, respectively) were substantially lower than the temporal variation over natural spatial gradients within a given year (mean range 56 days) or among years (mean range 32 days). Differences between snow study approaches need to be accounted for when projecting snow dynamics and their impact on ecosystems in future climates.

Summary: Preterm birth is a leading cause of death in children under five years of age. We hypothesized that sequential disruptions to inflammatory and angiogenic pathways during pregnancy increase the risk of placental insufficiency and spontaneous preterm labor and delivery. We conducted a secondary analysis of inflammatory and angiogenic analytes measured in plasma samples collected across pregnancy from 1462 Malawian women. Women with concentrations of the inflammatory markers sTNFR2, CHI3L1, and IL18BP in the highest quartile before 24 weeks gestation and women with anti-angiogenic factors sEndoglin and sFlt-1/PlGF ratio in the highest quartile at 28–33 weeks gestation had an increased relative risk of preterm birth. Mediation analysis further supported a potential causal link between early inflammation, subsequent angiogenic dysregulation detrimental to placental vascular development, and earlier gestational age at delivery. Interventions designed to reduce the burden of preterm birth may need to be implemented before 24 weeks of gestation.

Machine (especially deep) learning algorithms are changing the way wildlife imagery is processed. They dramatically speed up the time to detect, count, and classify animals and their behaviours. Yet, we currently have very few systematic literature surveys on its use in wildlife imagery. Through a literature survey (a ‘rapid’ review) and bibliometric mapping, we explored its use across: 1) species (vertebrates), 2) image types (e.g., camera traps, or drones), 3) study locations, 4) alternative machine learning algorithms, 5) outcomes (e.g., recognition, classification, or tracking), 6) reporting quality and openness, 7) author affiliation, and 8) publication journal types. We found that an increasing number of studies used convolutional neural networks (i.e., deep learning). Typically, studies have focused on large charismatic or iconic mammalian species. An increasing number of studies have been published in ecology-specific journals indicating the uptake of deep learning to transform the detection, classification and tracking of wildlife. Sharing of code was limited, with only 20% of studies providing links to analysis code. Much of the published research and focus on animals came from India, China, Australia, or the USA. There were relatively few collaborations across countries. Given the power of machine learning, we recommend increasing collaboration and sharing approaches to utilise increasing amounts of wildlife imagery more rapidly and transform and improve understanding of wildlife behaviour and conservation. Our survey, augmented with bibliometric analyses, provides valuable signposts for future studies to resolve and address shortcomings, gaps, and biases.

The use of online student response systems (OSRSs) is increasing within tertiary education providers, however, research investigating their potential to enhance student engagement is limited. The aim of the current study was to examine the impact of an OSRS using an experimental crossover design. Quantitative data measuring student engagement was compared from pre- to post-intervention. A qualitative analysis was used to further investigate student perceptions of the OSRS. The results from this study suggest that OSRSs may be appropriate tools to increase student engagement in undergraduate statistics classes. Despite no significant change in engagement scores observed when students were exposed to the OSRS than when they were not, students appreciated the novelty of the OSRS and perceived it to have had a positive impact on their learning experience. Suggestions for how to exploit the advantages of OSRSs and directions for further research are discussed.

Human disturbance, such as trampling, is an integral component of global change, yet we lack a comprehensive understanding of its effects on alpine ecosystems. Many alpine systems are seeing a rapid increase in recreation and in understudied regions, such as the Coast Mountains of British Columbia, yet disturbance impacts on alpine plants remain unclear. We surveyed disturbed (trail-side) and undisturbed (off-trail) transects along elevational gradients of popular hiking trails in the T’ak’t’ak’múy’in tl’a In’inyáxa7n region (Garibaldi Provincial Park), Canada, focusing on dominant shrubs (Phyllodoce empetriformis, Cassiope mertensiana, Vaccinium ovalifolium) and graminoids (Carex spp). We used a hierarchical Bayesian framework to test for disturbance by elevation effects on total plant percent cover, maximum plant height and diameter (growth proxies), and buds, flowers, and fruits (reproduction proxies). We found that trampling reduces plant cover and impacts all species, but that effects vary by species and trait, and disturbance effects only vary with elevation for one species’ trait. Growth traits are more sensitive to trampling than reproductive traits, which may lead to differential impacts on population persistence and species-level fitness outcomes. Our study highlights that disturbance responses are species-specific, and this knowledge can help land managers minimize disturbance impacts on sensitive vegetation types.

Previous research has indicated that nonattachment mediates the relationship between mindfulness and the ability to be adaptable. Additionally, adaptability has been associated with increased academic engagement and subsequently, higher grades. The current study combined these findings into a single model. In an undergraduate sample (N = 725), the results indicated that mindfulness and nonattachment were directly associated with greater adaptability and engagement. Increased adaptability was also directly associated with increased engagement, and engagement was associated with higher grades. Therefore, mindfulness and nonattachment were also found to be indirectly associated, albeit weakly, with higher grades. The current findings, therefore, add to the literature by indicating that mindfulness and nonattachment are both worthy of consideration in future research on student outcomes.

Abstract Although plant pathogens are traditionally controlled using synthetic agrochemicals, the availability of commercial bactericides is still limited. One potential control strategy could be the use of plant growth‐promoting bacteria (PGPB) to suppress pathogens via resource competition or the production of antimicrobial compounds. This study aimed to conduct in vitro and in vivo screening of eight Pseudomonas strains against Ralstonia solanacearum (the causative agent of bacterial wilt) and to investigate underlying mechanisms of potential pathogen suppression. We found that inhibitory effects were Pseudomonas strain‐specific, with strain CHA0 showing the highest pathogen suppression. Genomic screening identified 2,4‐diacetylphloroglucinol, pyoluteorin, and orfamides A and B secondary metabolite clusters in the genomes of the most inhibitory strains, which were investigated further. Although all these compounds suppressed R. solanacearum growth, only orfamide A was produced in the growth media based on mass spectrometry. Moreover, orfamide variants extracted from Pseudomonas cultures showed high pathogen suppression. Using the “Micro‐Tom” tomato cultivar, it was found that CHA0 could reduce bacterial wilt disease incidence with one of the two tested pathogen strains. Together, these findings suggest that a better understanding of Pseudomonas–Ralstonia interactions in the rhizosphere is required to successfully translate in vitro findings into agricultural applications.

Abstract Background Bacterial blotch is a group of economically important diseases affecting the cultivation of common button mushroom, Agaricus bisporus. Despite being studied for more than a century, the identity and nomenclature of blotch-causing Pseudomonas species is still unclear. This study aims to molecularly characterize the phylogenetic and phenotypic diversity of blotch pathogens in Western Europe. Methods In this study, blotched mushrooms were sampled from farms across the Netherlands, United Kingdom and Belgium. Bacteria were isolated from symptomatic cap tissue and tested in pathogenicity assays on fresh caps and in pots. Whole genome sequences of pathogenic and non-pathogenic isolates were used to establish phylogeny via multi-locus sequence alignment (MLSA), average nucleotide identity (ANI) and in-silico DNA:DNA hybridization (DDH) analyses. Results The known pathogens “Pseudomonas gingeri”, P. tolaasii, “P. reactans” and P. costantinii were recovered from blotched mushroom caps. Seven novel pathogens were also identified, namely, P. yamanorum, P. edaphica, P. salomonii and strains that clustered with Pseudomonas sp. NC02 in one genomic species, and three non-pseudomonads, i.e. Serratia liquefaciens, S. proteamaculans and a Pantoea sp. Insights on the pathogenicity and symptom severity of these blotch pathogens were also generated. Conclusion A detailed overview of genetic and regional diversity and the virulence of blotch pathogens in Western Europe, was obtained via the phylogenetic and phenotypic analyses. This information has implications in the study of symptomatic disease expression, development of diagnostic tools and design of localized strategies for disease management.

The use of online student response systems (OSRSs) is increasing within tertiary education providers, however, research investigating their potential to enhance student engagement is limited. The aim of the current study was to examine the impact of an OSRS using an experimental crossover design. Quantitative data measuring student engagement was compared from pre- to post-intervention. A qualitative analysis was used to further investigate student perceptions of the OSRS. The results from this study suggest that OSRSs may be appropriate tools to increase student engagement in undergraduate statistics classes. Despite no significant change in engagement scores observed when students were exposed to the OSRS than when they were not, students appreciated the novelty of the OSRS and perceived it to have had a positive impact on their learning experience. Suggestions for how to exploit the advantages of OSRSs and directions for further research are discussed.

Background: Malaria during pregnancy is a major contributor to the global burden of adverse birth outcomes including fetal growth restriction, preterm birth, and fetal loss. Recent evidence supports a role for angiogenic dysregulation and perturbations to placental vascular development in the pathobiology of malaria in pregnancy. The Angiopoietin-Tie2 axis is critical for placental vascularization and remodeling. We hypothesized that disruption of this pathway would contribute to malaria-induced adverse birth outcomes. Methods: Using samples from a previously conducted prospective cohort study of pregnant women in Malawi, we measured circulating levels of angiopoietin-1 (Angpt-1) and Angpt-2 by Luminex (n=1392). We used a preclinical model of malaria in pregnancy (Plasmodium berghei ANKA [PbA] in pregnant BALB/c mice), genetic disruption of Angpt-1 (Angpt1+/− mice), and micro-CT analysis of placental vasculature to test the hypothesis that disruptions to the Angpt-Tie2 axis by malaria during pregnancy would result in aberrant placental vasculature and adverse birth outcomes. Findings: Decreased circulating levels of Angpt-1 and an increased ratio of Angpt-2/Angpt-1 across pregnancy were associated with malaria in pregnancy. In the preclinical model, PbA infection recapitulated disruptions to the Angiopoietin-Tie2 axis resulting in reduced fetal growth and viability. Malaria decreased placental Angpt-1 and Tie2 expression and acted synergistically with reduced Angpt-1 in heterozygous dams (Angpt1+/−), to worsen birth outcomes by impeding vascular remodeling required for placental function. Interpretation: Collectively, these data support a mechanistic role for the Angpt-Tie2 axis in malaria in pregnancy, including a potential protective role for Angpt-1 in mitigating infection-associated adverse birth outcomes. Funding: This work was supported by the Canadian Institutes of Health Research (CIHR), Canada Research Chair, and Toronto General Research Institute Postdoctoral Fellowship Award. The parent trial was supported by the European & Developing Countries Clinical Trials Partnership and the Malaria in Pregnancy Consortium, which was funded by the Bill & Melinda Gates Foundation. The funders had no role in design, analysis, or reporting of these studies.

Evaluating the effectiveness of captive breeding programs is central to improving conservation outcomes in released animals. However, few studies have assessed the impact of the strategies and trade-offs involved in husbandry decisions and the selection of traits on the success of breeding programs. This study evaluated a range of husbandry features including an animal's environment, health, and traits of the released individual and its parents involved in the zoo-based Regent Honeyeater breed for release program to optimise individual reproductive success and survivability, leading to improved conservation outcomes in the wild. We analysed 285 birds using a penalised Cox proportional hazard model to assess survival and an ordinal logistic model to evaluate the reproductive success of zoo bred birds released to the wild. Key features identified by the study highlight the importance of having parents that are successful breeders and parents that have an overall higher lifetime reproductive output. However, there were associated quantity-quality trade-offs, as the success of young (i.e., released birds) produced by parents was negatively associated to the number of clutches per year (where one clutch per year was found optimal). The study demonstrated the importance of considering the parental effects on the traits of its offspring beyond its pedigree information and found there was an associated decline in fitness of its offspring with older fathers. Song tutoring using wild Regent Honeyeaters was also important for increased survival post-release. Other important factors are discussed within the review. In general, the study recommended that a multi-faceted approach in the assessment and evaluation of the captive breeding program, to identify markers that will improve conservation outcomes of future releases.

The Motivation and Engagement Scale-University/College (MES-UC) was used to identify student typologies on the basis of adaptive and maladaptive academic cognitions and behaviours. The sample comprised first-year (n = 390), second-year (n = 300), and third-year (n = 251) undergraduate students with 4 student typologies identified: high engagement/skills, low engagement/skills, and 2 moderately engaged groups distinguished by either high or low levels of maladaptive cognitions (e.g., anxiety). Additional analyses which displayed theoretically appropriate differences between these groups suggest that the MES-UC is suitable for identifying student typologies.

Bacterial blotch is a group of economically important diseases of the common button mushroom (Agaricus bisporus). Once the pathogens are introduced to a farm, mesophilic growing conditions (that are optimum for mushroom production) result in severe and widespread secondary infections. Efficient, timely and quantitative detection of the pathogens is hence critical for the design of localized control strategies and prediction of disease risk. This study describes the development of real-time TaqManTM assays that allow molecular diagnosis of three currently prevalent bacterial blotch pathogens: “Pseudomonas gingeri,” Pseudomonas tolaasii and (as yet uncharacterized) Pseudomonas strains (belonging to Pseudomonas salomonii and Pseudomonas edaphica). For each pathogen, assays targeting specific DNA markers on two different loci, were developed for primary detection and secondary verification. All six developed assays showed high diagnostic specificity and sensitivity when tested against a panel of 63 Pseudomonas strains and 40 other plant pathogenic bacteria. The assays demonstrated good analytical performance indicated by linearity across calibration curve (>0.95), amplification efficiency (>90%) and magnitude of amplification signal (>2.1). The limits of detection were optimized for efficient quantification in bacterial cultures, symptomatic tissue, infected casing soil and water samples from mushroom farms. Each target assay was multiplexed with two additional assays. Xanthomonas campestris was detected as an extraction control, to account for loss of DNA during sample processing. And the total Pseudomonas population was detected, to quantify the proportion of pathogenic to beneficial Pseudomonas in the soil. This ratio is speculated to be an indicator for blotch outbreaks. The multiplexed assays were successfully validated and applied by routine testing of diseased mushrooms, peat sources, casing soils, and water from commercial production units.

Abstract We describe an equitable transform that can be used to estimate missing data points, determine systematic patterns in data, observe baseline changes, and detect different amplitudes in replicated sequences. It is applicable to short discrete two‐ or three‐dimensional data sets such as biological life cycles or water content in similar media. The technique is independent of the continuity or ordering of sequences but is distinct from methods such as principal component analysis. It is ideally used to preprocess noisy or incomplete data sets prior to analysis with other well‐established techniques. This transformation maintains systematic differences between individual sequences when the underlying pattern is a separable function in two variables added to another function in one of these variables. The equitable transform partitions the original noisy data into the underlying signal determined from the data and its residuals. Points from one sequence can be transformed to any other sequence without losing any information. Information about one or more sequences can be used to infer others with missing data. A link to a github R package is provided so the transform can easily be run on any two‐dimensional data set. Simulated two‐dimensional data sets are used to demonstrate its utility in recovering missing data and scaling/offsetting in one of the dimensions. We used the transform to determine that winter temperatures at a High Arctic site have warmed by 1.8° ± 0.4°C/decade and summer temperatures by 1.1° ± 0.2°C/decade from 1986 to 2007. Applied to 18 yr of phenology data for the tundra plant Dryas integrifolia at the same site, we determined that the annual cycles of phenology events could be modeled accurately. Phenology, in some circumstances, can be described as offsetting and scaling the rate at which life cycle events occur. We introduce the idea of scaling and shifting the seasonal cycle of a reference plant via the equitable transform in order to approximate the behavior of multiple phenological cycles. Relative phenology rates of Dryas integrifolia were found to have increased over time indicating duration of phenological stages have become shorter in recent years, likely in response to the warming climate.

Abstract Background Chitinase-3-like 1 (CHI3L1) is a glycoprotein elevated in paediatric severe malaria, and an emerging urinary biomarker of acute kidney injury (AKI). Based on the hypothesis that elevated CHI3L1 levels in malaria are associated with disease severity, the relationship between plasma CHI3L1 levels, AKI and mortality was investigated in Ugandan children enrolled in a clinical trial evaluating inhaled nitric oxide (iNO) as an adjunctive therapy for severe malaria. Methods Plasma CHI3L1 levels were measured daily for 4 days in children admitted to hospital with severe malaria and at day 14 follow up. AKI was defined using the Kidney Disease: Improving Global Outcomes consensus criteria. This is a secondary analysis of a randomized double-blind placebo-controlled trial of iNO versus placebo as an adjunctive therapy for severe malaria. Inclusion criteria were: age 1–10 years, and selected criteria for severe malaria. Exclusion criteria included suspected bacterial meningitis, known chronic illness including renal disease, haemoglobinopathy, or severe malnutrition. iNO was administered by non-rebreather mask for up to 72 h at 80 ppm. Results CHI3L1 was elevated in patients with AKI and remained higher over hospitalization (p

BACKGROUND:Malaria in pregnancy is associated with adverse birth outcomes. However, the underlying mechanisms remain poorly understood. Tight regulation of angiogenic, metabolic, and inflammatory pathways are essential for healthy pregnancies. We hypothesized that malaria disrupts these pathways leading to preterm birth (PTB). METHODS AND FINDINGS:We conducted a secondary analysis of a randomized trial of malaria prevention in pregnancy conducted in Malawi from July 21, 2011, to March 18, 2013. We longitudinally assessed circulating mediators of angiogenic, metabolic, and inflammatory pathways during pregnancy in a cohort of HIV-negative women (n = 1,628), with a median age of 21 years [18, 25], and 562 (35%) were primigravid. Pregnancies were ultrasound dated, and samples were analyzed at 13 to 23 weeks (Visit 1), 28 to 33 weeks (Visit 2), and/or 34 to 36 weeks (Visit 3). Malaria prevalence was high; 70% (n = 1,138) had PCR-positive Plasmodium falciparum infection at least once over the course of pregnancy and/or positive placental histology. The risk of delivering preterm in the entire cohort was 20% (n = 304/1506). Women with malaria before 24 weeks gestation had a higher risk of PTB (24% versus 18%, p = 0.005; adjusted relative risk [aRR] 1.30, 95% confidence interval [CI] 1.04-1.63, p = 0.021); and those who were malaria positive only before week 24 had an even greater risk of PTB (28% versus 17%, p = 0.02; with an aRR of 1.67, 95% CI 1.20-2.30, p = 0.002). Using linear mixed-effects modeling, malaria before 24 weeks gestation was associated with altered kinetics of inflammatory (C-Reactive Protein [CRP], Chitinase 3-like protein-1 [CHI3L1], Interleukin 18 Binding Protein [IL-18BP], soluble Tumor Necrosis Factor receptor II [sTNFRII], soluble Intercellular Adhesion Molecule-1 [sICAM-1]), angiogenic (soluble Endoglin [sEng]), and metabolic mediators (Leptin, Angiopoietin-like 3 [Angptl3]) over the course of pregnancy (χ2 > 13.0, p ≤ 0.001 for each). Limitations include being underpowered to assess the impact on nonviable births, being unable to assess women who had not received any antimalarials, and, because of the exposure to antimalarials in the second trimester, there were limited numbers of malaria infections late in pregnancy. CONCLUSIONS:Current interventions for the prevention of malaria in pregnancy are initiated at the first antenatal visit, usually in the second trimester. In this study, we found that many women are already malaria-infected by their first visit. Malaria infection before 24 weeks gestation was associated with dysregulation of essential regulators of angiogenesis, metabolism, and inflammation and an increased risk of PTB. Preventing malaria earlier in pregnancy may reduce placental dysfunction and thereby improve birth outcomes in malaria-endemic settings.

The Buddhist notion of nonattachment relates to an engagement with experience with flexibility and without fixation on achieving specified outcomes. The present study sought to define, create and validate a new measure of nonattachment as it applies to notions of the self. A new construct of “nonattachment to self” (NTS) was developed, defined the absence of fixation on self-related concepts, thoughts and feelings, and a capacity to flexibly interact with these concepts, thoughts and feelings without trying to control them. Two studies were conducted in the development of the new scale. With expert consultation, study 1 (n = 445) established a single factor, internally consistent 7-item scale via exploratory factor analysis. Study 2 (n = 388, n = 338) confirmed the factor structure of the new 7-item scale using confirmatory factor analyses. Study 2 also found the new scale to be internally consistent, with evidence supporting its test-retest reliability, criterion, and construct validity. Nonattachment to self-emerged as a unique way of relating to the self, distinct from general nonattachment, that aligned with higher levels of well-being and adaptive functioning.

In every country the prosecution of criminal cases is governed by different laws, policies and processes. In South Africa, the National Prosecuting Authority (NPA) has the responsibility of planning and managing all prosecution functions. The NPA has certain unique characteristics that make it different from other similar organisations internationally. The development of a planning tool that the NPA could use to plan their future resource requirements over the short to medium term required extensive modelling, and its final form included features which, to the best knowledge of the development team, make it unique both locally and internationally. Model design was largely influenced by the challenges emanating from the special requirements and context of the problem. Resources were not forecasted directly, but were derived with the help of simulation models that traced docket flows through various resource-driven processes. Docket flows were derived as a proportion of reported crimes, and these were forecasted using a multivariate statistical model which could take into account explanatory variables as well as the correlations between the patterns observed within different crime categories. The simulation consisted of a number of smaller models which could be run independently, and not of one overarching model. This approach was found to make the best use of available data, and compensated for the fact that certain parameters, linking different courts and court types, were not available. In addition, it simplified scenario testing and sensitivity analysis. The various components of the planning tool, including inputs and outputs of the simulation models and the linkages between the forecasts and the simulation models, were implemented in a set of spreadsheets. By using spreadsheets as a common user interface, the planning tool could be used by prosecutors and managers who may not have extensive mathematical or modelling experience.

An 8× draft genome was obtained and annotated for Ralstonia solanacearum race 3 biovar 2 (R3B2) strain UW551, a United States Department of Agriculture Select Agent isolated from geranium. The draft UW551 genome consisted of 80,169 reads resulting in 582 contigs containing 5,925,491 base pairs, with an average 64.5% GC content. Annotation revealed a predicted 4,454 protein coding open reading frames (ORFs), 43 tRNAs, and 5 rRNAs; 2,793 (or 62%) of the ORFs had a functional assignment. The UW551 genome was compared with the published genome of R. solanacearum race 1 biovar 3 tropical tomato strain GMI1000. The two phylogenetically distinct strains were at least 71% syntenic in gene organization. Most genes encoding known pathogenicity determinants, including predicted type III secreted effectors, appeared to be common to both strains. A total of 402 unique UW551 ORFs were identified, none of which had a best hit or >45% amino acid sequence identity with any R. solanacearum predicted protein; 16 had strong (E < 10-13) best hits to ORFs found in other bacterial plant pathogens. Many of the 402 unique genes were clustered, including 5 found in the hrp region and 38 contiguous, potential prophage genes. Conservation of some UW551 unique genes among R3B2 strains was examined by polymerase chain reaction among a group of 58 strains from different races and biovars, resulting in the identification of genes that may be potentially useful for diagnostic detection and identification of R3B2 strains. One 22-kb region that appears to be present in GMI1000 as a result of horizontal gene transfer is absent from UW551 and encodes enzymes that likely are essential for utilization of the three sugar alcohols that distinguish biovars 3 and 4 from biovars 1 and 2.

The endogenous metabolites excreted by organisms into their surrounding environment, termed the exometabolome, are important for many processes including chemical communication. In fish biology, such metabolites are also known to be informative markers of physiological status. While metabolomics is increasingly used to investigate the endogenous biochemistry of organisms, no non-targeted studies of the metabolic complexity of fish exometabolomes have been reported to date. In environmental chemistry, Chemcatcher® (Portsmouth, UK) passive samplers have been developed to sample for micro-pollutants in water. Given the importance of the fish exometabolome, we sought to evaluate the capability of Chemcatcher® samplers to capture a broad spectrum of endogenous metabolites excreted by fish and to measure these using non-targeted direct infusion mass spectrometry metabolomics. The capabilities of C18 and styrene divinylbenzene reversed-phase sulfonated (SDB-RPS) Empore™ disks for capturing non-polar and polar metabolites, respectively, were compared. Furthermore, we investigated real, complex metabolite mixtures excreted from two model fish species, rainbow trout (Oncorhynchus mykiss) and three-spined stickleback (Gasterosteus aculeatus). In total, 344 biological samples and 28 QC samples were analysed, revealing 646 and 215 m/z peaks from trout and stickleback, respectively. The measured exometabolomes were principally affected by the type of Empore™ (Hemel Hempstead, UK) disk and also by the sampling time. Many peaks were putatively annotated, including several bile acids (e.g., chenodeoxycholate, taurocholate, glycocholate, glycolithocholate, glycochenodeoxycholate, glycodeoxycholate). Collectively these observations show the ability of Chemcatcher® passive samplers to capture endogenous metabolites excreted from fish.

Premise of the study: Next-generation sequencing (NGS) data are widely used for single-nucleotide polymorphism discovery and genetic marker development in species with limited available genome information. We developed microsatellite primers for the Proteaceae nut crop species Macadamia integrifolia and assessed cross-species transferability in all congeners to investigate genetic identification of cultivars and gene flow. Methods and Results: Primers were designed from both raw and assembled Illumina NGS paired-end reads. The final 12 microsatellite markers selected were polymorphic among wild individuals of all four Macadamia species—M. integrifolia, M. tetraphylla, M. ternifolia, and M. jansenii—and in commercial macadamia cultivars including hybrids. Conclusions: We demonstrate the utility of raw and assembled Illumina NGS reads from total genomic DNA for the rapid development of microsatellites in Macadamia. These primers will facilitate future studies of population structure, hybridization, parentage, and cultivar identification in cultivated and wild Macadamia populations.