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Modern Applied Statistics with S

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Abstract

A guide to using S environments to perform statistical analyses providing both an introduction to the use of S and a course in modern statistical methods. The emphasis is on presenting practical problems and full analyses of real data sets.

Chapters (6)

Statistics is fundamentally about understanding data. We start by looking at how data are represented in S, then move on to importing, exporting and manipulating data.
In linear regression the mean surface is a plane in sample space; in non-linear regression it may be an arbitrary curved surface but in all other respects the models are the same. Fortunately the mean surface in most non-linear regression models met in practice will be approximately planar in the region of highest likelihood, allowing some good approximations based on linear regression to be used, but non-linear regression models can still present tricky computational and inferential problems.
We collect together several ways to handle linear and non-linear models with random effects, possibly as well as fixed effects.
Multivariate analysis is concerned with datasets that have more than one response variable for each observational or experimental unit. The datasets can be summarized by data matrices X with n rows and p columns, the rows representing the observations or cases, and the columns the variables. The matrix can be viewed either way, depending on whether the main interest is in the relationships between the cases or between the variables. Note that for consistency we represent the variables of a case by the row vector x.
Classification is an increasingly important application of modern methods in statistics. In the statistical literature the word is used in two distinct senses. The entry (Hartigan, 1982) in the original Encyclopedia of Statistical Sciences uses the sense of cluster analysis discussed in Section 11.2. Modern usage is leaning to the other meaning (Ripley, 1997) of allocating future cases to one of g prespecified classes. Medical diagnosis is an archetypal classification problem in the modern sense. (The older statistical literature sometimes refers to this as allocation.)
Statisticians1 often under-estimate the usefulness of general optimization methods in maximizing likelihoods and in other model-fitting problems. Not only are the general-purpose methods available in the S environments quick to use, they also often outperform the specialized methods that are available. A lot of the software we have illustrated in earlier chapters is based on the functions described in this. Code that seemed slow when the first edition was being prepared in 1993 now seems almost instant.
... Sublineage size was defined as the number of uniquely sampled descendants within a subtree defined by the Canadian introductory node. A negative binomial model of sublineage size by TMRCA was generated, adjusted by whether a sublineage was active (had any sampled cases in the previous 2 months) or extinct, using the R package MASS (Venables and Ripley, 2002). Since the data was downloaded on 15 June, but restricted to dates before 1 March, the effect of sequence deposition delay on sublineage lifespan was partially mitigated. ...
... (Pagès et al., 2020), phytools 0.7-70 (Revell, 2012), phangorn 2.5.5 (Schliep et al., 2017), tidyverse 1.3.1 (Wickham et al., 2019), coronavirus 0.3.0.9000 (Krispin and Byrnes, 2020), lubridate 1.7.9.2 (Grolemund and Wickham, 2011), zoo 1.8-8 (Zeileis and Grothendieck, 2005), RColorBrewer 1.1-2 (Neuwirth, 2014), cowplot 1.1.1 (Wilke, 2020), ggstance 0.3.5 (Henry et al., 2020), ggalluvial 0.12.3 (Brunson, 2020), ggridges 0.5.3 (Wilke, 2021), ggtree 2.2.4 (Yu et al., 2016), ggplotify 0.0.5 (Yu, 2020), ggrepel 0.9.1 (Slowikowski, 2021), MASS 7.3-53 (Venables andRipley, 2002), and treemapify 2.5.5 (Wilkins, 2021). Additional R packages used to generate the maps included rgeos 0.5-5 (Bivand and Rundel, 2018b), maptools 1.0-2 (Bivand and Lewin-Koh, 2018a), ggsn 0.5.0 (Baquero, 2017), broom 0.7.6 (Couch, 2021), and rgdal 1.5-18 (Bivand et al., 2017). ...
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Tracking the emergence and spread of SARS-CoV-2 lineages using phylogenetics has proven critical to inform the timing and stringency of COVID-19 public health interventions. We investigated the effectiveness of international travel restrictions at reducing SARS-CoV-2 importations and transmission in Canada in the first two waves of 2020 and early 2021. Maximum likelihood phylogenetic trees were used to infer viruses' geographic origins, enabling identification of 2263 (95% confidence interval: 2159-2366) introductions, including 680 (658-703) Canadian sublineages, which are international introductions resulting in sampled Canadian descendants, and 1582 (1501-1663) singletons, introductions with no sampled descendants. Of the sublineages seeded during the first wave, 49% (46-52%) originated from the USA and were primarily introduced into Quebec (39%) and Ontario (36%), while in the second wave, the USA was still the predominant source (43%), alongside a larger contribution from India (16%) and the UK (7%). Following implementation of restrictions on the entry of foreign nationals on 21 March 2020, importations declined from 58.5 (50.4-66.5) sublineages per week to 10.3-fold (8.3-15.0) lower within 4 weeks. Despite the drastic reduction in viral importations following travel restrictions, newly seeded sublineages in summer and fall 2020 contributed to the persistence of COVID-19 cases in the second wave, highlighting the importance of sustained interventions to reduce transmission. Importations rebounded further in November, bringing newly emergent variants of concern (VOCs). By the end of February 2021, there had been an estimated 30 (19-41) B.1.1.7 sublineages imported into Canada, which increasingly displaced previously circulating sublineages by the end of the second wave.Although viral importations are nearly inevitable when global prevalence is high, with fewer importations there are fewer opportunities for novel variants to spark outbreaks or outcompete previously circulating lineages. Editor's evaluation This study provides important observations about the transmission of SARS-CoV-2 lineages within Canada and the importation of lineages into Canada over the first year of the COVID-19 pandemic. This information is critical for understanding SARS-CoV-2 evolution and epidemiology, including the potential impacts of travel restrictions.
... Following the principle of parsimony, stepwise selection of covariates enables the identification of the combination of variables that minimises BIC values, and the covariates that show no significant correlation with the points are excluded during the process. BIC and stepwise model selection can be performed with the R package MASS function stepAIC (Akaike Information Criterion) (Venables & Ripley, 2002). The significance of BIC-selected covariates was validated against the stationary model (Model 0), using BIC weights. ...
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In the Northern Apennines, significant modifications to the characteristic historical features of landscapes have occurred since the 1950s as agriculture declined in importance and villages were progressively depopulated. Today, European policies are promoting the repopulation of these regions to help preserve the cultural identity of territories and reduce demographic pressure in urban areas. Such initiatives increase the need for cultural and natural landscape management to be better integrated using interdisciplinary approaches. Sustainable landscape management is a dynamic process involving the formulation of strategies to underpin the preservation of landscape heritage and foster local development based on the values and opportunities provided by landscapes themselves. This study uses landscape archaeology and spatial statistics to provide insights into which parts of the historic landscape retain the greatest time-depth and which parts reflect the more recent radical change, enabling an understanding which goes beyond the basic spatial relationships between landscape components.
... 39 . Ordinal logistic regression analyses (function polr from the MASS package, Venables and Ripley 2002) were carried out to relate volume estimates obtained at T 1 to MRS at T 2 . In line with previous structural imaging studies 32,41 , the patients' group was split by the median into two subsets per volume (larger and smaller regional volumes compared to the median) to improve statistical power. ...
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The concept of brain reserve capacity positively influencing the process of recovery after stroke has been continuously developed in recent years. Global measures of brain health have been linked with a favourable outcome. Numerous studies have evidenced that the cerebellum is involved in recovery after stroke. However, it remains an open question whether characteristics of cerebellar anatomy, quantified directly after stroke, might have an impact on subsequent outcome after stroke. Thirty-nine first-ever ischemic non-cerebellar stroke patients underwent MRI brain imaging early after stroke and longitudinal clinical follow-up. Structural images were used for volumetric analyses of distinct cerebellar regions. Ordinal logistic regression analyses were conducted to associate cerebellar volumes with functional outcome 3-6 months after stroke, operationalized by the modified Rankin Scale. Larger volumes of cerebellar lobules IV, VI and VIIIB were positively correlated with favourable outcome, independent of the severity of initial impairment, age and lesion volume (P < 0.01). The total cerebellar volume did not exhibit a significant structure-outcome association. The present study reveals that pre-stroke anatomy of distinct cerebellar lobules involved in motor and cognitive functioning might be linked to outcome after acute non-cerebellar stroke, thereby promoting the emerging concepts of structural brain reserve for recovery processes after stroke.
... Descriptive statistics, hypothesis tests, and multinomial logistic regression were the main techniques used. This analysis was performed using the free software R (R Core Team 2021), using the nnet (Venables and Ripley 2002), DescTools (Signorell 2017), and car (Fox and Weisberg 2019) packages. The significance level adopted in this study was 5% for all the tests. ...
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Human comfort outdoors is widely investigated, but most studies explore the comfort domains singularly. This paper aimed to evaluate human comfort in parks, verifying the importance of using a multi-domain (simultaneously evaluating thermal, visual, acoustic, and air quality) and multi-disciplinary (combining environmental and social fields) approach. A walk through a pre-defined path from one park to another was repeated twice per day on four consecutive days in June, with three participants per walk. The two investigated parks are in central Italy and were chosen because they differ in their design and spatial characteristics. Environmental data were recorded with an innovative wearable device during the whole walk, and surveys were used to assess people’s perceptions of the parks. Despite observed differences in collected physical parameters, the survey’s responses were similar, and different comfort domains showed dependence on each other in the two parks. Logistic regression models were developed for each park, and they revealed that the qualitative information predicted the overall comfort level more accurately than the environmental data. In detail, the models based on environmental data resulted in R 2 equal to 0.126 and 0.111 in Parks 1 and 2, respectively, whereas using the survey answers increased it up to 0.820 (Park 1) and 0.806 (Park 2). This study contributes to addressing the gap in multi-domain comfort studies outdoors and confirms the importance of using multi-disciplinary and multi-domain approaches for a complete comfort analysis, supporting holistic human-biometeorology-oriented models and forecasting opportunities that can promote improvements in urban environmental quality and liveability.
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Predation is one of the key factors shaping the dynamics of animal populations. In birds, nest loss due to predation can be a significant cause of low reproductive success. Ground‐nesting birds are among the bird groups most susceptible to predation, mainly because their nests are easily accessible to a broad suite of potential predators. For these birds, anthropogenic disturbances can generate changes in nest predation risk by altering their antipredator behaviour and also by altering behaviour of the predator species – i.e. the predator becoming much more aware of predation opportunities due to frequent disturbances and/or motivated to repeat predation attempts when some are successful. To date, most previous studies investigating this have focused on a single effect, either predation or disturbance, on chick survival. It remains unknown how the risk of predation with and without disturbance varies with chick age. In this study, we used behavioural observations to assess how the interaction between predators and disturbance affects predation risk in chicks and how this interacts with chick age. Specifically, we investigated the effect of disturbance caused by humans and stray dogs on the predation of Slender‐billed Gull (Chroicocephalus genei) chicks by Yellow‐legged Gulls (Larus michahellis), and whether this depended on the age of the chicks. Our results revealed that disturbance had a significant positive effect on predation measures of Slender‐billed Gull chicks by Yellow‐legged Gulls, but that this effect was mediated both by disturbance type and the age of chicks. Stray dogs entering the colony had a stronger disturbance effect on chicks than passing humans, increasing predation risk by Yellow‐legged Gulls. Our results also showed that chick age interacts with disturbance type to determine the predation risk. This is probably mediated by chicks’ capacity to escape predation by gathering in a single large crèche that runs into the water when disturbed. To preserve Slender‐billed Gull colonies in one of its few remaining breeding sites in Tunisia, and as gulls tend to react even when the disturbance occurs relatively far from the colonies, it is crucial to (1) restrict human access to dikes and islets where large colonies breed, and (2) construct artificial islets attractive to gulls and inaccessible to stray dogs.
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Background Metabolic activity and environmental energy are two of the most studied putative drivers of molecular evolutionary rates. Their extensive study, however, has resulted in mixed results and has rarely included the exploration of interactions among various factors impacting molecular evolutionary rates across large clades. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with proxies of metabolic demands imposed by flight (wing loading and wing shape) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). Results We found weak evidence of a positive effect of environmental and morphological variables on mitochondrial substitution rates. Additionally, we found that temperature and UV radiation interact to explain molecular rates at nucleotide sites affected by selection and population size (non-synonymous substitutions), contrary to the expectation of their impact on sites associated with mutation rates (synonymous substitutions). We also found a negative interaction between wing shape (as described by the hand-wing index) and body mass explaining mitochondrial molecular rates, suggesting molecular signatures of positive selection or reduced population sizes in small-bodied species with greater flight activity. Conclusions Our results suggest that the demands of flight and environmental energy pose multiple evolutionary pressures on the genome either by driving mutation rates or via their association with natural selection or population size. Data from whole genomes and detailed physiology across taxa will bring a more complete picture of the impact of metabolism, population size, and the environment on avian genome evolution.
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Global change in climate and land use has profound effects on species' geographic and elevational distributions. In European birds, while species are predicted to track their climatic niches upslope, lowland agricultural intensification and high‐elevation land abandonment can drive elevational shifts. Species traits that can predict response to change in climate and land use can inform conservation, but a thorough examination of their relationships with elevational shifts in European birds is lacking. We estimate the change in the elevational distributions of 71 species from 1996 to 2016 in a region of the western Palearctic with wide elevational gradients (approximately 3000 m) and large changes in temperature. We model the relationships between elevational shifts and species traits associated with resource preference and adaptive capacity at five reference points including the cool edge, warm edge, and the core of species' elevational distributions. When intermediate reference points were removed, changes to the results were negligible, indicating that three reference points are likely sufficient. We found significant upslope and downslope shifts in 56% and 23% of our study species, respectively. Asymmetric rates of shifts in the cool and warm edges caused significant contractions in elevational extent in 30% of our study species. The effect of elevational preference (i.e., midpoint elevation) was habitat dependent. Movement in alpine birds was unidirectionally upslope, with nearly half displaying significant or apparent elevational range contractions. In woodland birds, asymmetries of shifts in reference points led to expansions in extent in low‐elevation species and contractions in high‐elevation species. Generally, migrants, species with smaller mass, smaller relative brain size, smaller hand‐wing index, and generalists in diet, habitat, and elevation had greater upslope shifts. While elevational shifts in European birds were heterogenous and species‐specific, many were rapid, and species traits associated with resource preference and adaptive capacity were associated with common patterns of elevation.
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We describe a new species of the genus Conraua from the Fouta Djallon Highlands in Guinea. The species is recognised as distinct from nominotypical C. alleni, based on morphological evidence and is supported by a recent species delimitation analysis, based on DNA sequence data. The new species is distinguished from its congeners by the unique combination of the following characters: medium body size, robust limbs, only one instead of two palmar tubercles, the first finger webbed to below the first subarticular tu-bercle, presence of a lateral line system, indistinct tympanum, two subarticular tubercles on fingers III and IV, venter in adults white with dark brown spots or dark brown with grey or whitish spots. The new species differs from all congeners by more than 6% in the DNA sequence of mitochondrial ribosomal 16S. We discuss isolation in Pliocene and Pleistocene forest refugia as a potential driver of speciation in the C. alleni complex. We also emphasise the importance of conserving the remaining forest fragments in the Fouta Djallon Region for the preservation of both its unique biodiversity and its valuable water sources for local people. Resumé Nous décrivons une nouvelle espèce du genre Conraua des hauts plateaux du Fouta Djallon en Guinée. L'espèce est reconnue comme distincte du C. alleni nominotypique, sur la base de preuves morphologiques et est soutenue par une analyse récente de délimitation des espèces, basée sur des données de séquence d'ADN. La nouvelle espèce se distingue de ses congénères par la combinaison unique des caractères suivants: taille moyenne du corps, membres robustes, un seul tubercule palmaire au lieu de deux, premier doigt palmaire jusqu'en dessous du premier tubercule subarticulaire, présence d'un système de lignes latérales, tympan indistinct, deux tubercules subarticulaires sur les doigts III et IV, ventre blanc avec des taches brun foncé ou brun foncé avec des taches gris ou blanchâtre chez les adultes. La nouvelle espèce diffère de ses congénères avec plus de 6% de sa séquence d'ADN du ribosome mitochondrial 16S. Nous discutons de l'isolement dans les refuges forestiers du Pliocène et du Pléistocène comme facteur potentiel de spéciation dans le complexe C. alleni. Nous soulignons également l'importance de conserver les fragments de forêt restants dans la région du Fouta Djallon pour préserver à la fois sa biodiversité unique et ses sources d'eau précieuses pour les populations locales.
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Ocean acidification may have deleterious effects on many species, but anticipating long-term changes in the abundance of populations will require an understanding of ocean acidification as an evolutionary force. Here, I show that ocean acidification alters natural selection on offspring size and is likely to drive contemporary evolution. In a detailed study of a coastal fish species (California grunion), I demonstrate that larval mortality is highly sensitive to ocean acidification and that mortality rates are lower for larger larvae. However, these effects are countered by tradeoffs between offspring size and number, suggesting that measurements of maternal fitness are critical for quantifying selection through ocean acidification. Measurements of selection and genetic variation were used to project the evolution of larval size as seawater conditions changed incrementally over many decades. Results for California grunion suggest that contemporary evolution may offset the projected decline in reproductive success by about 50%.
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The Vestibular/Ocular-Motor Screening (VOMS), an important component in acute (<72 h) sport-related concussion (SRC) assessment, is increasingly used alongside the Sport Concussion Assessment Tool (SCAT) and as part of the Military Acute Concussion Evaluation 2 (MACE2). VOMS demonstrates clinically useful diagnostic accuracy for acute SRC and improves the overall utility when added to the SCAT3. However, potential overlap among VOMS’s vestibular and oculomotor items suggests the possibility of a more efficient version. VOMS and SCAT3 scores were analyzed for 3,958 preseason (47.8% female) and 496 acute-SRC (37.5% female) NCAA-DoD Concussion Assessment, Research, and Education (CARE) consortium collegiate athlete evaluations. Analyses revealed very large effect sizes (d = 2.39–2.45) and high correlations (rho = 0.95–0.99) among all VOMS items except near point of convergence distance (d = 0.79, rho ≤ 0.341). Receiver operating characteristic (ROC) curve analyses showed clinically useful discriminative utility for VOMS Total (AUC = 0.85) and the VOMS Total change score, where pretest symptoms were incorporated (AUC = 0.81). A modified VOMS (mVOMS) consisting of four items (smooth pursuits, horizontal saccades, horizontal vestibulo-ocular reflex, visual motion sensitivity) yielded identical AUCs to VOMS Total. Integer cutoff analyses suggest a score of ≥4 for VOMS Total and ≥4 for mVOMS Total optimizes concussion identification. Incorporating VOMS or mVOMS into SCAT3 (AUC = 0.79) significantly improved the combined tool’s acute utility for acute concussion identification by a maximum of 4% (SCAT3+VOMS AUC = 0.84, SCAT3+mVOMS AUC = 0.83). Future versions of SCAT or MACE may want to consider incorporating a more parsimonious VOMS for the purpose of identifying acute concussion.
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Background Australia has had a framework for legal medicinal cannabis since 2016, yet prior online surveys in 2016 and 2018 indicated that most consumers continued to use illicit medical cannabis products. Regulatory data indicate an increase in the prescription of medicinal cannabis since 2019, and this survey examines consumer experiences of prescribed and illicit medical cannabis (MC) use in Australia. Methods A cross-sectional anonymous online survey was administered September 2020 to January 2021. Recruitment via social media, professional and consumer forums, and medical practices. Participant eligibility: ≥ 18 years; used a cannabis product for self-identified medical reason(s) in the past year, and resident in Australia. Outcome measures included c onsumer characteristics, conditions treated, source and patterns of MC use, and perspectives on accessing MC. Results Of the 1600 participants (mean age 46.4 ± 14.3 years, 53% male), 62.4% ( n = 999) reported using only illicit and 37.6% ( n = 601) used prescribed MC in the past year. MC was used on a median of 28 (IQR: 12, 28) of the past 28 days and cost $AUD 74 ± 72 weekly (median = $40, IQR: $7, $100). Prescribed participants were more likely to treat pain conditions than those using illicit MC (52% v 40%, OR = 1.7, 1.3–2.1) and less likely to treat sleep conditions (6% v 11%, OR = 0.5, 0.3–0.8), with mental health conditions also a common indication in both groups (26%, 31%). Prescribed MC was consumed predominately by oral routes (72%), whereas illicit MC was most commonly smoked (41%). Prescribed MC was ‘mainly THC’ (26%), ‘equal THC/CBD’ (40%), ‘mainly CBD’ (31%) and ‘uncertain’ (3%), while 34% of those using illicit MC were ‘uncertain’ of the cannabinoid profile. Cost and difficulties finding medical practitioners to prescribe remain significant barriers to accessing prescribed MC, and few (10.8%) described the existing model for accessing prescribed MC as ‘straightforward or easy’. Conclusions There has been a notable shift from illicit to prescribed MC by many consumers compared to prior surveys. Consumers using prescribed MC reported a range of advantages compared to illicit MC, including safer routes of administration, and greater certainty regarding access and composition of products.
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Sweet potato is a valuable staple crop that guarantees food security to a large segment of the world population. The wide phenotypic and genetic variability of this species is an indication of its high adaptation capacity to diverse environmental conditions. In Colombia, it is a neglected and underutilized crop, mainly managed by traditional knowledge. The aim of this study was to recognize the contribution of in situ conservation and to characterize the habitats and the traditional uses to shed light on the design of their management and conservation strategies. Germplasm and data collection were conducted in the Caribbean and Andean regions of the country. This collection resulted in 750 accessions from 131 municipalities, belonging to 19 departments of the two regions. In these regions, sweet potato has been conserved in situ in a wide spatial and altitudinal distribution. The major collection sources were wild and cultivated habitats, which highlight the invaluable contribution of farmers and communities in the preservation of this species and its associated knowledge. In situ conservation seemed to be an efficient strategy for conserving and using plant genetic resources; therefore, it should be considered by conservation efforts.
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Incorporating non-crop habitats around cropping fields is often promoted to enhance biodiversity and deter crop pests. However, few studies have investigated how these habitats influence the overwintering success of pest populations. In this study, we investigate how a specialist insect pest, the asparagus beetle (Crioceris asparagi, Coleoptera: Chrysomelidae), uses local and landscape resources for overwintering. We surveyed beetles in 2019–2020 at 11 asparagus farms in Michigan, USA, and conducted experiments to compare overwintering survival of adult beetles in five substrates commonly found in asparagus agroecosystems. We compared the overwintering number of beetles across three habitat types: asparagus field, weedy margin, and woodlot. Overwintering asparagus beetle abundance was highest within sites with deciduous leaves and decomposing asparagus stalks. We found a negative relationship between the abundance of dead trees in adjacent woodlots and adult beetle abundance. We then expanded beyond the woodlots with a landscape analysis conducted at multiple spatial scales. Landscape analysis indicated that deciduous forest within 1250 m of sites increased beetle abundance in focal asparagus fields, while asparagus production at spatial scales greater than 1500 m suppressed their populations. Our findings indicate that certain specialist pests, like asparagus beetles, depend on host resources for overwintering, but non-host habitat from the surrounding landscape is also important to their success. Practically, removal of host and non-host debris (leaf litter) from asparagus fields may lead to decreased survival and lower pest pressures. In addition, crop-dominated landscapes may not require in-field habitat management of overwintering substrates to the same extent as more diverse landscapes with higher proportions of non-host habitat (deciduous forest). Ultimately, we argue that the net positive and negative impact of increasing non-host habitat at the landscape level should be considered when developing integrated pest management strategies for specialists at the local scale.
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As growing urban populations have fewer chances to experience nature, i.e., ‘the extinction of experience’, the subsequent loss of emotional affinities for biodiversity (biophilia) pose major challenges to environmental conservation. Gardening, as an everyday nature interaction and window into invertebrate ecological functioning may offer opportunities to develop biophilia. However, the associations between gardening and biophilia/biophobia towards invertebrates remains untested. We conducted an online survey (n = 443) with adults in Japan about their nature and gardening experiences, demographics, and species identification knowledge in relation to their biophilia (like) and biophobia (dislike, fear, and disgust) towards invertebrates. We also asked participants about their perceptions of invertebrates as ‘beneficials’ or ‘pests’. From responses, we ranked invertebrates according to the attitudes held towards them. We found that frequent gardeners were more likely to express biophilia and perceive invertebrates as beneficial, and generally less likely to express biophobia towards invertebrates. Frequency of visits to recreational parks, but not national/state parks was associated with increased biophilia and reduced dislike and fear of invertebrates. Our results suggest that gardening, in addition to localised nature experiences, acts as a possible pathway towards appreciation of invertebrate biodiversity. We recommend that policymakers and conservation organisations view urban gardening as a potential tool to minimise the negative impacts of the extinction of experience. Implications for insect conservation As people are more likely to conserve what they love, finding ways to nurture positive attitudes towards insects is critical for the public support needed for successful insect conservation. Considering gardening is a relatively accessible form of nature connection even in cities, our findings of the association between gardening and biophilia towards invertebrates holds promise for potential pathways towards fostering support for insect conservation now and into the future.
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Small ruminant lentiviruses (SRLV) belong to the Retroviridae family and can cause various diseases. One of the most impacting diseases is visna-maedi, a complex disease characterized by long latencies and chronic progressive inflammatory events affecting the nervous system, lungs, mammary gland, and articular joints. A single nucleotide polymorphism (rs408593969, c.103G>A, missense mutation E35K) in the ovine transmembrane protein gene 154 (TMEM154) was identified as protective against small ruminant lentivirus infection in different herds worldwide. However, there is evidence in the scientific literature of a breed-specificity of this protective effect and, furthermore, there are still limited studies regarding the association between the animal genotype and the infecting virus genotype. Thus, the aim of this study was to further investigate the association between the animal genotype for the suggested protective mutation and the infecting virus genotype, in three different sheep breeds reared in northern Italy. The results obtained only partially confirmed the data available in the literature, as the protective effect was confirmed only for SRLV genotype A clusters, while other genotypes (namely B and E) infected AA and GA animals. Further studies with an experimental infection of specific virus genotypes in hosts with specific genotypes are required to confirm the larger number of cases the results obtained in this study.
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1. Litter quality has been related to broiler performance, behaviour, welfare, dust and ammonia (NH3) emissions. Drier litter leads to a reduction in NH3 emissions and reduces the formation of foot- and hock lesions. However, maintaining good litter quality is often challenging. This study investigated the effects of different bedding materials on litter quality and NH3 concentrations at litter level, broiler performance, foot- and hock lesions, plumage cleanliness and breast skin irritation.2. A total of 2160 Ross 308 male broilers were randomly assigned to 36 floor pens. There were six replications for each of the following six litter treatments: wood shavings, flax, peat, corn silage, chopped wheat straw and flax pellets.3. For the total period, the highest feed intake and body weight was obtained for broilers housed on peat. The NH3 concentrations measured at litter level was highest for peat and chopped wheat straw at 36 d of age and numerically the lowest for flax at 30 and 36 d of age. Corn silage remained friable, but did not result in lower NH3 concentrations compared to wood shavings. Chopped wheat straw and wood shavings gave rise to the highest incidence of foot lesions at 38 d of age, while broilers kept on flax, peat, corn silage and flax pellets had the lowest incidence of foot lesions at the end of the rearing period.4. The results of the current study suggest a complicated relationship between the type of bedding material, litter conditions and NH3 volatilized from the litter.
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Objective Cannabis and alcohol co-use is highly prevalent and confers a host of risk factors that outweigh those related to the use of either substance alone; however, few studies have examined associations between varying levels of co-use intensity (i.e., frequency) and clinical variables. The present study characterizes the effects of co-use across varying levels of cannabis use frequency in a large sample of heavy drinkers. Methods Comparisons among co-use groups (i.e., no, light-to-moderate, and moderate-to-heavy cannabis use; N = 863; 33.95% female) on demographic and clinical variables consisted of one-way analyses of variance for continuous outcomes or Chi-Square tests for dichotomous outcomes. Multinomial logistic regression modeling was used to examine the relationship between demographic and clinical variables and co-use group membership. Multiple linear regression was used to explore associations among variables of interest and cannabis use days. Results Despite relatively low levels of cannabis use overall in the present sample, younger age, identification with male gender, treatment seeking for AUD, and concurrent tobacco use were robust predictors of co-use. Individuals reporting more frequent cannabis use also reported increased levels of alcohol craving and more heavy drinking days, as compared to those who reported fewer or no cannabis use days. Drinking days and treatment seeking for AUD significantly predicted increases in cannabis use days. Conclusion In clinical practice, younger age, male gender, and comorbid tobacco use represent identifiable risk factors for cannabis and alcohol co-use. While in treatment for AUD, reducing drinking days may be an intervention target to mitigate co-use.
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Osteoarthritis (OA) is one of the most prevalent age-related chronic conditions that afflict companion dogs, and multiple joint supplements are available to prevent or treat OA, though the efficacy of these treatments is controversial. While the demographic factors that are associated with OA diagnosis are well established, the factors that are associated with joint supplement use are not as well studied. Using data collected from the Dog Aging Project, we analyzed owner survey responses regarding joint supplement administration and OA diagnosis for 26,951 adult dogs. In this cross-sectional analysis, logistic regression models and odds-ratios (OR) were employed to determine demographic factors of dogs and their owners that were associated with joint supplement administration. Forty percent of adult dogs in our population were given some type of joint supplement. Perhaps not surprisingly, dogs of older age, larger size, and those that were ever overweight were more likely to receive a joint supplement. Younger owner age, urban living, owner education, and feeding commercial dry food were associated with a reduced likelihood of administration of joint supplements to dogs. Interestingly, mixed breed dogs were also less likely to be administered a joint supplement (OR: 0.73). Dogs with a clinical diagnosis of OA were more likely to receive a joint supplement than those without a reported OA diagnosis (OR: 3.82). Neutered dogs were more likely to have a diagnosis of OA, even after controlling for other demographic factors, yet their prevalence of joint supplement administration was the same as intact dogs. Overall, joint supplement use appears to be high in our large population of dogs in the United States. Prospective studies are needed to determine if joint supplements are more commonly administered as a preventative for OA or after an OA clinical diagnosis.
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Quinoa consumption has increased in worldwide importance due to an extraordinary nutritional value and public acceptance as alternative food. Fatty acid profiles of 10 quinoa varieties grown in the same geographical location were analyzed using different chemometric multivariate approaches [variable in importance partial least square discriminant analysis (VIP-PLS-DA), stepwise linear discriminant analysis (S-LDA), linear discriminant analysis (LDA), random forests (RF) and canonical analysis of principal components (CAP)]. The application of variable selection approaches such as S-LDA and LDA significantly increased the classification accuracy (78 % and 74 % respectively) of the samples according to their variety. The S-LDA approach allowed to reduce the number of selected fatty acids, representing those fatty acids with higher statistical significance when applying other random and non-random approaches. These fatty acid profiles also allowed to estimate the nutritional lipid profiles of each variety for suitability in human diet, providing insights on the various nutritional qualities of each quinoa variety. It is proposed that these results can be used to facilitate selection of varieties with optimized economic value.
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The NIH Toolbox includes a cognitive battery that provides an Early Childhood Composite score for children age 3-7. However, very few studies have evaluated feasibility when it is used in the youngest segment of this age range-3-year-olds. The current study evaluated performance on the four cognitive subtests composing the early childhood composite, two of which assess executive function, in a large sample of 3-year-olds enrolled in a Vanguard pilot of the National Children's Study. Results found that in a cohort of 609 3-year-olds (mean age = 39.6 months, SD = 1.6, 53% male, 64% White, 87% Non-Hispanic) who were administered four subtests included in the Early Childhood Composite, up to approximately 30% were unable to pass practice items on the Flanker, Dimensional Change Card Sort, and Picture Sequence Memory, whereas only approximately 3% were unable to pass practice items on the Picture Vocabulary Test. Furthermore, of those that did pass practice and achieve scores on the subtests, approximately 70% and 80% performed at or below chance level on the executive function tasks (Flanker and Dimensional Change Card Sort) and Picture Sequence Memory, respectively. Ultimately, the average 3-year-old has difficulty with three of the four NIH Toolbox tasks composing the Early Childhood Composite and may not yet have developed the requisite skills. These findings indicate that changes compatible with the developmental level of preschoolers are recommended to increase the feasibility and effectiveness of the NIH Toolbox in measuring individual cognition differences in 3-year-old children.
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The late Miocene is a period of increasing aridity and habitat openness in the south-eastern Mediterranean region. The impact of these changes has not been fully explored regarding rhinocerotids’ ecology, although rhinoceroses were a major and diverse component of the Miocene mammalian faunas. Here, we investigate the palaeoecology of rhinocerotid specimens coming from 12 localities throughout the Balkan-Iranian zoogeographic province, and covering a large part of the late Miocene (MN9 to MN13). Microwear textures confirmed the hypothesised niche partitioning between the two main rhinocerotid species – Ceratotherium [Ce.] neumayri (mixed-feeder including grasses) and Dihoplus pikermiensis (browser) – but highlighted dietary overlap between Ce. neumayri and the co-occurring chilothere species at Maragheh, Samos and Pentalophos-1. Although microwear did not reveal clear spatiotemporal differences, we found obvious discrepancies regarding hypoplasia prevalence: Vallesian rhinocerotid teeth displayed more defects (Xirochori and Pentalophos-1: 16.26% of teeth affected) than Turolian specimens (all other localities: 9.72%). Similarly, rhinocerotid teeth from eastern localities (Samos and Maragheh; supposedly more arid), had a higher hypoplasia prevalence (13.52%) than their western counterparts (6.90%). Insights from rhinocerotids’ ecology thus challenged space and time homogeneity within Balkan-Iranian province, and the associated savanna habitat, at least regarding the sample studied here.
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Accurate and up‐to‐date land cover maps are vital for underpinning evidence‐based landscape management decision‐making. However, the technical skills required to extract tailored information about land cover dynamics from these open‐access geospatial data often limit their use by those making landscape management decisions. Using Dartmoor National Park as an example, we demonstrate an open‐source toolkit which uses open‐source software (QGIS and RStudio) to process freely available Sentinel‐2 and public LiDAR data sets to produce fine scale (10 m2 grain size) land cover maps. The toolbox has been designed for use by staff within the national park, for example, enabling land cover maps to be updated as required in the future. An area of 945 km2 was mapped using a trained random forest classifier following a classification scheme tailored to the needs of the national park. A 2019 land cover map had an overall user's accuracy of 79%, with 13 out of 17 land cover classes achieving greater than 70% accuracy. Spatially, accuracy was related via logistical regression to blue band surface reflectance in the spring and topographic slope derived from LiDAR (1 m resolution), with greater accuracy in steeper terrain and areas exhibiting higher blue reflectance. Between an earlier (2017–2019) and later (2019–2021) time frame, 8% of pixels changed, most of the change by area occurred in the most common classes. However, the largest proportional increase occurred in Upland Meadows, Lowland Meadows and Blanket Bog, all habitats subject to restoration efforts. Identifying areas of change enables future field work to be better targeted. We discuss the application of this mapping to land management within the Dartmoor national park and of the potential of tailored land cover and land cover change mapping, via this toolbox, to evidence‐based environmental decision‐making more widely. Customizable land cover & change toolbox for non‐specialists using open‐source data and software with a step‐by‐step guide: map what habitats are where in the area you manage, shown here for Dartmoor (England).
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Introduction: Monocyte distribution width (MDW), a parameter generated alongside full blood counts (FBC) in new-generation haematology analysers, has been proposed as a diagnostic test for severe infection/sepsis. It represents the standard deviation (SD) of the monocyte mean volume (MMV). Methods: This study aimed to compare monocyte volumetric parameters retrieved by the UniCel DxH 900 haematology analyser (MMV and MDW) against corresponding parameters from the same sample measured using flow cytometry (forward scatter [FSC] mean and SD) in combination with phenotypic characterization of monocyte subtypes. We analysed blood samples from healthy individuals (n = 11) and patients with conditions associated with elevated MDW: sepsis (n = 26) and COVID-19 (n = 15). Results: Between-instrument comparisons of monocyte volume parameters (MMV vs. FSC-mean) showed relatively good levels of correlation, but comparisons across volume variability parameters (MDW vs. FSC-SD) were poor. Stratification on sample type revealed this lack of correlation only within the sepsis group. Flow cytometry analysis revealed that in healthy controls intermediate monocytes are the largest and non-classical the smallest cells. In each disease state, however, each monocyte subset undergoes different changes in volume and frequency that together determine the overall configuration of the monocyte population. Increased MDW was associated with reduced classical monocyte frequency and increased intermediate monocyte size. In COVID-19, the range of monocyte sizes (smallest to largest) reduced, whereas in sepsis it increased. Conclusion: Increased MDW in COVID-19 and sepsis has no single flow cytometric phenotypic correlate. It represents-within a single value-the delicate equipoise between monocyte subset frequency and size.
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In Arequipa, Peru, a large-scale vector control campaign has successfully reduced urban infestations of the Chagas disease vector, Triatoma infestans . In addition to preventing new infections with Trypanosoma cruzi (etiological agent of Chagas disease), the campaign produced a wealth of information about the distribution and density of vector infestations. We used these data to create vector infestation risk maps for the city in order to target the last few remaining infestations, which are unevenly distributed and difficult to pinpoint. Our maps, which are provided on a mobile app, display color-coded, individual house-level estimates of T . infestans infestation risk. Entomologic surveillance personnel can use the maps to select homes to inspect based on estimated risk of infestation, as well as keep track of which parts of a given neighborhood they have inspected to ensure even surveillance throughout the zone. However, the question then becomes, how do we encourage surveillance personnel to actually use these two functionalities of the risk map? As such, we carried out a series of rolling trials to test different incentive schemes designed to encourage the following two behaviors by entomologic surveillance personnel in Arequipa: (i) preferential inspections of homes shown as high risk on the maps, and (ii) even surveillance across the geographical distribution of a given area, which we term, ‘spatial coverage.’ These two behaviors together constituted what we termed, ‘optimal map use.’ We found that several incentives resulted in one of the two target behaviors, but just one incentive scheme based on the game of poker resulted in optimal map use. This poker-based incentive structure may be well-suited to improve entomological surveillance activities and other complex multi-objective tasks.
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Solifugae are a group of arachnids with strong chelicerae and absence of venom, diverse in the tropics and subtropics, tolerant to levels of humidity, and adapted to coastal ecosystems. The ecological characteristics of Ammotrechella manggi Acosta-Berrocal et al. 2017 in mangrove fragments from the southern Morrosquillo Gulf, Colombian Caribbean, were evaluated. The solifuges were collected in four fragments of mangrove forests, between November 2015 and July 2016 in different climatic seasons. A total of 81 individuals were collected, and the occurrence and abundance of solpugids in the evaluated mangrove forest fragments may be influenced by precipitation, height, and bark humidity. A. manggi exhibited a preference for fallen trees with or without decomposed areas located in floodable areas at heights between 0.5-2.7 meters and fallen trunks located on sandbars at lower heights of 1.5 m. The mangrove forest fragments offer the conditions and resources for the occurrence of the populations of A. manggi, determined by the availability of microhabitats that provide protection, shelter, and nesting sites.
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Purpose There is increasing interest in developing new methods to improve sensitivity in detecting subtle cognitive deficits associated with cancer and its treatments. The current study aimed to evaluate the ability of a novel computerized battery of cognitive neuroscience–based tests to discriminate between cognitive performance in breast cancer survivors and controls. Methods Breast cancer survivors (N = 174) and age-matched non-cancer controls (N = 183) completed the Enformia Cogsuite Battery of cognitive assessments, comprised of 7 computerized tests of multiple cognitive domains. Primary outcome measures included accuracy, reaction times (RT), and coefficients of variation (CV) for each task, as well as global scores of accuracy, RT, and CV aggregated across tests. Results Linear regressions adjusting for age, education, and remote vs. in-office administration showed that compared to non-cancer controls, survivors had significantly lower performance on measures of attention, executive function, working memory, verbal ability, visuospatial ability, and motor function. Survivors had significantly greater CV on measures of attention, working memory, and processing speed, and significantly slower RT on measures of verbal fluency. Conclusions The Cogsuite battery demonstrates sensitivity to cancer-related cognitive dysfunction across multiple domains, and is capable of identifying specific cognitive processes that may be affected in survivors. Implications for Cancer Survivors The sensitivity of these tasks to subtle cognitive deficits has advantages for initial diagnosis of cancer-related cognitive dysfunction, as well as detecting changes in survivors’ cognitive function over time. The remote delivery of the battery may help overcome barriers associated with in-office administration and increase access to neurocognitive evaluation.
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This study aims to elucidate the structure of support for social policies (redistribution and free competition), focusing on the role of community interests (especially demographic decline). To this end, Japan was selected as a case study because it has the highest proportion of the elderly population in the world. The author analyzed data from the National Survey of Social Stratification and Social Mobility in 2015 and the Population Census for the same year, employing ordered logit models. The results revealed that people living in demographically declining communities were more likely to support redistribution and less likely to endorse free competition, compared to individuals from other communities. Furthermore, compared to the underprivileged, wealthy individuals were more likely to consider community interests irrespective of individual benefits. This finding demonstrates that community interests may have a significant influence on individuals’ policy preferences.
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Global climate change has profound effects on species, especially those in habitats already altered by humans. Tropical ectotherms are predicted to be at high risk from global temperature increases, particularly those adapted to cooler temperatures at higher altitudes. We investigated how one such species, the water anole (Anolis aquaticus), is affected by temperature stress similar to that of a warming climate across a gradient of human-altered habitats at high elevation sites. We conducted a field survey on thermal traits and measured lizard critical thermal maxima across the sites. From the field survey, we found that (1) lizards from the least disturbed site and (2) operative temperature models of lizards placed in the least disturbed site had lower temperatures than those from sites with histories of human disturbance. Individuals from the least disturbed site also demonstrated greater tolerance to high temperatures than those from the more disturbed sites, in both their critical thermal maxima and the time spent at high temperatures prior to reaching critical thermal maxima. Our results demonstrate within-species variability in responses to high temperatures, depending on habitat type, and provide insight into how tropical reptiles may fare in a warming world.
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Machine learning algorithms have shown several advantages compared to humans, namely in terms of the scale of data that can be analysed, delivering high speed and precision. However, it is not always possible to understand how algorithms work. As a result of the complexity of some algorithms, users started to feel the need to ask for explanations, boosting the relevance of Explainable Artificial Intelligence. This field aims to explain and interpret models with the use of specific analytical methods that usually analyse how their predicted values and/or errors behave. While prediction analysis is widely studied, performance analysis has limitations for regression models. This paper proposes a rule‐based approach, Error Distribution Rules (EDRs), to uncover atypical error regions, while considering multivariate feature interactions without size restrictions. Extracting EDRs is a form of subgroup mining. EDRs are model agnostic and a drill‐down technique to evaluate regression models, which consider multivariate interactions between predictors. EDRs uncover regions of the input space with deviating performance providing an interpretable description of these regions. They can be regarded as a complementary tool to the standard reporting of the expected average predictive performance. Moreover, by providing interpretable descriptions of these specific regions, EDRs allow end users to understand the dangers of using regression tools for some specific cases that fall on these regions, thaṯ is, they improve the accountability of models. The performance of several models from different problems was studied, showing that our proposal allows the analysis of many situations and direct model comparison. In order to facilitate the examination of rules, two visualization tools based on boxplots and density plots were implemented. A network visualization tool is also provided to rapidly check interactions of every feature condition. An additional tool is provided by using a grid of boxplots, where comparison between quartiles of every distribution with a reference is performed. Based on this comparison, an extrapolation of counterfactual examples to regression was also implemented. A set of examples is described, including a setting where regression models performance is compared in detail using EDRs. Specifically, the error difference between two models in a dataset is studied by deriving rules highlighting regions of the input space where model performance difference is unexpected. The application of visual tools is illustrated using EDRs examples derived from public available datasets. Also, case studies illustrating the specialization of subgroups, identification of counter factual subgroups and detecting unanticipated complex models are presented. This paper extends the state of the art by providing a method to derive explanations for model performance instead of explanations for model predictions.
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In the era of urban tourism expansion, restaurants in major cities of former Yugoslavia (Belgrade, Zagreb, Ljubljana, Sarajevo, Skopje, Podgorica, which are also the capitals of the newly emerged countries) are very important factors in meeting the needs of tourists. The Internet with specialized websites and social networks provides a wealth of information to potential restaurant visitors. Tripadvisor is one of the most popular hospitality websites that gives its users an insight into past experiences of restaurant customers. Previous research has shown that there is a close relationship between the number of reviews on the website and the financial performance of restaurants. The aim of this paper is to examine the relationship of visitor satisfaction between the mentioned capitals, as well as the trends in the number of reviews and satisfaction over time, including the correlation between the number of written comments and visitor satisfaction via the analysis of ratings and comments left on the Tripadvisor site.
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Successful adaptive behavior requires efficient attentional and locomotive systems. Previous research has thoroughly investigated how we achieve this efficiency during natural behavior by exploiting prior knowledge related to targets of our actions (e.g., attending to metallic targets when looking for a pot) and to the environmental context (e.g., looking for the pot in the kitchen). Less is known about whether and how individual nontarget components of the environment support natural behavior. In our immersive virtual reality task, 24 adult participants searched for objects in naturalistic scenes in which we manipulated the presence and arrangement of large, static objects that anchor predictions about targets (e.g., the sink provides a prediction for the location of the soap). Our results show that gaze and body movements in this naturalistic setting are strongly guided by these anchors. These findings demonstrate that objects auxiliary to the target are incorporated into the representations guiding attention and locomotion.
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The invasive alien species Harmonia axyridis (Coleoptera: Coccinellidae) was first observed in the UK in 2004. Previous studies have demonstrated the adverse effects on other species of H. axyridis during its early stages of establishment. However, habitat factors are important in determining distribution and population trends of ladybirds. Whilst the abundance of H. axyridis is well known in the UK within urban and other managed habitats, much less is known about its abundance in the wider countryside. Here we present the results of surveys from rural woodland habitats to assess whether or not H. axyridis dominates coccinellid communities in these rural habitats. Additionally, we explored the relationship between coccinellid and aphid abundance within these habitats. All field sites were in Cambridgeshire or Suffolk, East Anglia, UK and were surveyed between May and October 2016 and 2017. Three deciduous sites and three coniferous sites were included in the study. Surveys were conducted using a standardised approach involving sweep-netting within grass margins and tree beating to sample ladybirds from trees. Three distinct vegetation structures or layers were surveyed within both the coniferous and deciduous sites; tree, shrub and herb layer. All captured coccinellids were identified to species-level. Seventeen species of coccinellid and over 1300 individuals were recorded during the study period from two distinct site types (deciduous, coniferous). Species richness was lower at deciduous sites (n = 12) in comparison to coniferous (n = 16) sites. The coccinellid community also did not appear to be dominated by H. axyridis at rural sites, in contrast to urban areas. Deciduous woodland appeared to be a lesser preferred habitat of H. axyridis than coniferous woodland. Additionally, there was a distinct difference in the coccinellid community in relation to vegetation structure (across the tree, shrub and herb layers) between coniferous and deciduous sites. Our results indicate that there appear to be distinct native coccinellid communities at deciduous and coniferous sites. We discuss the way in which rural woodlands could act as a refuge for some native coccinellids.
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Pyrethroid insecticides are widely used to control mosquitoes that transmit pathogens such as West Nile virus (WNV) to people. Single nucleotide polymorphisms (SNP) in the knockdown resistance locus ( kdr ) of the voltage gated sodium channel ( Vgsc ) gene in Culex mosquitoes are associated with knockdown resistance to pyrethroids. RNAseq was used to sequence the coding region of Vgsc for Culex tarsalis Coquillett and Culex erythrothorax Dyar, two WNV vectors. The cDNA sequences were used to develop a quantitative reverse transcriptase PCR assay that detects the L1014F kdr mutation in the Vgsc . Because this locus is conserved, the assay was used successfully in six Culex spp . The resulting Culex RT kdr assay was validated using quantitative PCR and sequencing of PCR products. The accuracy of the Culex RT kdr assay was 99%. The L1014F kdr mutation associated with pyrethroid resistance was more common among Cx . pipiens than other Culex spp. and was more prevalent in mosquitoes collected near farmland. The Culex RT kdr assay takes advantage of the RNA that vector control agencies routinely isolate to assess arbovirus prevalence in mosquitoes. We anticipate that public health and vector control agencies may employ the Culex RT kdr assay to define the geographic distribution of the L1014F kdr mutation in Culex species and improve the monitoring of insecticide resistance that will ultimately contribute to effective control of Culex mosquitoes.
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Background and Aims Nitrogen (N2) fixation through endophytic diazotrophs within the non-nodulated plants has been considered a novel source of N inputs in terrestrial ecosystems. However, little is known about the composition and diversity of endophytic diazotrophs within the non-nodulated plants, especially when compared with the diazotrophs in nodulated plants. Methods High-throughput nifH amplification sequencing was conducted to characterize endophytic diazotrophs within different tissues (leaf, stem, and root) of non-nodulated plants (Salix rehderiana Schneid, S. ernestii Schneid, and Populus purdomii Rehd.) and nodulated plants (Astragalus mahoshanicus and Hippophae rhamnoides L.) which dominate in the newly formed N-limited glacier floodplain in the eastern Qinghai-Tibetan Plateau. Results We found endophytic diazotrophs, primarily Proteobacteria, in all tissue types of non-nodulated plants and leaf and stem of nodulated plants. The dominant genera were Bradyrhizobium, Ideonella, Azotobacter, and Geobacter. In comparison, diazotrophs within the nodule of leguminous Astragalus mahoshanicus and actinorhizal Hippophae rhamnoides were predominantly of genera Rhizobium and Frankia, respectively. Further, the community composition of diazotrophs was structured by plant species (P = 0.001), tissue types (P = 0.001), and nutrient concentrations (P = 0.001). Leaves of non-nodulated plants exhibited higher Chao1 indices and lower Simpson and Shannon indices than their stem and root, but these were not significantly different among different tissue types of nodulated plants. Conclusions Endophytic diazotrophs might be prevalent in pioneer plants occurring in the N-limited habitat and have a high degree of host specificity; these findings could help to understand the ability of those pioneer plants to acquire N.
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Context Power line corridors have been repeatedly assessed as habitat for wild bees; however, few studies have examined them as bee habitat relative to nearby crop fields and surrounding landscape context. Objectives We surveyed bee communities in power line corridors near to and isolated from lowbush blueberry fields in two landscape contexts in Maine, U.S.A. We examined the influences of blooming plant abundance and diversity and bee life-history traits including sociality, nesting preference, and body size. Methods We surveyed wild bees and blooming plants in power line corridors from 2013 to 2015. We calculated landscape composition surrounding sites at multiple scales and gathered bee trait information from the literature. We assessed differences in bee communities owing to landscape context with generalized linear models. Results We collected 125 wild bee species and observed a rare plant-pollinator relationship within power line corridors. We found greater bee abundance and species richness throughout a complex, resource-rich landscape, while mass-flowering lowbush blueberry fields enhanced bee species richness only in a simple, resource-poor landscape. Landscape composition and blooming plant diversity varied with landscape context, though only landscape composition influenced bee communities. Solitary and ground-nesting species were more sensitive to landscape context than social or cavity-nesting species. Conclusions Power line corridors provide crucial refugia for crop pollinating wild bees in agricultural landscapes with resource-poor natural habitat, while bees may selectively forage in power line corridors within agricultural landscapes containing resource-rich natural habitat. We found high-quality forage within corridors; quantifying nesting resources could clarify corridor use by wild bees.
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Paratuberculosis is a chronic enteric progressive disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP). Despite cultural methods being considered the gold standard for the diagnosis of paratuberculosis, quantitative PCR (qPCR) assays have been developed for this purpose. These assays showed sensitivity and specificity comparable to cultural method but provide more rapid analysis results. Aim of our work was the validation of an IS900-qPCR assay for detection of MAP in faeces according to the OIE guidelines relative to the validation of assays for infectious diseases. The analytical and diagnostic characteristics and the reproducibility of the qPCR method were assessed. The robustness of the assay was evaluated using two extraction methods (silica column and magnetic beads DNA capture) and two qPCR systems (STEPONETM and CFX96TM). According to our validation, the analytical specificity, inclusivity and exclusivity were found to be appropriate for the use of this qPCR assay as a diagnostic test. Specifically, the limit of detection was approximately 100 CFU/g or even less if binomial approaches were used for the determination of the 95% probability of detection (logit and clog-log models) with sufficient repeatability and reproducibility. Estimation of test accuracy was performed using a Bayesian two latent class model, in various scenarios combining different priors for prevalence and accuracy of the two tests used. All models were run considering three different cut-offs for qPCR. Our validation study underlines the good performance of this IS900-qPCR assay for diagnosis of MAP representing a valid and robust alternative to culture. Moreover, coupled with the semiautomatic magnetic beads DNA extraction method, this assay allows the rapid processing of numerous samples.
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Introduction Specialist management of asthma has been shown to associate with socioeconomic status (SES). However, little is known about the influence of SES on care burden in universal healthcare settings. Methods Patients aged 18–45 years using inhaled corticosteroids (ICS) were followed in national databases. Impact of asthma was investigated using negative binomial regression adjusted for age, sex, comorbidity, and GINA 2020 Step. Uncontrolled asthma was defined as >600 annual SABA puffs, ≥2 prednisolone courses and/or ≥1 hospitalization. Results A total of 60,534 (55% female, median age 33 (IQR 25–39)) patients were followed for 10.1 years (IQR 5.2–14.3)). Uncontrolled asthma resulted in 6.5 and 0.51 additional annual contacts to primary care and pulmonologists, respectively. Unscheduled and primary care burden was dependent on SES, increasing with rural residence, lower education, income and receiving welfare. Differences in planned respiratory care were slight, only seen among divorced, low income- or welfare recipients. Lower SES was consistently associated with an increased utilization of SABA and prednisolone. No dose–response relationship between ICS use and SES could be identified. Conclusion Lower SES in asthma is a risk factor for a predominance of unscheduled care and adverse outcomes, warranting further attention to patients’ background when assessing asthma care.
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Prior expectations strongly structure the way we perceive the world and ourselves. For instance, action-outcome prediction can modulate time perception and causal experience. We designed a study that allowed us to investigate whether action-outcome prediction has similar effects on time perception and intentional causality. Participants viewed a stimulus that was consistent or inconsistent with the action they, or another agent executed. The stimulus preceded or followed these actions and participants reported simultaneity or causal judgments. Observers were more likely to report the consistent outcomes as being generated by the action, even when the outcomes actually preceded the action. However, outcome consistency did not modulate simultaneity judgments. These results shed insight on the relationship between time and causal experience. It suggests that time perception and causal experience do not rely in the same way on temporal information, the latter being more permeable to contextual cues such as action-outcome consistency.
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Orchid bees (Euglossini) are pollinators sensitive to landscape pressures related to agricultural land use, such as coffee farming. Coffee crops occupy a large land area in Brazil, and understanding the effects of coffee farming on bee communities is essential to pollinator conservation in modified landscapes. Here, we evaluated the Euglossini communities in forest patches surrounded by coffee crops in the Atlantic Forest. We hypothesized the negative effects of coffee cover (%) on euglossine richness and abundance. The euglossine males were sampled at a sampling point within forest patches of 15 landscapes in southeastern Brazil. A total of 1890 euglossine males in four genera and 14 species were sampled. Eulaema nigrita Lepeletier, 1841 was the dominant species (55.1%), followed by Euglossa cordata (Linnaeus, 1758) (25.5%). We found a new record for Euglossa liopoda Dressler, 1982, increasing the species’ known range in the Atlantic Forest. The results showed that the euglossine richness and species abundance decreased in forest patches surrounded by a high coffee cover (%). These negative effects of coffee cover on the Euglossini communities are related to forest cover substitution by monocultures with low or no floral attractiveness for these bees. This study highlights that forest patches in agricultural landscapes sustain high levels of euglossine richness. Thus, we indicate the conservation importance of these Atlantic Forest patches for bee species requirements.
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Background and objectives: Major depressive disorder (MDD) is a common and severe psychiatric disorder that has enormous economical and societal costs. As pharmacogenetics is one of the key tools of precision psychiatry, we analyze the cost-utility of test screening of CYP2C19 and CYP2D6 for patients suffering from major depressive disorder (MDD) and try to understand the main drivers that influence the cost-utility. Methods: We developed two pharmacoeconomic nonhomogeneous Markov models to test the cost-utility, from an Italian societal perspective, of pharmacogenetic testing genetic to characterize the metabolizing profiles of cytochrome P450 (CYP) 2C19 and CYP2D6 in a hypothetical case study of patients suffering from major depressive disorder (MDD). The model considers different scenarios of adjustment of antidepressant treatment according to the patient's metabolizing profile or treatment over a period of 18 weeks. The uncertainty of model parameters is tested through both a probabilistic sensitivity analysis and a one-way deterministic sensitivity analysis, and these results are used in a post-hoc analysis to understand the main drivers of three alternative cost-effectiveness levels ("poor," "standard," and "high"). These drivers are first evaluated from an exploratory multidimensional perspective and next from a predictive perspective as the probability that a patient belongs to a specific cost-effectiveness level is estimated on the basis of a restricted set of parameters used in the original pharmacoeconomic model. Results: The models for CYP2C19 and CYP2D6 indicate that screening has an incremental cost-effectiveness ratio of 60,000€ and 47,000€ per quality-adjusted life year (QALY), respectively. The probabilistic sensitivity analysis shows that the treatments are cost-effective for a 75,000€ willingness to pay (WTP) threshold in 58% and 63% of the Monte Carlo replications, respectively. The post-hoc analysis highlights the factors that allow us to clearly discriminates poor cost-effectiveness from high cost-effectiveness scenarios and demonstrates that it is possible to predict with reasonable accuracy the cost-effectiveness of a genetic test and the associated therapeutic pattern. Conclusions: Our findings suggest that screenings for both CYP2C19 and CYP2D6 enzymes for patients with MDD are cost-effective for a WTP threshold of 75,000€ per QALY, and provide relevant suggestions about the most important aspects to be further explored in clinical studies aimed at addressing the cost-effectiveness of genetic testing for patients diagnosed with MDD.
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Some children are more affected by specific family environments than others, as a function of differences in their genetic make-up. However, longitudinal studies of genetic moderation of parenting effects during early childhood have not been conducted. We examined developmental profiles of child behavior problems between 18 months and age 8 in a longitudinal parent–offspring sample of 361 adopted children. In toddlerhood (18 months), observed structured parenting indexed parental guidance in service of task goals. Biological parent psychopathology served as an index of genetic influences on children’s behavior problems. Four profiles of child behavior problems were identified: low stable (11%), average stable (50%), higher stable (29%), and high increasing (11%). A multinominal logistic regression analysis indicated a genetically moderated effect of structured parenting, such that for children whose biological mother had higher psychopathology, the odds of the child being in the low stable group increased as structured parenting increased. Conversely, for children whose biological mother had lower psychopathology, the odds of being in the low stable group was reduced when structured parenting increased. Results suggest that increasing structured parenting is an effective strategy for children at higher genetic risk for psychopathology, but may be detrimental for those at lower genetic risk.
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This study presents a novel ensemble regression model for forecasts of the hypoxic area (HA) in the Louisiana–Texas (LaTex) shelf. The ensemble model combines a zero-inflated Poisson generalized linear model (GLM) and a quasi-Poisson generalized additive model (GAM) and considers predictors with hydrodynamic and biochemical features. Both models were trained and calibrated using the daily hindcast (2007–2020) by a three-dimensional coupled hydrodynamic–biogeochemical model embedded in the Regional Ocean Modeling System (ROMS). Compared to the ROMS hindcasts, the ensemble model yields a low root-mean-square error (RMSE) (3256 km2), a high R2 (0.7721), and low mean absolute percentage biases for overall (29 %) and peak HA prediction (25 %). When compared to the shelf-wide cruise observations from 2012 to 2020, our ensemble model provides a more accurate summer HA forecast than any existing forecast models with a high R2 (0.9200); a low RMSE (2005 km2); a low scatter index (15 %); and low mean absolute percentage biases for overall (18 %), fair-weather summer (15 %), and windy-summer (18 %) predictions. To test its robustness, the model is further applied to a global forecast model and produces HA prediction from 2012–2020 with the adjusted predictors from the HYbrid Coordinate Ocean Model (HYCOM). In addition, model sensitivity tests suggest an aggressive riverine nutrient reduction strategy (92 %) is needed to achieve the HA reduction goal of 5000 km2.
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Stress hormones and their impacts on whole organism metabolic rates are usually considered as appropriate proxies for animal energy budget that is the foundation of numerous concepts and models aiming at predicting individual and population responses to environmental stress. However, the dynamics of energy re-allocation under stress make the link between metabolism and corticosterone complex and still unclear. Using ectopic application of corticosterone for 3, 11 and 21 days, we estimated a time effect of stress in a lizard (Zootoca vivipara). We then investigated whole organism metabolism, muscle cellular O2 consumption and liver mitochondrial oxidative phosphorylation processes (O2 consumption and ATP production) and ROS production. The data showed that while skeletal muscle is not impacted, stress regulates the liver mitochondrial functionality in a time-dependent manner with opposing pictures between the different time expositions to corticosterone. While 3 days exposition is characterized by lower ATP synthesis rate and high H2O2 release with no change in the rate of oxygen consumption, the 11 days exposition reduced all three fluxes of about 50%. Oxidative phosphorylation capacities in liver mitochondria of lizard treated with corticosterone for 21 days was similar to the hepatic mitochondrial capacities in lizards that received no corticosterone treatment but with 40% decrease in H2O2 production. This new mitochondrial functioning allows a better capacity to respond to the energetic demands imposed by the environment but do not influence whole organism metabolism. In conclusion, global mitochondrial functioning has to be considered to better understand the proximal causes of the energy budget under stressful periods.
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Parasitism among individuals in a population often varies more than expected by chance only, leading to parasite aggregation, which is a parameter of paramount importance in parasite population dynamics and particularly in vector-borne epidemiology. However, the origin of this phenomenon is yet not fully elucidated. An increasing body of literature has demonstrated that individuals vary consistently in their behaviour, which is referred to as animal personality. Such behavioural variation could potentially lead to different encounter rates with parasites. To test this hypothesis, the relationship between personality and burden with ticks (Ixodes spp.) in the bank vole, Myodes glareolus (Schreber), was assessed. Wild rodents (eight females and 18 males) were live-trapped, identified, sexed, weighted, and inspected for ticks. Behavioural profiling was then performed using standardised tests measuring activity/exploration and boldness with a combination of automatically and manually recorded behavioural variables summarised using multivariate analyses. The resulting personality descriptors and questing tick variables were used as explanatory variables in negative binomial generalised linear models of tick burden and Bayesian simulations were performed to better estimate coefficients. Tick burden was associated to body mass and sex, but not to personality descriptors, which was mainly associated to activity/exploration. These results are discussed regarding the complex relationships among individual personality, physiological status, space use and health status.
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