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R: A Language and Environment for Statistical Computing

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... The slope was obtained from linear regression with the lm function in R (4.0.3; R Development Core Team, 2017) using temperature as an ordered categorical variable (6°C < 16°C). ...
... Correlations were calculated as Pearson's correlations using the cor function in R (4.0.3; R Development Core Team, 2017). Population structure may confound the correlation between phenotype and climate. ...
... The variance decomposition for initial size into variance explained by winter temperature and seed size was done with a randomeffect model where initial size was explained by winter temperature and seed size, using the lmer and VarCorr functions from the lme4 package (1.1.27.1; Bates et al., 2015) in R (4.0.3; R Development Core Team, 2017). The seed size-corrected correlation between initial size and winter temperature was estimated with the lme function from the nlme package (3.1.152; ...
Article
We investigated early vegetative growth of natural Arabidopsis thaliana accessions in cold, nonfreezing temperatures, similar to temperatures these plants naturally encounter in fall at northern latitudes. We found that accessions from northern latitudes produced larger seedlings than accessions from southern latitudes, partly as a result of larger seed size. However, their subsequent vegetative growth when exposed to colder temperatures was slower. The difference was too large to be explained by random population differentiation, and is thus suggestive of local adaptation, a notion that is further supported by substantial transcriptome and metabolome changes in northern accessions. We hypothesize that the reduced growth of northern accessions is an adaptive response and a consequence of reallocating resources toward cold acclimation and winter survival.
... Pre-processing of the data, such as the elimination of the non-informative peaks, QC-based robust LOESS (locally estimated scatterplot smoothing) signal correction (QC-RLSC) [36], the normalization by IS and sample weight, was performed using the in-house script written in R (version 4.0.3) [37] and run in RStudio [38]. LOESS smoothing was applied to the pooled QC data with a smoother span value of 0.5 and spline interpolation. ...
... The statistical test was conducted in R (version 4.0.3) [37] using the FSA package [39]. ...
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Lipids are biochemical compounds that are substantially present in coffee beans. However, lipids in coffee have not been comprehensively studied thus far and have not been used to differentiate its geographical origin. This study aimed to investigate the applicability of lipid profiling for use in coffee origin authentication. In this study, Indonesian superior coffee originating from six major producing regions was used. Lipid extraction from roasted coffee was subjected to a high-performance liquid chromatography coupled with triple-quadrupole mass spectrometry (LC–MS/MS). The obtained data were analyzed using the multivariate approach, including partial least squares discriminant analysis (PLS-DA), principal component analysis, and clustering analysis. The LC–MS/MS analysis tentatively identified 85 lipid species from five global lipid classes, such as neutral lipids, sphingolipids, sterol, glycerophospholipids, and glyceroglycolipids. The PLS-DA model exhibited an accuracy of 90%–100% in discriminating the origins of coffee based on receiver operating characteristics–area under the curve analysis. Therefore, the lipid profile obtained from the LC–MS/MS analysis can be applied to determine the geographical origin of coffee. The selected features showed high reliability as descriptor compounds in the validation analysis, as indicated on the natural separation of the unsupervised model. The results of this research provide solid evidence for the discrimination of the origin of coffee based on its lipid profile. Moreover, it might benefit the coffee industry to establish an advanced method for determining the origin of coffee.
... -In the Appendix, following the excellent approach from [49], we provide the implementations of the most interesting algorithms. For that, we use the R [397] and C++11 programming language. In the latter case, the Rcpp package classes [177] are used as a link between these two languages. ...
... [397] environment handles vector and matrix computations. In particular: -The set of natural numbers, {1, 2, . . . ...
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A proper fusion of complex data is of interest to many researchers in diverse fields, including computational statistics, computational geometry, bioinformatics, machine learning, pattern recognition, quality management, engineering, statistics, finance, economics, etc. It plays a crucial role in: synthetic description of data processes or whole domains, creation of rule bases for approximate reasoning tasks, reaching consensus and selection of the optimal strategy in decision support systems, imputation of missing values, data deduplication and consolidation, record linkage across heterogeneous databases, and clustering. This open-access research monograph integrates the spread-out results from different domains using the methodology of the well-established classical aggregation framework, introduces researchers and practitioners to Aggregation 2.0, as well as points out the challenges and interesting directions for further research.
... The data have been examined on the R statistic platform adopting linear mixed-effects modeling utilizing the lme4 (Bates et al., 2015) and lmerTest packages (Kuznetsova et al., 2015;R Core Team, 2016). Mixed-effects modeling enabled both random and fixed effects to be included. ...
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The present study investigated the effects of L1-L2 congruency, collocation type, and restriction on L2 collocational processing. Advanced Chinese learners of English and native English-speaking controls performed an online acceptability judgment task to investigate how advanced L2 learners processed congruent (sharing the same meaning and structure in L1 language) collocations and English-only (not equivalent in L1 construction) collocations with the same node (right) word and a different collocate (left). The experimental materials included verb-noun (VN), adjective-noun (AN) collocations, free (less fixed), and restricted (more fixed) collocations chosen from BNC. The results revealed that (i) The non-native speakers were sensitive to L1-L2 congruency, but the native speakers were not. (ii) The native speakers were sensitive to collocation restriction, whereas the non-native speakers were not. These results lend initial support to the mapping hypothesis and open choice principle of L2 collocational processing for Chinese English learners.
... We built generalized linear models (GLMs) between each landscape metric and each response variable using the multifit function 60 in R version 3.3.2 61 . We built one GLM for each buffer size, thereby testing 544 models in all (17 buffers × 4 response variables × 8 landscape metrics). ...
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Reversing large-scale habitat degradation and deforestation goes beyond what can be achieved by site-level ecological restoration and a landscape ecology perspective is fundamental. Here we assess the relative importance of tree cover and its configuration on forest-dependent birds and late-successional tree seedlings in restoration sites in southern Costa Rica. The abundance and species richness of birds increased in landscapes with more corridors, higher tree cover, and lower levels of fragmentation, highlighting the importance of riparian corridors for connectivity, and continuous tree cover as suitable habitat. Landscape variables affected abundance and species richness of seedlings similarly, but effects were weaker, possibly because seedlings face establishment limitation in addition to dispersal limitation. Moreover, the scale of landscape effects on seedlings was small, likely because proximal individual trees can significantly influence recruitment in restoration plots. Results underscore the importance of incorporating landscape-level metrics to restoration projects, as knowing the extent, and how the landscape may affect restoration outcomes can help to infer what kind of species will arrive to restoration plots.
... We used R software 25 for the data analyses. ...
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Background The Omicron wave of COVID-19 in England peaked in January 2022 resulting from the rapid transmission of the Omicron BA.1 variant. We investigate the spread and dynamics of the SARS-CoV-2 epidemic in the population of England during February 2022, by region, age and main SARS-CoV-2 sub-lineage. Methods In the REal-time Assessment of Community Transmission-1 (REACT-1) study we obtained data from a random sample of 94,950 participants with valid throat and nose swab results by RT-PCR during round 18 (8 February to 1 March 2022). Findings We estimated a weighted mean SARS-CoV-2 prevalence of 2.88% (95% credible interval [CrI] 2.76–3.00), with a within-round effective reproduction number (R) overall of 0.94 (0·91–0.96). While within-round weighted prevalence fell among children (aged 5 to 17 years) and adults aged 18 to 54 years, we observed a level or increasing weighted prevalence among those aged 55 years and older with an R of 1.04 (1.00–1.09). Among 1,616 positive samples with sublineages determined, one (0.1% [0.0–0.3]) corresponded to XE BA.1/BA.2 recombinant and the remainder were Omicron: N=1047, 64.8% (62.4–67.2) were BA.1; N=568, 35.2% (32.8–37.6) were BA.2. We estimated an R additive advantage for BA.2 (vs BA.1) of 0.38 (0.34–0.41). The highest proportion of BA.2 among positives was found in London. Interpretation In February 2022, infection prevalence in England remained high with level or increasing rates of infection in older people and an uptick in hospitalisations. Ongoing surveillance of both survey and hospitalisations data is required. Funding Department of Health and Social Care, England.
... transformed to control for heteroscedasticity) and richness of ants at each sampling point were used as response variables with vertical height as a continuous explanatory variable and horizontal position of vertical transects as a categorical explanatory variable.To explore vertical and horizontal ant assemblage composition, we used nonmetric multidimensional scaling (NMDS) ordination of both abundance-based (ln[x + 1] transformed) assemblages (Bray-Curtis distances) and species presence/absence data (Jaccard distances) assemblages at each sampling point. Because results from ordinations using abundance and presence-absence dissimilarities were similar, we mainly present abundance-based ordination results.To increase sample size within groups for the vertical analyses, and so statistical power, we assigned all sampling points within 10 m bins to the same groups (i.e., 0-10 m, 10-20 m, etc.), testing for differences among these groupings using PERMANOVA (adonis function in the vegan package, 999 permutations;Oksanen et al., 2013, R Development Core Team, 2019. ...
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Abiotic and biotic factors structure species assembly in ecosystems both horizontally and vertically. However, the way community composition changes along comparable horizontal and vertical distances in complex three-dimensional habitats, and the factors driving these patterns, remains poorly understood. By sampling ant assemblages at comparable vertical and horizontal spatial scales in a tropical rainforest, we tested hypotheses that predicted differences in vertical and horizontal turnover explained by different drivers in vertical and horizontal space. These drivers included environmental filtering, such as microclimate (temperature, humidity, and photosynthetic photon flux density) and microhabitat connectivity (leaf area), which are structured differently across vertical and horizontal space. We found that both ant abundance and richness decreased significantly with increasing vertical height. Although the dissimilarity between ant assemblages increased with vertical distance, indicating a clear distance-decay pattern, the dissimilarity was higher horizontally where it appeared independent of distance. The pronounced horizontal and vertical structuring of ant assemblages across short distances is likely explained by a combination of microclimate and microhabitat connectivity. Our results demonstrate the importance of considering three-dimensional spatial variation in local assemblages and reveal how highly diverse communities can be supported by complex habitats.
... All of the data processing and statistical analyses were performed using the statistical software program R (version 4.1.1 [27]). First, reads that were not able to be identified to species level were removed. ...
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Microbiomes are essential to a host’s physiology and health. Despite the overall importance of microbiomes to animal health, they remain understudied in wildlife. Microbiomes function as physical barriers to invading pathogens, and changes in the diversity or composition of microbes within a host may disrupt this barrier. In order to use microbiomes in wildlife ecology, knowledge of the natural variation within and among species is essential. We compare the diversity and composition of two avian species that share the same habitat and niche in our study area, the western screech-owl ( Megascops kennicottii ) and the whiskered screech-owl ( M. trichopsis ). We used a targeted 16S sequencing method to improve the taxonomic resolution of microbiomes. We found similar measures of alpha diversity between species and sample types (cloacal samples vs. fecal samples). However, there were significant differences in bacterial species richness among nestlings from different nest boxes, and the composition differed between the two bird species and among nestlings from different nest boxes. Western screech-owls had more variation in alpha diversity and composition and had fewer bacterial species in their core microbiome than whiskered screech-owls. Siblings are likely to yield similar findings for microbiomes; thus, sampling nestlings from different nests may be most informative for monitoring population-level changes.
... In this paper, we introduce an open source R-script and package [16] designed as an assistant tool, AquaDesign, to facilitate development of new animal species productions in monoculture and polyculture based on niche analyses [17,18]. Our goal is to use the large amount of biogeographic and environmental information available in public databases to provide a pragmatic and operational way to highlight species or species combination that could be further considered in new aquaculture developments. ...
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Farming new species and promoting polyculture can enhance aquaculture sustainability. This implies to define the rearing conditions that meet the ecological requirements of a target species and/or to assess if different species can live in the same farming environment. However, there is a large number of rearing conditions and/or taxon combinations that can be considered. In order to minimise cumbersome and expensive empirical trials to explore all possibilities, we introduce a tool, AquaDesign. It is based on a R-script and package which help to determine farming conditions that are most likely suitable for species through in silico assessment. We estimate farming conditions potentially suitable for an aquatic organism by considering the species niche. We define the species n-dimensional niche hypervolume using a correlative approach in which the species niche is estimated by relating distribution data to environmental conditions. Required input datasets are mined from several public databases. The assistant tool allows users to highlight (i) abiotic conditions that are most likely suitable for species and (ii) combinations of species potentially able to live in the same abiotic environment. Moreover, it offers the possibility to assess if a particular set of abiotic conditions or a given farming location is potentially suitable for the monoculture or the polyculture of species of interest. Our tool provides useful pieces of information to develop freshwater aquacultures. Using the large amount of biogeographic and abiotic information available in public databases allows us to propose a pragmatic and operational tool even for species for which abiotic requirements are poorly or not available in literature such as currently non-produced species. Overall, we argue that the assistant tool can act as a stepping stone to promote new aquatic productions which are required to enhance aquaculture sustainability.
... Furthermore, partial η 2 was used as a measure of the effect size of each independent variable (27). The analysis was performed with the R Project for statistical computing, version 4.0.5 (28 or using hormonal contraception or hormonal replacement therapy were enrolled in our study. Eight patients were admitted after relapsing while using long-term maintenance antidepressant treatment; two patients were not administered any medication before admission. ...
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Objectives Osteocalcin is a protein secreted by osteoblasts with a versatile endocrine role. Several domains in which it plays a role—stress response, monoamine synthesis, and cognitive functioning—are implicated also in the pathophysiology of major depressive disorder. In search of possible objective biomarkers of depression, the aim of the study was to assess the relationship between osteocalcin and depressive symptoms during the treatment of depressive episode.Methods The study included female inpatients with at least moderate depressive episode. In these patients, depression severity was measured using the Montgomery-Åsberg Depression Rating Scale (MADRS), and osteocalcin levels were assessed before the stabilization of antidepressive treatment and after 6 weeks. Relationships between osteocalcin levels and symptoms were analyzed with mixed-effect and linear models, taking into account age, menopausal status, and body mass index.ResultsIn 11 out of 13 enrolled inpatients, osteocalcin levels decreased during the first 6 weeks of treatment; this decrease was significant according to the mixed-effects model (t = −2.345, p = 0.019). According to the linear model, this decrease was significantly associated with reduction in depressive symptom severity (t = 2.673, p = 0.028). Osteocalcin was not associated with initial depressive symptom severity, and initial osteocalcin levels did not predict response to treatment. Limitations of the study include low sample size and inclusion of both pre- and postmenopausal women of various ages.Conclusions This preliminary study suggests that osteocalcin may be a candidate biomarker of antidepressive treatment response and that this topic warrants further investigation.
... Thus, we conducted a total of 54 analyses for both scales of our bobcat study (27 bobcats x 2 scales). All statistical analyses were performed and figures were created in program R 3.5.1 [50]. ...
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Understanding habitat selection of top predators is critical to predict their impacts on ecological communities and interactions with humans, particularly in recovering populations. We analyzed habitat selection in a recovering population of bobcats ( Lynx rufus ) in south-central Indiana using a Random Forest model. We predicted that bobcats would select forest habitat and forest edges but avoid agriculture to maximize encounters with prey species. We also predicted that bobcats would avoid developed areas and roads to minimize potential antagonistic interactions with humans. Results partially supported our predictions and were consistent with bobcats in the early stages of population expansion. Bobcats exhibited elevated use near forest edges, thresholds of avoidance near agriculture, and thresholds of selection for low and intermediate habitat heterogeneity. Bobcats exhibited peak probability of use 1–3 km from major roads, >800 m from minor roads, and <1km from developed areas, suggesting tradeoffs in reward for high-quality hunting areas and mortality risk. Our Random Forest model highlighted complex non-linear patterns and revealed that most shifts in habitat use occurred within 1 km of the edge of each habitat type. These results largely supported previous studies in the Midwest and across North America but also produced refinements of bobcat habitat use in our system, particularly at habitat boundaries. Refined models of habitat selection by carnivores enable improved prediction of the most suitable habitat for recovering populations and provides useful information for conservation.
... Bayesian Information Criterion (BIC), a model selection criterion, identified four, possibly five genetic clusters as the best model fit for the number of the principal components (Supplementary Figure S1) (Peiffer et al., 2014). The first principal component separated Brazilian accessions from the rest of the TSC panel [ Figure 4A generated using R-ArcGIS (R Core Development Team, 2015)], and with four principal components, Figure 4B demonstrates that, first, lowland vs. highland accessions can be separated by a major principal component; second, Caribbean accessions are genetically distinguishable from Mexican accessions; and third, northern South American maize could be a genetic mixture of lowland Mexican and Caribbean maize. These findings support that the spread of Mesoamerican lowland landraces was through Central America to South America (yellow dots of Figure 4B) (Vigouroux et al., 2008). ...
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The tar spot complex (TSC) is a devastating disease of maize ( Zea mays L.), occurring in 17 countries throughout Central, South, and North America and the Caribbean, and can cause grain yield losses of up to 80%. As yield losses from the disease continue to intensify in Central America, Phyllachora maydis , one of the causal pathogens of TSC, was first detected in the United States in 2015, and in 2020 in Ontario, Canada. Both the distribution and yield losses due to TSC are increasing, and there is a critical need to identify the genetic resources for TSC resistance. The Seeds of Discovery Initiative at CIMMYT has sought to combine next-generation sequencing technologies and phenotypic characterization to identify valuable alleles held in the CIMMYT Germplasm Bank for use in germplasm improvement programs. Individual landrace accessions of the “Breeders' Core Collection” were crossed to CIMMYT hybrids to form 918 unique accessions topcrosses (F1 families) which were evaluated during 2011 and 2012 for TSC disease reaction. A total of 16 associated SNP variants were identified for TSC foliar leaf damage resistance and increased grain yield. These variants were confirmed by evaluating the TSC reaction of previously untested selections of the larger F1 testcross population (4,471 accessions) based on the presence of identified favorable SNPs. We demonstrated the usefulness of mining for donor alleles in Germplasm Bank accessions for newly emerging diseases using genomic variation in landraces.
... where h (height) is the depth of a rooted soil patch [m], and r (radius) is half of the length of a rooted soil patch [m]. The direct correlation of soil penetration resistance with sedimentation and wild boar rooting (rooting-ring-control comparisons) were analyzed by Generalized Estimating Equations (GEE) in R [27], with the "geepack" package [28]. Since these compaction values were highly autocorrelated in similar depths, GEE was an appropriate method to handle issues related to any type of temporal or spatial autocorrelation [29] by selecting the best working correlation structure by the QIC (quasi-likelihood under the independence model criterion) value of each equation. ...
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Forest soils are shaped by various processes, like runoff, erosion, sedimentation and bioturbation. A better understanding of the interactions between abiotic and biotic soil-forming processes, including wild boar (Sus scrofa) rooting (i.e., subsurface foraging), enhances adequate management of forest ecosystems. We hypothesized that intense soil sedimentation influences wild boar rooting occurrence and that wild boars modify the outcome of the sedimentation process by redistributing soil layers. This study was conducted in the Babat Valley, Hungary. We estimated the availability of sedimented and non-sedimented patches and the occurrence of boar rooting. Surveys and samplings were done along transects, over consecutive months, where the impact of rooting on the physical and chemical characteristics of soil was measured by comparing them between control and rooted sites. We found that non-sedimented, steep areas were preferred areas for rooting. Sedimentation processes have a higher impact on soil chemical characteristics and soil layer composition than wild boar rooting. We conclude that mitigation of soil degradation can be more effective by reducing adverse abiotic processes rather than wild boar population control.
... Additionally, influence diagnostic tests were done. Analyses were conducted with SAS 9.4 (SAS Institute, Cary, NC) or the R platform (21). No imputation was done for missing data, considering the exploratory nature of the study, overall low occurrence of missing CGM data, and plausibility that data are, for practical purposes, missing completely at random. ...
... For the statistical analyses, OK and IDW interpolations were performed using the "gstat" packages in R 4.0.4 [39] and RStudio (version 1.3.1093, Boston, MA, USA) [40]. ...
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Agricultural development in northern polar areas has potential as a result of global warming. Such expansion requires modern soil surveys and large-scale maps. In this study, the abandoned arable experimental field founded by I.G. Eichfeld one century ago in Salekhard city (Russian Arctic), located in the polar circle, was investigated. Our aims were to assess the nutritional soil properties and their spatial variability. For spatial assessment and mapping, ordinary kriging (OK) and inverse distance-weighted (IDW) methods were employed. We found that due to long-term agriculture use, the soil cover was represented by a unique Plaggic Podzol (Turbic) that is not typical of the region. The soil was characterized by relatively low soil organic carbon (SOC) content, high acidity and a high content of plant-available forms of phosphorus in the humus-accumulative horizon. The results showed that some properties (pH H2O, pH CaCl2) were characterized by large-scale heterogeneity and showed clear spatial dependence. However, some properties (ammonium and nitrate nitrogen, basal respiration) showed a pure-nugget effect, presumably due to experimentation with fertilizer over a long period of time.
... The means were compared using the Tukey test (p≤0.05). All analyzes were performed using R statistical software, version 3.6.1 [25]. Weight loss was not influenced by the application of phytoregulators (Fig. 1). ...
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Aims: This work aimed to verify the efficiency of the phytoregulators naphthalene acetic acid (NAA) and methyl jasmonate (MeJa) in maintaining the postharvest quality of 'Laetitia' plum fruits, stored under refrigeration. Study design: The experimental design used was completely randomized with three treatments and five repetitions of 30 fruits/repetition. Place and Duration of Study: The experiment was carried out with 'Laetitia' plums from a commercial orchard in the municipality of Catanduvas, SC (27° 4' 3'' S and 51° 39' 47'' W), during the 2017/18 harvest. Methodology: The fruits were treated with distilled water (control), MeJa (10-4 M), and NAA (10 mg. L-1); and stored in chambers with Biochemical Oxygen Demand (BOD), maintained at a temperature of 4±1°C and relative humidity of 85±3%, for 35 days and another three days at ambient conditions (23±1°C). The main quality attributes were evaluated after storage. Results: Weight loss, soluble solids content, and pulp firmness are not affected by the application Original Research Article Gularte et al.; JEAI, X(X): xxx-xxx, 20YY; Article no.JEAI.90306 2 of phytoregulators. The application of NAA 10 mg.L-1 accelerated fruit ripening and showed no positive effects. Treatment of 'Laetitia' plums with MeJa 10-4 M decreases ethylene production, respiration, and lipid peroxidation. This treatment also increased the concentration of antioxidants and total phenolic compounds. Fruit treatment with MeJa 10-4 M significantly reduced the incidence and severity of internal browning of the 'Laetitia' plum. Conclusion: The treatment of 'Laetitia' plums with MeJa 10-4 M has positive effects on post-harvest storage, mainly reducing internal browning.
... All analyses and figures were carried out using the R software program, version 3.2.2 [33]. ...
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Background Incisional hernia (IH) is a common complication after abdominal surgery. Prevention of IH is matter of intense research. Prophylactic mesh reinforcement (PMR) has been shown to be promising in the minimization of IH risk after elective midline laparotomy. Methods Systematic review and meta-analysis of randomized controlled trials (RCTs) comparing PMR vs. primary suture closure (PSC). Risk ratio (RR) and standardized mean difference (MD) were used as pooled effect size measures whereas 95% confidence intervals (95%CI) were used to assess relative inference. Results Fourteen RCTs (2332 patients) were included. Overall, 1280 (54.9%) underwent PMR while 1052 (45.1%) PSC. Postoperative follow-up ranged from 12 to 67 months. The incidence of IH was reduced for PMR vs. PSC (13.4% vs. 27.5%). The estimated pooled IH RR for PMR vs. PSC is 0.38 (95% CI 0.24–0.58; p < 0.001). Stratified subgroup analysis according to mesh location shows a risk reduction for intraperitoneal (RR = 0.65; 95% CI 0.48–0.89), preperitoneal (RR = 0.18; 95% CI 0.04–0.81), retromuscular (RR = 0.47; 95% CI 0.24–0.92) and onlay (RR = 0.24; 95% CI 0.12–0.51) compared to PSC. The seroma RR was higher for PMR (RR = 2.05; p = 0.0008). No differences were found for hematoma (RR = 1.49; p = 0.34), surgical site infection (SSI) (RR = 1.17; p = 0.38), operative time (OT) (MD = 0.27; p = 0.413), and hospital length of stay (HLOS) (MD = -0.03; p = 0.237). Conclusions PMR seems effective in reducing the risk of IH after elective midline laparotomy compared to PSC in the medium-term follow-up. While the risk of postoperative seroma appears higher for PMR, hematoma, SSI, HLOS and OT seems comparable.
... [23], accessed through R (version 3.6.1) [24]. Data and code are provided in S2 Appendix. ...
Article
BACKGROUND: Prospective malaria public health interventions are initially tested for entomological impact using standardised experimental hut trials. In some cases, data are collated as aggregated counts of potential outcomes from mosquito feeding attempts given the presence of an insecticidal intervention. Comprehensive data i.e. full breakdowns of probable outcomes of mosquito feeding attempts, are more rarely available. Bayesian evidence synthesis is a framework that explicitly combines data sources to enable the joint estimation of parameters and their uncertainties. The aggregated and comprehensive data can be combined using an evidence synthesis approach to enhance our inference about the potential impact of vector control products across different settings over time. METHODS: Aggregated and comprehensive data from a meta-analysis of the impact of Pirimiphos-methyl, an indoor residual spray (IRS) product active ingredient, used on wall surfaces to kill mosquitoes and reduce malaria transmission, were analysed using a series of statistical models to understand the benefits and limitations of each. RESULTS: Many more data are available in aggregated format (N = 23 datasets, 4 studies) relative to comprehensive format (N = 2 datasets, 1 study). The evidence synthesis model had the smallest uncertainty at predicting the probability of mosquitoes dying or surviving and blood-feeding. Generating odds ratios from the correlated Bernoulli random sample indicates that when mortality and blood-feeding are positively correlated, as exhibited in our data, the number of successfully fed mosquitoes will be under-estimated. Analysis of either dataset alone is problematic because aggregated data require an assumption of independence and there are few and variable data in the comprehensive format. CONCLUSIONS: We developed an approach to combine sources from trials to maximise the inference that can be made from such data and that is applicable to other systems. Bayesian evidence synthesis enables inference from multiple datasets simultaneously to give a more informative result and highlight conflicts between sources. Advantages and limitations of these models are discussed.
... Collected data were analyzed by following statistical package software R version 3.6.2 [43][44][45]. Means were separated by Least Significant Difference (LSD) test with P < 0 05 and the analysis of variance was done as per the procedure described [46]. Nei's [47] genetic distance value was computed using the PowerMarker version 3.25 software [45]. ...
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Pummelo is one of the basic citrus species of horticultural importance for human health and nutrition security. It has wide genetic diversity due to its breeding behavior during the domestication process. The present research was performed to study the fruits traits and characterization of the studied 21 pummelo genotypes with morphological, fruit quality parameters, and SSR markers. Principal component analysis (PCA) was done to get PC individual plot and clustering the genotypes in five main clusters based on 17 morphological traits. The highest number (08) of genotypes was grouped in cluster V and the lowest (01) in cluster III. Genotypes resided with the highest genetic distance in the individual biplots are promising for suitable parents. Again, molecular characterization or cluster analysis was performed with 5 SSR markers. The PIC values ranged from a low of 0.66 (CAC23) to a high of 0.8787 (TAA41) and averaged 0.78. TAA41 presented the second largest (47 bp) difference among allele size range and the largest (11) number of alleles with the highest gene diversity value (0.88). The average genetic distance among the 21 pummelo genotypes were 0.8362. The NJ cluster analysis led to the grouping of the pummelo genotypes in three major clusters (I, II, and III). The genotypes resided in the similar cluster should be avoided for pummelo improvement. The findings of this research would be useful to select desirable parents for future pummelo breeding program.
... The data analysis in this paper was mainly conducted in R 4.0.3 73 , with support of Microsoft Excel (Microsoft 365) and Stata (v16.0). The inequality measures IOV and POL were calculated using the R Package Agrmt 1.42.4 74 . ...
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Water security requires not only sufficient availability of and access to safe and acceptable quality for domestic uses, but also fair distribution within and across populations. However, a key research gap remains in understanding water security inequality and its dynamics, which in turn creates an impediment to tracking progress towards sustainable development. Therefore, we analyse the inequality of water security using data from 7603 households across 28 sites in 22 low- and middle-income countries, measured using the Household Water Insecurity Experiences Scale. Here we show an inverted-U shaped relationship between site water security and inequality of household water security. This Kuznets-like curve suggests a process that as water security grows, the inequality of water security first increases then decreases. This research extends the Kuznets curve applications and introduces the Development Kuznets Curve concept. Its practical implications support building water security and achieving more fair, inclusive, and sustainable development. A new study considering data from 7603 households across 28 sites in 22 low- and middle-income countries show that inequality of household water security follows a Development Kuznets Curve.
... Two simulations were set up using R statistical language [21] with parameters selected to closely resemble the observed results of the RECOVERY trial. The first of these simulations was based on two arms of the RECOVERY trial: namely the dexamethasone arm and the control arm. ...
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Background The Randomised Evaluation of COVID-19 Therapy (RECOVERY) trial is aimed at addressing the urgent need to find effective treatments for patients hospitalised with suspected or confirmed COVID-19. The trial has had many successes, including discovering that dexamethasone is effective at reducing COVID-19 mortality, the first treatment to reach this milestone in a randomised controlled trial. Despite this, it continues to use standard or ‘fixed’ randomisation to allocate patients to treatments. We assessed the impact of implementing response adaptive randomisation within RECOVERY using an array of performance measures, to learn if it could be beneficial going forward. This design feature has recently been implemented within the REMAP-CAP platform trial. Methods Trial data was simulated to closely match the data for patients allocated to standard care, dexamethasone, hydroxychloroquine, or lopinavir-ritonavir in the RECOVERY trial from March-June 2020, representing four out of five arms tested throughout this period. Trials were simulated in both a two-arm trial setting using standard care and dexamethasone, and a four-arm trial setting utilising all above treatments. Two forms of fixed randomisation and two forms of response-adaptive randomisation were tested. In the two-arm setting, response-adaptive randomisation was implemented across both trial arms, whereas in the four-arm setting it was implemented in the three non-standard care arms only. In the two-arm trial, randomisation strategies were performed at the whole trial level as well as within three pre-specified patient subgroups defined by patients’ respiratory support level. Results All response-adaptive randomisation strategies led to more patients being given dexamethasone and a lower mortality rate in the trial. Subgroup specific response-adaptive randomisation reduced mortality rates even further. In the two-arm trial, response-adaptive randomisation reduced statistical power compared to FR, with subgroup level adaptive randomisation exhibiting the largest power reduction. In the four-arm trial, response-adaptive randomisation increased statistical power in the dexamethasone arm but reduced statistical power in the lopinavir arm. Response-adaptive randomisation did not induce any meaningful bias in treatment effect estimates nor did it cause any inflation in the type 1 error rate. Conclusions Using response-adaptive randomisation within RECOVERY could have increased the number of patients receiving the optimal COVID-19 treatment during the trial, while reducing the number of patients needed to attain the same study power as the original study. This would likely have reduced patient deaths during the trial and lead to dexamethasone being declared effective sooner. Deciding how to balance the needs of patients within a trial and future patients who have yet to fall ill is an important ethical question for the trials community to address. Response-adaptive randomisation deserves to be considered as a design feature in future trials of COVID-19 and other diseases.
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The present dissertation investigates the development in the production and perception of inflectional morphology in second-language learners of English and the role of their mother tongue during this development. The data analysed in this thesis stem from three psycholinguistic experiments that examine the production and comprehension of English novel words (thus investigating the sublexicon without the activation of word meaning). The first experiment focuses on the perception of inflectional morphemes in English novel words in L2 students at the A0 to C1 proficiency levels. Reaction-times analysis has shown that L2 learners seem to be (similarly to native speakers (e.g., Post et al., 2008)) sensitive to the presence of morphosyntactic information at the sublexical level, and they appear to decompose inflected forms into stems and affixes during perception and conduct an implicit phonetic analysis of the stem. The presence of these patterns across all levels suggests that L2 performance might be influenced by L1: Czech is morphologically much richer than English, and Czech speakers might thus be in general sensitive to morphological analysis of words. The second experiment investigates the production of inflected forms, more specifically those of past tense, in L2 learners of English at the A1 to C1 levels (and in a control group of English native speakers) with an elicitation task. The analysis of produced forms has shown that the L2 learners display a progressive development from the application of default rules (at the A1 to B1 levels) to the use of analogy (in more proficient B2 and C1 levels), a procedure that is used productively by native speakers. Reaction-times analysis has shown that L1 Czech functions as a facilitator at the lowest language levels (items that are phototactically legal in both Czech and English are analysed more quickly). Given the findings of the first two experiments (pointing in partly different directions), I suggest the presence of redundant processing, which enables parallel activation of two (redundant) mechanisms. The third experiment focuses on language transfer, using a lexical decision task with the novel verbs from Experiment 2, paired with existing English words, and it assesses L2 learners distributed on a proficiency scale. Reaction-times analysis has shown that Czech has a mild facilitatory effect on performance, not only for the lowest language levels but also for more proficient learners, suggesting that transfer effects are not limited to non-proficient speakers. Altogether, the findings of this thesis offer complex look into how inflectional morphology develops in L2 learners from the lowest to the proficient levels and also into the role of L1. In the last chapter, I additionally discuss possible pedagogical implementations of these findings into an L2 classroom.
Thesis
Our everyday listening environment is a complex acoustic mixture that needs to be processed and filtered in order to access relevant auditory information. Cognitive resources are then required for the selective processing of a particular sound stream, and simultaneous filtering of irrelevant information. The engagement of these cognitive resources to understand an auditory message, leads to listening effort, especially in noisy environments. Listening effort has been investigated in the last two decades, using a large panel of methods. The work of this thesis aims at bringing new insights on the investigation of listening effort, first with the use of pupillometry, then based on the complementarity of different measures (subjective, behavioral and objective). A methodological investigation was first conducted on pupillometry data recorded during a word-in-noise task, among older hearing-impaired patients, with and without hearing-aids. Several analysis methods were compared, including different normalization techniques, baseline periods, and baseline durations. While the different normalization methods and baseline durations showed similar results, the choice of the baseline period turned out to have a crucial influence on conclusions. Indeed, anticipatory, pre-stimulus cognitive processes, such as attention mobilization were observed on pupil dilation when the baseline period was the most anterior, relative to the stimulus onset. The differences in pupil dilation were observed even at perfect intelligibility, highlighting the relevance of pupillometry as an objective measure of listening effort. The second axis of this work focused on the results of empirical studies in which several measures, including pupillometry, were concurrently used to assess listening effort. Empirical studies were conducted (1) in older hearing-impaired patients using subjective measures of effort and pupillometry during a word-in-noise task, (2) in normal-hearing young adults using pupillometry and sclap electroencephalography during a discrimination in noise task. The lack of correlation between self-assessed difficulty of the task and pupil responses in hearing-impaired listeners, suggests that the two measures address different aspects of effortful listening. Pupil responses allowed for the observation of anticipation processes, even at perfect intelligibility, while subjective measures described the overall perceived effort during the task. In normal-hearing young adults, the modulations of the cortical responses observed thanks to electroencephalography, were linked to the processing of the stimulation and the inhibition of the irrelevant sound source during discrimination. Pupillary responses, recorded simultaneously, brought information on participants' arousal state during the task. Results of both studies then suggest that the different measures complement each other, and that their combination can help for the understanding of the different cognitive processes involved during effortful listening. Overall, this PhD work brings insights on the use and processing of the pupillometric signal to explore listening effort. It also underlines the relevance of the use of pupillometry and its contribution for the study of listening effort, among distinct populations. Finally, it shows the complementarity of subjective and objective measures during the assessment of listening effort, supporting the idea that it is a multidimensional construct.
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Seed dispersal via dung (endozoochorous seed dispersal) is one of the vital impacts imposed by herbivores on rangeland habitats. The present research was aimed to assess the potential seed dispersal of plant species by different-sized herbivores of hare (Lepuscapensis), Persian gazelle (Gazelle subguttrosa) and wild goat (Capra aegagrus) in rangeland habitats of Central Iranin Kolah-Ghazi National Park. The number of five main habitats were selected for each herbivore.. Seed content of dung samples were determined in greenhouse germination experiments over a period of 8 months. In total, 3766 seedlings from 60 plant species (19, 43 and 45 seed species in dung samples of cape hare, Persian gazelle and wild goat, respectively), mainly annual with attractive inflorescence and small seeds were recorded in dung samples of the three herbivore species. Seed content found in all herbivores dung were differed significantly.in addition, number of dispersedseedlings was correlated to herbivores size. However, the observed differences in dung seed density of herbivore species was not related to their sizes; so that the highest and the least number of seeds were recorded in dung samplesof wild goat and Persian gazelle, respectively. Given that most of plant species recorded in the Park regenerate by seeds, and that seeds of different plant species dispersed by herbivore species, seed dispersal via dung of different-sized herbivores may play an important role in vegetation conservation and dynamics of these rangelands habitats, only if necessary environmental factors met. While increasing knowledge of plant seed dispersal, results of the present research can be specially applied in managing country’s protected ecosystems and rangeland habitats.
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The application of environmental DNA (eDNA) metabarcoding has revolutionised large scale biodiversity monitoring of aquatic ecosystems. Validation studies have been performed mainly in laboratories and mesocosm experiments, however large-scale field experiments are necessary to verify the robustness of eDNA based monitoring for more specific applications and different environmental conditions. Here, eDNA samples were collected from three fishponds with high fish density and broad species diversity during summer and autumn. This sampling design included a large number of spatial replicates evenly spaced across the pond surface and samples from the inflow, while pooled samples were used to test the effect of filtration volumes on detectability. Most common species were detected using eDNA, but rare species were often missed out under these high stocking densities. Average read counts and site occupancy positively correlated strongly with species abundance and biomass, with the exception of samples affected by PCR inhibition. Higher diversity detections were observed in autumn compared to summer samplings and in running compared to standing water. Fish communities detected in pooled samples reflect the overall community structure, and the species detectability increases with higher filtration volumes. This work highlights how eDNA based surveys can be optimised based on sampling conditions to achieve the highest overall detection, which has important implications for applying this method to aid management and policy initiatives.
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Herbivores face a broad range of defences when feeding on plants. By mixing diets, polyphagous herbivores are assumed to benefit during their development by gaining a better nutritional balance and reducing the intake of toxic compounds from individual plant species. Nevertheless, they also show strategies to metabolically cope with plant defences. In this study, we investigated the development of the polyphagous tansy leaf beetle, Galeruca tanaceti (Coleoptera: Chrysomelidae), on mono diets consisting of one plant species [cabbage (Brassica rapa), Brassicaceae; lettuce (Lactuca sativa), or tansy (Tanacetum vulgare), Asteraceae] vs. two mixed diets, both containing tansy. Leaves of the three species were analysed for contents of water, carbon and nitrogen, the specific leaf area (SLA) and trichome density. Furthermore, we studied the insect metabolism of two glucosinolates, characteristic defences of Brassicaceae. Individuals reared on cabbage mono diet developed fastest and showed the highest survival, while the development was slowest for individuals kept on tansy mono diet. Cabbage had the lowest water content, while tansy had the highest water content, C/N ratio and trichome density and the lowest SLA. Lettuce showed the lowest C/N ratio, highest SLA and no trichomes. Analysis of insect samples with UHPLC-DAD-QTOF-MS/MS revealed that benzyl glucosinolate was metabolised to N-benzoylglycine, N-benzoylalanine and N-benzoylserine. MALDI-Orbitrap-MS imaging revealed the localisation of these metabolites in the larval hindgut region. 4-Hydroxybenzyl glucosinolate was metabolised to N-(4-hydroxybenzoyl)glycine. Our results highlight that G. tanaceti deals with toxic hydrolysis products of glucosinolates by conjugation with different amino acids, which may enable this species to develop well on cabbage. The high trichome density and/or specific plant chemistry may lower the accessibility and/or digestibility of tansy leaves, leading to a poorer beetle development on pure tansy diet or diet mixes containing tansy. Thus, diet mixing is not necessarily beneficial, if one of the plant species is strongly defended.
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Drought is expected to increase in future climate scenarios. Although responses to drought of individual functional traits are relatively well-known, simultaneous changes across multiple traits in response to water scarcity remain poorly understood despite its importance to understand alternative strategies to resist drought. We grew 52 herbaceous species in monocultures under drought and control treatments and characterized the functional space using seven measured above- and below-ground traits: plant height, leaf area, specific leaf area, leaf dry matter content, specific root length, average root diameter, and root dry matter content. Then, we estimated how each species occupied this space and the amount of functional space occupied in both treatments using trait probability density functions. We also estimated intraspecific trait variability (ITV) for each species as the dissimilarity in trait values between the individuals of each treatment. We then mapped drought resistance and ITV in the functional space using generalized additive models. The response of species to drought strongly depended on their traits, with species that invested more in root tissues and conserved small size being both more resistant to drought and having higher ITV. We also observed a significant trend of trait displacement towards less conservative strategies. However, these changes depended strongly on the trait values of species in the control treatment, with species with different traits having opposing responses to drought. These contrasting responses resulted in lower trait variability in the species pool in drought compared to control conditions. Our results suggest strong trait filtering acting on conservative species as well as the existence of an optimal part in the functional space to which species converge under drought. Our results show that changes in species trait-space occupancy are key to understand plant strategies to withstand drought, highlighting the importance of individual variation in response to environmental changes, and suggest that community-wide functional diversity and biomass productivity could decrease in a drier future. Knowing these shifts will help to anticipate changes in ecosystem functioning facing climate change.
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Interspecific hybridization has varied consequences for offspring fitness, with implications for the maintenance of species integrity. Hybrid vigour, when it occurs, can peak in first-generation (F1) hybrids and then decline in advanced-generation (F2+) hybrids. This hybrid breakdown, together with the processes affecting patterns of hybridization and hybrid fitness, determine the evolutionary stability of hybrid zones. An extensive hybrid zone in North America involving the cattails Typha latifolia, T. angustifolia, and their invasive hybrid T. × glauca is characterized by hybrid vigour among F1s, but the fitness of advanced-generation hybrids has not been studied. We compared seed germination and plant growth of T. latifolia (parental L), F1 T. × glauca (F1), hybrid backcrosses to T. angustifolia (bcA) and T. latifolia (bcL), and advanced-generation (F2) hybrids. Consistent with expectations under hybrid breakdown, we found reduced plant growth for F2 hybrids in comparison with F1s (plant height and above-ground biomass) and parental Ls (above-ground biomass). Backcrossed hybrids had intermediate measures of plant growth and bcLs were characterized by reduced seed germination in comparison with parental Ls. Hybrid breakdown could make the formation of F1s in North America finite because (1) hybridization among cattails is asymmetric, with T. angustifolia but not T. latifolia subject to genetic swamping, and (2) T. angustifolia is less common and subject to competitive displacement by F1s. Hybrid breakdown is therefore expected to reduce hybrid frequencies over time, contributing to the long-term maintenance of T. latifolia – the only native cattail in the study region.
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Little is known about the effects of bilingualism and distributional properties of word relationships on children's development of semantic convergence, operationalized as children's ability to produce word associates that mirror adults’ responses in a word association task. Forty-five Mandarin–English bilingual, 32 Spanish–English bilingual, and 28 English-speaking monolingual children, aged 4 to 7, produced three associates to each of 15 single-word cues in English. Children's productions were compared against adult responses to the same cues in the “Small World of Words” Norm. Three scoring methods comparing similarities of children's responses to adults’ showed consistent bilingual disadvantages in producing adult-like responses. Follow-up analyses targeted the three most predominant responses adults produced for each cue and addressed factors predicting children's likelihood to produce these responses. Results showed additional effects of cue-associate relationships measured by co-occurrence and semantic relatedness. The findings highlight the multi-faceted nature of knowledge development of word relationship and semantic convergence.
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Introduction: Alterations in the microbiome contribute to the pathogenesis of many gastrointestinal diseases. However, the composition of the microbiome in gallbladder disease is not well described. Methods: We aimed to characterize the biliary microbiome in cholecystectomy patients. Bile and biliary stones were collected at cholecystectomy for a variety of surgical indications between 2017 and 2019. DNA was extracted and metagenomic sequencing was performed with subsequent taxonomic classification using Kraken2. The fraction of bacterial to total DNA reads, relative abundance of bacterial species, and overall species diversity were compared between pathologies and demographics. Results: A total of 74 samples were obtained from 49 patients: 46 bile and 28 stones, with matched pairs from 25 patients. The mean age was 48 years, 76% were female, 29% were Hispanic, and 29% of patients had acute cholecystitis. The most abundant species were Klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus pasteurianus. The bacterial fraction in bile and stone samples was higher in acute cholecystitis compared to other non-infectious pathologies (p < 0.05). Neither the diversity nor differential prevalence of specific bacterial species varied significantly between infectious and other non-infectious gallbladder pathologies. Multivariate analysis of the non-infectious group revealed that patients over 40 years of age had increased bacterial fractions (p < 0.05). Conclusions: Metagenomic sequencing permits characterization of the gallbladder microbiome in cholecystectomy patients. Although a higher prevalence of bacteria was seen in acute cholecystitis, species and diversity were similar regardless of surgical indication. Additional study is required to determine how the microbiome can contribute to the development of symptomatic gallbladder disease.
Thesis
Genomische Selektion ist ein Routine-Verfahren bei verschiedenen Nutztierarten, aber noch nicht bei der Honigbiene wegen der Besonderheiten dieser Spezies. Für die Zuchtwertschätzung bei der Honigbiene ist eine spezielle genetische Verwandtschaftsmatrix erforderlich, da die Paarungsbiologie dieser Spezies ungesicherte Vaterschaft, diploide Königinnen und haploide Drohnen umfasst. Die Arbeit präsentiert einen neu-entwickelten Algorithmus zur effizienten Berechnung der Inversen der genetischen Verwandtschaftsmatrix und der Inzuchtkoeffizienten auf großen Datensätzen. Die Methode wurde zur Voraussage von genomischen und Stammbaum-basierten Zuchtwerten in einer Simulationsstudie genutzt. Die Genauigkeit und die Verzerrung der geschätzten Zuchtwerte wurden ausgewertet unter Berücksichtigung verschiedener Größen der Referenzpopulation. Außerdem wurde der Zuchtfortschritt im ersten Durchlauf von Zuchtprogrammen ausgewertet, die Zuchtschemata mit genomischer oder Stammbaum-basierter Selektion nutzten. Ein erheblich größerer Zuchtfortschritt als bei Stammbaum-basierter Selektion wurde mit genomischer Vorselektion erzielt, für die junge Königinnen genotypisiert wurden, und nur die Kandidaten mit den höchsten genomischen Zuchtwerten zur Anpaarung oder Leistungsprüfung zugelassen wurden. Für einen realen Datensatz von ungefähr 3000 genotypisierten Königinnen wurden Stammbaum-basierte und genomische Zuchtwerte für sechs wirtschaftlich bedeutende Merkmale vorhergesagt. Drei Merkmale zeigten eine signifikant höhere Vorhersagegenauigkeit bei genomischer Zuchtwertschätzung gegenüber Stammbaum-basierten Verfahren und die Unterschiede zwischen allen sechs Merkmalen konnten im Wesentlichen aus den genetischen Parametern der Merkmale und der begrenzten Größe der Referenzpopulation erklärt werden. Damit zeigt die Arbeit, dass die genomische Selektion bei der Honigbiene genutzt werden kann, den Zuchtfortschritt zu erhöhen.
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Extracellular vesicles (EVs) are blood-borne messengers that coordinate signalling between different tissues and organs in the body. The specificity of such crosstalk is determined by preferential EV docking to target sites, as mediated through protein-protein interactions. As such, the need to structurally characterize the EV surface precedes further understanding of docking selectivity and recipient-cell uptake mechanisms. Here, we describe an intact extracellular vesicle crosslinking mass spectrometry (iEVXL) method that can be applied for structural characterization of protein complexes in EVs. By using a partially membrane-permeable disuccinimidyl suberate crosslinker, proteins on the EV outer-surface and inside EVs can be immobilized together with their interacting partners. This not only provides covalent stabilization of protein complexes before extraction from the membrane-enclosed environment, but also generates a set of crosslinking distance restraints that can be used for structural modelling and comparative screening of changes in EV protein assemblies. Here we demonstrate iEVXL as a powerful approach to reveal high-resolution information, about protein determinants that govern EV docking and signalling, and as a crucial aid in modelling docking interactions.
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