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R: A Language and Environment for Statistical Computing

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... Statistical analyses were conducted for each experimental task following the same procedure. Mixed model analyses were conducted on R software (R Core Team, 2017), using lmer and glmer functions from the lme4 package (Bates et al., 2015). Indeed, through these models, the potential variability across participants, items and schools was considered for each experimental task through random intercepts: the random effect structure model included at least random intercepts for participants and for items. ...
Thesis
The contribution of orthography has been reported for learning of low-frequency words in native language (L1; Rosenthal & Ehri, 2008) and of pseudowords (Ricketts, Bishop, & Nation, 2009) by using a paired-associate learning paradigm (PAL). These studies cannot fully account for foreign language (L2) word learning, for which both L2 spoken and written forms have to be linked into a pre-existing concept, which in turn, is already connected to phonological and (sometimes) to an orthographic representation in L1. Besides, L2 learning confronts children to different challenges, such as incongruent letter/sound mapping with L1, due to the larger overlap on written than on spoken modality between languages (Marian et al., 2012). Therefore, this doctoral work aimed to explore the benefit of orthography on L2 word learning in children and to determine whether this advantage was modulated by L1 reading skills. We also sought to determine the moderating effect of incongruent letter/sound mappings with L1 on L2 learning. Using a PAL, we conducted three main L2 vocabulary learning studies by contrasting two learning methods, both simultaneous presentation of spoken and written (orthographic method) vs spoken forms only (non-orthographic method). As for learning phase, we made two groups of children (third vs. fifth graders) learn 16 (Study 1a) or 24 German words (Study 1b, Study 2). As for testing, we assessed learning performance with three main experimental tasks: a forced-choice picture recognition task (choose the correct image corresponding to the spoken form), a go/no-go spoken recognition task (discrimination between spoken German words and close phonological distractors) and an orthographic judgment task (select the correct German written form among three written distractors). We reported a consistent benefit of orthography on all three experimental tasks in both groups, supporting that children relied on written information at early steps of L2 learning. Still, contradictory results were reported for phonological learning in fifth graders, given that the benefit of orthography was only retrieved when increasing the learning load (Study 1b). Interestingly, although fifth graders outperformed the third graders on all experimental tasks, we reported a comparable amplitude for the orthographic facilitation in both groups. Measures of L1 reading skills were not (consistently) correlated with L2 vocabulary learning, supporting that a minimal amount of orthographic knowledge was enough to trigger an orthographic facilitation. A moderating effect of incongruent letter/sound mappings with L1 was restricted to L2 phonological learning, with larger discriminative performance for congruent compared to incongruent L2 words immediately after learning (Study 2), but disappeared after a one-week delay, aiming for a differential time-course for the encoding of congruent and incongruent L2 words, an assumption that was discussed in regards to the ontogenetic model of L2 lexical representation (Bordag, Gor, & Opitz, 2021) and to the L2 lexical fuzziness (Kapnoula, 2021). Study 3 was conducted during an Indoc mobility and explored whether the bilingual advantage on L3 vocabulary learning might be extended to children attending a classroom-immersion to L2 and whether this advantage was reinforced by the cross-linguistic similarities conveyed by cognate words. We reported a generalized advantage and cognate facilitation was restricted to the learning of novel L3 written form. In light of these results, this doctoral work reinforced the need for developmental models of bilingualism to consider the lexical and sublexical processing at early steps of L2 acquisition.
... Data were analyzed using statistical and graphical procedures in R [63], including rLakeAnalyzer [64] and gStat [65]. Inverse distance weighting (IDW) procedures for spatial data analysis employed a pixel size of 10 m. ...
Article
Hypoxia is common to shallow ice-covered lakes during the winter season, and restorative actions to prevent impacts to aquatic ecosystems are desired yet untested in remote settings. The use of a solar photovoltaic circulator was investigated for reoxygenation in a shallow hypoxic lake in the northern Rocky Mountains. During the fall of 2019, a solar powered lake circulator (SolarBee SB10000LH; hereinafter circulator) was installed near the center of Upper Red Rock Lake, Montana USA (latitude 44° 36’N) and dissolved oxygen (DO), temperature, turbidity, and changes to ice formation were monitored until ice-out the following spring of 2020 using an array of real-time and data logging sondes. Observations indicate the circulator formed a polynya that lasted until late November, did not increase lake turbidity, and facilitated oxygen exchange through the circulator-created-polynya for at least 3 weeks after an adjacent lake became ice covered. Thereafter, operation of the solar circulator failed from accumulation of snow and ice on the solar panels such that the lake froze completely over during a period of low light in December. From that point on throughout the winter, DO subsequently declined from supersaturation to hypoxia over a 41-day period and remained that way for nearly four months until ice-out in April. Based on this outcome, additional work is required to improve the solar-powered circulator design before attempting comparable applications elsewhere as a means of reducing the severity of hypoxia in shallow-lake systems during winter.
... The simulation model and analyses of its output were implemented in R V.3.6.2. 16 Visual outcomes were compared between the delayed treatment models with the no treatment delay model using the z-test. Graphs were generated using the ggplot2 package. ...
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Objectives To report the reduction in new neovascular age-related macular degeneration (nAMD) referrals during the COVID-19 pandemic and estimate the impact of delayed treatment on visual outcomes at 1 year. Design Retrospective clinical audit and simulation model. Setting Multiple UK National Health Service (NHS) ophthalmology centres. Participants Data on the reduction in new nAMD referrals were obtained from four NHS Trusts comparing April 2020 with April 2019. To estimate the potential impact on 1-year visual outcomes, a stratified bootstrap simulation model was developed drawing on an electronic medical records dataset of 20 825 nAMD eyes from 27 NHS Trusts. Main outcome measures Simulated mean visual acuity and proportions of eyes with vision ≤6/60, ≤6/24 and ≥6/12 at 1 year under four hypothetical scenarios: 0-month, 3-month, 6-month and 9-month treatment delays. Estimated additional number of eyes with vision ≤6/60 at 1 year nationally. Results The number of nAMD referrals dropped on average by 72% (range 65%–87%). Simulated 1-year visual outcomes for 1000 nAMD eyes with a 3-month treatment delay suggested an increase in the proportion of eyes with vision ≤6/60 from 15.5% (13.2%–17.9%) to 23.3% (20.7%–25.9%), and a decrease in the proportion of eyes with vision ≥6/12 (driving vision) from 35.1% (32.1%–38.1%) to 26.4% (23.8%–29.2%). Outcomes worsened incrementally with longer modelled delays. Assuming nAMD referrals are reduced to this level for 1 month nationally, these simulated results suggest an additional 186–365 eyes with vision ≤6/60 at 1 year. Conclusions We report a large decrease in nAMD referrals during the COVID-19 lockdown and provide an important public health message regarding the risk of delayed treatment. As a conservative estimate, a treatment delay of 3 months could lead to a >50% relative increase in the number of eyes with vision ≤6/60 and 25% relative decrease in the number of eyes with driving vision at 1 year.
... Statistical analyses were conducted using R (R version 4.1.0) (26). We analyzed the agreement of each possible observer pair with Spearman's rank correlation coefficients. ...
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The well-being of animals kept by humans in laboratories, farms, or as pets should always be of the highest importance, and a prerequisite for this is adequate housing. To assess the potential indicators for animal well-being, ideally simple, non-invasive, and reliable methods are necessary. Here, we propose a novel plumage scoring system for small songbirds, using the example of the Zebra Finch, and examine its reliability in comparison with a well-known body condition index, that is, the fat score. We used up to five different observers of different experience levels to assess inter- and intra-observer reliability of the proposed plumage score and also the fat score. We found substantial inter-observer reliability for the proposed novel plumage score, and lower inter-observer reliability for the fat score, which seems to require more training of observers. The intra-observer reliability of the experienced observer who trained the others also showed a very strong reliability for the plumage score and for the fat score. Thus, we conclude that our proposed novel plumage score is a simple, reliable, and non-invasive way to estimate an important indicator of captive Zebra Finches' well-being. Furthermore, the plumage score can be reliably taught to other observers. The plumage score, maybe in combination with the fat score, may be an important tool to reliably assess well-being on a regular basis in captive populations in zoos, laboratories, or pet stocks.
... 14 Finally, we investigated the representativeness of our sample within BADBIR using classic statistical tests. All statistical analysis was performed in R. 15 ...
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Despite some evidence that psoriatic arthritis (PsA) may increase psychological burden in psoriasis, the mental health of this subpopulation is under‐investigated. To investigate whether PsA is associated with higher depression and anxiety in moderate‐to‐severe psoriasis; explore whether pain mediates these associations; and estimate the prevalence of undiagnosed and untreated depression. Baseline data from British Association of Dermatologists Biologic and Immunomodulators Register (BADBIR) participants completing the Hospital Anxiety and Depression Scale (HADS) were analysed. 707 patients (n = 540 with psoriasis only; n = 167 with PsA) were included. Depression prevalence was higher in patients with than without PsA, when a HADS‐depression subscale cut‐off ≥8 was used (33% vs. 23%, adjusted Odds Ratio [OR] (95% Confidence Intervals [CI]) = 1.64 (1.09–2.45)), but did not differ using the HADS cut‐off ≥ 11. Anxiety prevalence was higher among PsA patients, regardless of HADS cut‐off (cut‐off ≥11: adjusted OR (95% CI) = 1.62 (1.07–2.45)). Pain fully mediated the effect of PsA on depression and anxiety in psoriasis. 53.6% of participants identified as depressed did not have a known psychiatric disorder; two thirds of depressed participants were not treated. PsA comorbidity in psoriasis is associated with higher anxiety; its association with depression appears to be robust when milder depressive syndromes are included, but less consistent for higher‐threshold depression definitions. Depression remains unrecognized and untreated in over half of moderately‐to‐severe psoriasis patients. Routine depression and anxiety screening is recommended in psoriasis and PsA. PsA comorbidity may increase depression and anxiety in psoriasis through pain experience.
... The identified PI SNP pairs were then tested for their LE. These tests were performed using in-house scripts written in R3.5 [65]. The P-values were adjusted to minimize false discovery rate (FDR) for multiple testing [66]. ...
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Candida auris is a recently emerged, multidrug-resistant pathogenic yeast capable of causing a diversity of human infections worldwide. Genetic analyses based on whole-genome sequences have clustered strains in this species into five divergent clades, with each clade containing limited genetic variation and one of two mating types, MTL a or MTL α. The patterns of genetic variations suggest simultaneous emergence and clonal expansion of multiple clades of this pathogen across the world. At present, it is unclear whether recombination has played any role during the evolution of C. auris. In this study, we analyzed patterns of associations among single nucleotide polymorphisms in both the nuclear and the mitochondrial genomes of 1,285 strains to investigate potential signatures of recombination in natural C. auris populations. Overall, we found that polymorphisms in the nuclear and mitochondrial genomes clustered the strains similarly into the five clades, consistent with a lack of evidence for recombination among the clades after their divergence. However, variable percentages of SNP pairs showed evidence of phylogenetic incompatibility and linkage equilibrium among samples in both the nuclear and the mitochondrial genomes, with the percentages higher in the total population than those within individual clades. Our results are consistent with limited but greater frequency of recombination before the divergence of the clades than afterwards. SNPs at loci related to antifungal resistance showed frequencies of recombination similar to or lower than those observed for SNPs in other parts of the genome. Together, though very limited, evidence for the observed recombination for both before and after the divergence of the clades suggests the possibility for continuous genetic exchange in natural populations of this important yeast pathogen.
... The statistical analysis was carried out using R version 4.1.0 [24]. The full R code is available on the GitHub website [25]. ...
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In this meta-analysis, we aimed to estimate the diagnostic accuracy of machine learning models on digital mammograms and tomosynthesis in breast cancer classification and to assess the factors affecting its diagnostic accuracy. We searched for related studies in Web of Science, Scopus, PubMed, Google Scholar and Embase. The studies were screened in two stages to exclude the unrelated studies and duplicates. Finally, 36 studies containing 68 machine learning models were included in this meta-analysis. The area under the curve (AUC), hierarchical summary receiver operating characteristics (HSROC) curve, pooled sensitivity and pooled specificity were estimated using a bivariate Reitsma model. Overall AUC, pooled sensitivity and pooled specificity were 0.90 (95% CI: 0.85–0.90), 0.83 (95% CI: 0.78–0.87) and 0.84 (95% CI: 0.81–0.87), respectively. Additionally, the three significant covariates identified in this study were country (p = 0.003), source (p = 0.002) and classifier (p = 0.016). The type of data covariate was not statistically significant (p = 0.121). Additionally, Deeks’ linear regression test indicated that there exists a publication bias in the included studies (p = 0.002). Thus, the results should be interpreted with caution.
... For all statistical analyses, the R software was used 34 . To examine whether there is variation in utilized temperature among individuals within each species, we built General Linear Mixed Models (GLMMs). ...
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We used observational data collected during a mark-recapture study that generated a total of 7503 captures of 6108 unique individuals representing three endangered butterfly species to quantify inter-and intraindividual variation in temperature utilization and examine how activity patterns vary according to season, time of day, and ambient temperature. The Marsh Fritillary, the Apollo, and the Large Blue differed in utilized temperatures and phenology. Their daily activity patterns responded differently to temperature, in part depending on whether they were active in the beginning, middle or end of the season, in part reflecting interindividual variation and intraindividual flexibility, and in part owing to differences in ecology, morphology, and colouration. Activity temperatures varied over the season, and the Apollo and the Large Blue were primarily active at the highest available ambient temperatures (on the warmest days and during the warmest part of the day). The Marsh Fritillary was active early in the season and decreased activity during the highest temperatures. The relationship between individual lifespan and the average temperature was qualitatively different in the three species pointing to species-specific selection. Lifespan increased with an increasing range of utilized temperatures in all species, possibly reflecting that intra-individual flexibility comes with a general survival benefit.
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Locomotion, as a fundamental function in mammals directly associated with the use of ecological resources, is expected to have anatomical structures functionally committed that evolved under intense selective pressure, possibly carrying specializations for different locomotor habits. Among caviomorph rodents, the family Echimyidae stands out for having the greatest species richness, with relatively well-resolved phylogenetic relationships, wide variation in body mass, and remarkable diversity of locomotor habits, including arboreal, scansorial, semi-aquatic, semifossorial, and terrestrial forms. Thus, Echimyidae constitutes a promising model for understanding how phylogenetic, allometric, and ecological factors affect the evolution of postcranial structures directly linked to locomotor function. We investigated the influence of these three factors on scapular and humeral morphological variation in 38 echimyid species using two-dimensional geometric morphometry and phylogenetically informed comparative methods. Scapular and humeral shape variation had a low correlation with body mass and structure size, conveying a small or negligible allometric effect. Conversely, a significant moderate to strong phylogenetic signal was detected in both structures, suggesting that an important part of their morphometric variation results from shared evolutionary history. Notably, morphological variation of the scapula was extensively structured by phylogeny, without the marked influence of locomotor habits, suggesting that its shape may be a suitable taxonomic marker. Finally, locomotor habits were important in structuring the morphological variation of the humerus. Our results suggest that the morphologies of the scapula and humerus, despite being anatomically and functionally interconnected, were differentially shaped by ecological factors associated with locomotor habits.
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Emotion recognition abilities are fundamental to our everyday social interaction. A large number of clinical populations show impairments in this domain, with emotion recognition atypicalities being particularly prevalent among disorders exhibiting a dopamine system disruption (e.g., Parkinson's disease). Although this suggests a role for dopamine in emotion recognition, studies employing dopamine manipulation in healthy volunteers have exhibited mixed neural findings and no behavioural modulation. Interestingly, whilst a dependence of dopaminergic drug effects on individual baseline dopamine function has been well established in other cognitive domains, the emotion recognition literature so far has failed to account for these possible interindividual differences. The present within-subjects study therefore tested the effects of the dopamine D2 antagonist haloperidol on emotion recognition from dynamic, whole-body stimuli while accounting for interindividual differences in baseline dopamine. 33 healthy male and female adults rated emotional point-light walkers (PLWs) once after ingestion of 2.5 mg haloperidol and once after placebo. To evaluate potential mechanistic pathways of the dopaminergic modulation of emotion recognition, participants also performed motoric and counting-based indices of temporal processing. Confirming our hypotheses, effects of haloperidol on emotion recognition depended on baseline dopamine function, where individuals with low baseline dopamine showed enhanced, and those with high baseline dopamine decreased emotion recognition. Drug effects on emotion recognition were related to drug effects on movement-based and explicit timing mechanisms, indicating possible mediating effects of temporal processing. Results highlight the need for future studies to account for baseline dopamine and suggest putative mechanisms underlying the dopaminergic modulation of emotion recognition.Significance statementA high prevalence of emotion recognition difficulties amongst clinical conditions where the dopamine system is affected suggests an involvement of dopamine in emotion recognition processes. However, previous psychopharmacological studies seeking to confirm this role in healthy volunteers thus far have failed to establish whether dopamine affects emotion recognition and lack mechanistic insights. The present study uncovered effects of dopamine on emotion recognition in healthy individuals by controlling for interindividual differences in baseline dopamine function and investigated potential mechanistic pathways via which dopamine may modulate emotion recognition. Our findings suggest that dopamine may influence emotion recognition via its effects on temporal processing, providing new directions for future research on typical and atypical emotion recognition.
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The concept of mindfulness has been discussed as being a promising pathway to strenghten pro-environmental behavior, that is at the same time related to personal well-being. Several studies identified correlations between trait mindfulness and pro-environmental behavior (PEB) and identified different mediators. To obtain better, fine-grained insights into this connection, the present study investigated mindfulness as a predictor of same-day connectedness to nature, personal ecological norm activation (PENA), PEB and well-being on a within-person level. In a daily diary study (N = 183, days = 1197), multilevel regression analysis showed: (i) positive same-day within-person relationships between mindfulness and PENA, connectedness to nature and well-being; (ii) a significant effect of mindfulness on next-day PEB; (iii) relationships between regular mind-body practices, such as mindfulness meditation, and daily PEB. Path analysis showed, (iv) a path from mindfulness to PEB mediated by connectedness to nature and PENA. The study confirms the significance of mindfulness in every-day life for connectedness to nature, PENA and well-being. Furthermore, the study points out the relevance of investigating predictors of PEB on a within-person level
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The Central Mineral Belt (CMB) in Labrador, Canada, hosts multiple U (±base ± precious metal) showings, prospects and deposits in metamorphosed and variably hydrothermally altered Neoarchean to Mesoproterozoic, igneous and sedimentary rocks. Previous work has recognized U mineralization locally associated with Fe-Ca and alkali metasomatism typical of metasomatic iron oxide and alkali-calcic alteration systems (IOAA) that host iron oxide-copper-gold (IOCG) and affiliated critical metal deposits. However, the type, extent and temporal or genetic relationships between the diverse Fe, Ca and alkali metasomatism and the regionally distributed U mineralization remains poorly understood. Combined unsupervised machine-learning and classification of alteration from a large geochemical dataset distinguish the main alteration phases in the CMB, identify compositional changes related to U mineralization, and infer lithological/mineralogical information from samples with censored (i.e., missing), limited and/or inaccurate metadata. Weak to intense Na and Na + Ca-Fe (Mg) metasomatism in the southwest (Two-Time and Moran Lake areas) and eastern (Michelin area) portions of the CMB pre-dates U mineralization and Fe-oxide breccia development, similar to albitite-hosted U and IOCG deposits globally. Rare earth elements and spider diagrams highlight both preservation and disruption of normally immobile elements. Principal component and cluster analysis indicate significant variations in Fe-Mg ± Na contents in the rocks from combinations of Na, Ca, Fe, and Mg-rich alteration, while protolith REE signatures can be locally preserved even after pervasive albitization-hematization. Cluster analysis identifies mineralized felsic and mafic rocks in the Michelin deposit and Moran Lake area, facilitating inference of relevant lithological/mineralogical information from samples lacking or with limited meta-data. The methods outlined provide rapid and relatively inexpensive means to optimize identification of mineral systems within large geochemical datasets, verify drill core or field observations, highlight potentially overlooked alteration, and refine economic mineral potential assessments. Based on our results and previous work, we suggest the mineral potential of the southwestern and eastern CMB needs to be re-assessed with modern exploration models for IOAA ore systems and their iron oxide-poor variants.
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Halo effects refer to a common source of error in human judgment. In rater-mediated assessments where each rater assigns multiple scores to examinees, raters subject to halo tend to give similar scores on conceptually distinct traits, dimensions, or criteria. An intricate problem with empirically detecting halo effects concerns the separation between illusory halo due to judgmental biases or cognitive distortions, and true halo, due to actual overlap between the traits or criteria used for scoring examinee performances. The present research used the mixture Rasch facets model for halo effects (MRFM-H; Jin & Chiu, 2022) to detect illusory halo. In two separate studies, raters scored examinees' writing performances on a set of criteria using a four-category rating scale. Halo parameters were estimated building on Bayesian Markov chain Monte Carlo methods implemented in the freeware JAGS run within the R environment. The findings revealed that (a) the MRFM-H fit the data well but not better than the basic Rasch facets model (RFM), (b) in Study 2, we identified three raters that may have been subject to illusory halo effects. The discussion focuses on practical implications for ensuring high rating quality in performance assessments.
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Magnolia sinica is one of the most endangered Magnoliaceae species in China. Seed biology information concerning its long-term ex situ conservation and utilization is insufficient. This study investigated dormancy status, germination requirements and storage behavior of M. sinica. Freshly matured seeds germinated to ca. 86.5% at 25/15 C but poorly at 30 C; GA 3 and moist chilling promoted germination significantly at 20 C. Embryos grew at temperatures (alternating or constant) between 20 C and 25 C, but not at 5 C or 30 C. Our results indicate that M. sinica seeds possibly have non-deep simple mor-phophysiological dormancy (MPD). Seeds survived desiccation to 9.27% and 4.85% moisture content (MC) as well as a further 6-month storage at À20 C and in liquid nitrogen, including recovery in vitro as excised embryos. The established protocol ensured that at least 58% of seedlings were obtained after both cold storage and cryopreservation. These results indicate that both conventional seed banking and cryopreservation have potential as long-term ex situ conservation methods, although further optimized approaches are recommended for this critically endangered magnolia species.
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(200/200) Purpose : Vaccinations are reported at the state level, but services are delivered at the county level through health departments (HD). This research contributes statistical models to predict county level HPV vaccination. Methods : Using a cross sectional study design, secondary data were analyzed for the years 2016 to 2018 for all counties of GA. Study population was male and female adolescents aged 13-17 who received the tetanus, diphtheria and pertussis (Tdap) vaccine. The number of administered HPV vaccine doses and HPV vaccination coverage rate were modeled using indicators of HD clinic access, age, sex, race/ethnicity, socioeconomic status, education, median household income, health insurance and urban/rural residence. Results : By county the number of administered HPV vaccine doses showed a statistically significant positive association with indicators of HD clinic access: public transit and the number of HD private clinics. HPV vaccination coverage showed a statistically significant negative association with White race and rural residency. Conclusion : Examining Tdap vaccinated adolescents conservatively predicted HPV vaccination and controlled for multiple confounders such as vaccination ineligibility, vaccine exemption, and vaccine opposition. Within this population, public health professionals and clinicians could use these statistical models to target HPV vaccination efforts among non-Hispanic whites and rural communities at the county level.
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A considerable proportion of tropical protected areas are Sustainable Use Reserves (SURs), where socio-biodiversity protection and sustainable resource extraction are the main goals. Subsistence hunting is the most widespread form of subcanopy forest resource extraction, and often depletes game populations within SURs, but the degree to which these extractive activities are sustainable remains questionable. To assess patterns of hunting sustainability within SURs, we systematically examined the local ecological knowledge of 211 resident hunters living in 93 communities located within and immediately outside nine SURs of Brazilian Amazonia. We used mixed models to assess the effects of settlement features (distance to reserve boundaries, size, age, distance to urban centers, and extent of floodplain areas) on local perceptions of game abundance, the prey profile of the most consumed game species, and overall levels of local game depletion. Hunters consistently reported that game populations were less impacted within communal catchment areas containing larger amounts of floodplain habitat and farther from urban centers. In these areas the overall game abundance was perceived to be higher, low-fecundity species were most consumed, and harvest-sensitive species were least depleted. Local SUR communities within this context accrued higher benefits from higher wild-meat availability, but settlement age and size had no effects on hunted species. Evidence-based conservation management plans in tropical protected areas should focus on reducing wild meat demand in urban areas and managing both, the local aquatic animal protein in floodplain areas to relieve pressure on terrestrial game species, and the offtake of game populations at inland sites lacking access to aquatic animal protein.
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The widespread use of ITS2 as a potential marker in insects has accelerated species-level phylogenetic studies. Reliable and quality data can be obtained thanks to the features such as rapid evolution and secondary structure of this marker. This paper presents the phylogenetic relationship among 36 individuals of Dolerus Panzer, 1801 (Hymenoptera: Tenthredinidae) collected between 2002 and 2018 to obtain the first data on ITS2 secondary structure. Aligned of ITS2 data were analyzed by application of maximum likelihood method to reveal phylogenetic relationship among the specimens. Also, the structural properties, length variation and presence of compensatory base changes make the ITS2 useful marker in determination of species boundaries of closely related species.
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Background: Coronavirus disease 2019 (COVID-19) is a pandemic that has affected the daily life, governments and economies of many countries all over the globe. Ghana is currently experiencing a surge in the number of cases with a corresponding increase in the cumulative confirmed cases and deaths. The surge in cases and deaths clearly shows that the preventive and management measures are ineffective and that policy makers lack a complete understanding of the dynamics of the disease. Most of the deaths in Ghana are due to lack of adequate health equipment and facilities for managing the disease. Knowledge of the number of cases in advance would aid policy makers in allocating sufficient resources for the effective management of the cases. Methods: A predictive tool is necessary for the effective management and prevention of cases. This study presents a predictive tool that has the ability to accurately forecast the number of cumulative cases. The study applied polynomial and spline models on the COVID-19 data for Ghana, to develop a generalized additive model (GAM) that accurately captures the growth pattern of the cumulative cases. Results: The spline model and the GAM provide accurate forecast values. Conclusion: Cumulative cases of COVID-19 in Ghana are expected to continue to increase if appropriate preventive measures are not enforced. Vaccination against the virus is ongoing in Ghana, thus, future research would consider evaluating the impact of the vaccine.
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Background Drug-related cue-reactivity, dysfunctional negative emotion processing, and response-disinhibition constitute three core aspects of methamphetamine use disorder (MUD). These phenomena have been studied independently, but the neuroscientific literature on their interaction in addictive disorders remains scant. Methods 62 individuals with MUD were scanned when responding to the geometric Go or No-Go cues superimposed over blank, neutral, negative-emotional and drug-related background images. Neural correlates of drug and negative-emotional cue-reactivity, response-inhibition and their interactions were estimated, and methamphetamine cue-reactivity was compared between individuals with MUD and 23 healthy controls. Relationships between behavioral characteristics and observed activations were investigated. Results Individuals with MUD had longer reaction times and more errors in drug and negative-emotional compared to blank blocks, and more omission errors in drug compared to neutral blocks. They showed higher drug cue-reactivity than controls across prefrontal, fusiform, and visual regions (Z>3.1, p-corrected<0.05). Response-inhibition was associated with precuneal, inferior parietal, anterior cingulate, temporal, and inferior frontal activations (Z>3.1, p-corrected<0.05). Response-inhibition in drug cue blocks coincided with higher activations in the visual cortex and lower activations in the paracentral lobule and superior and inferior frontal gyri, while inhibition during negative-emotional blocks led to higher superior parietal, fusiform, and lateral occipital activations (Z>3.1, p-corrected<0.05). Conclusion Drug cue-reactivity may impair response inhibition partly through activating dis-inhibitory regions, while temporal and parietal activations associated with response-inhibition in negative blocks suggest compensatory activity. Results suggest that drug and negative-emotional cue-reactivity influence response-inhibition, and the study of these interactions may aid mechanistic understanding of methamphetamine use disorder.
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Metazoans host complex communities of microorganisms that include dinoflagellates, fungi, bacteria, archaea and viruses. Interactions among members of these complex assemblages allow hosts to adjust their physiology and metabolism to cope with environmental variation and occupy different habitats. Here, using reciprocal transplantation across depths, we studied adaptive divergence in the corals Orbicella annularis and O. franksi , two young species with contrasting vertical distribution in the Caribbean. When transplanted from deep to shallow, O. franksi experienced fast photoacclimation and low mortality, and maintained a consistent bacterial community. By contrast, O. annularis experienced high mortality and limited photoacclimation when transplanted from shallow to deep. The photophysiological collapse of O. annularis in the deep environment was associated with an increased microbiome variability and reduction of some bacterial taxa. Differences in the symbiotic algal community were more pronounced between coral species than between depths. Our study suggests that these sibling species are adapted to distinctive light environments partially driven by the algae photoacclimation capacity and the microbiome robustness, highlighting the importance of niche specialization in symbiotic corals for the maintenance of species diversity. Our findings have implications for the management of these threatened Caribbean corals and the effectiveness of coral reef restoration efforts.
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Negative affect facilitates conflict processing. Here we sought to assess whether symmetrically, its downregulation by means of reappraisal could lower it. To this end, 105 participants performed the confound-minimized Stroop task eliciting negative affect that was followed by a simple reward-related visual discrimination task. Conflict processing was induced with the former task. Half of them (experimental group) were instructed to use this second task to downregulate negative affect arising from the Stroop task. The other half (control group) did not receive these appraisal-related instructions. Group comparisons showed that negative affect and the conflict effect were similar for these two groups. However, when we added and modeled the subjective ratings related to emotion regulation, we found that conflict processing significantly improved for participants who reported using reappraisal spontaneously, and this gain occurred irrespective of negative affect. These results suggest that reappraisal can influence conflict processing but this change does not depend on negative affect.
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Background and aimsSoil-borne diseases are an increasingly serious threat to agriculture systems. Organic fertilization would improve soil quality and microbial community as well, and thus is appreciated a promising control strategy for soil-borne diseases. Yet, how soil microbial communities mediate disease control under organic fertilization remains largely unknown. Here, we aimed to explore the microbial mechanism of controlling soil-borne diseases by organic fertilization.Methods We investigated the effects of various fertilization regimes on the soil suppressiveness toward pathogenic fungi in the peanut rhizosphere. The fertilization regimes tested were organic fertilizer, chemical fertilizers, and a combination of both.ResultsUninterrupted application of organic fertilizer in peanut field plots for seven planting seasons resulted in a control of peanut root rot, with a significantly higher peanut yield. Upon organic fertilization, bacterial microbiome assembly in the rhizosphere played a key role in developing soil suppressiveness against peanut root rot; upon chemical fertilization, the potential fungal pathogens dominated the fungal microbiome assembly in the rhizosphere to boost root rot. Further, structural equation model revealed that the rhizosphere bacterial community contributed to the control of root rot. Furthermore, upon organic fertilization, the rhizosphere bacterial community strongly suppressed mycelial growth and spore germination of Fusarium sp. ACCC 36194.Conclusions Collectively, in a monocropping system, persistent organic fertilization favors the development of a protective microbial shield in the plant rhizosphere, maintaining the rhizosphere health.
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Bacterial cell-based biosensors have been widely developed for detecting environmental toxic materials. The znt-operon in Escherichia coli is a Zn(II)-responsive genetic system and is employed in Zn(II), Cd(II), and Hg(II)-sensing biosensors. In this study, point mutations were introduced in the regulatory protein ZntR to modulate its target selectivity, and metal ion-exporting genes, such as copA and zntA, in host cells were deleted to increase cellular metal ion levels and enhance specificity. Thus, the overall responses of the E. coli cell-based biosensors toward metal(loid) ions were increased, and their selectivity, which was originally for Cd(II) and Hg(II), was shifted to Pb(II). The gene encoding ZntA, known as the Zn(II)-translocating P-type ATPase, showed an impact on the ability of E. coli to export Pb(II), whereas copA deletion showed no significant impact. Noteworthily, the newly generated biosensors employing ZntR Cys115Ile showed the capacity to detect under 5 nM Pb(II) in solution, without response to other tested metal ions within 0–100 nM. To understand the marked effect of single point mutations on ZntR, computational modeling was employed. Although it did not provide clear answers, changes in the sequences of the metal-binding loops of ZntR modulated its transcriptional strength and target selectivity. In summary, the approaches proposed in this study can be valuable to generate new target-sensing biosensors with superior selectivity and specificity, which can in turn broaden the applicability of cell-based biosensors to monitor Pb(II) in environmental systems.
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Chapter
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Thesis
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Ecology is fundamental in the development, transmission, and perpetuity of primate technology. Previous studies on tool site selection have addressed the relevance of targeted resources and raw materials for tools, but few have considered the broader foraging landscape. In this landscape-scale study of the ecological contexts of wild chimpanzee ( Pan troglodytes verus ) tool use, we investigated the conditions required for nut-cracking to occur and persist in discrete locations at the long-term field site of Bossou, Guinea. We examined this at three levels: selection, frequency of use, and inactivity. We collected data on plant foods, nut trees, and raw materials using transect and quadrat methods, and conducted forest-wide surveys to map the location of nests and watercourses. We analysed data at the quadrat level ( n = 82) using generalised linear models and descriptive statistics. We found that, further to the presence of a nut tree and availability of raw materials, abundance of food-providing trees as well as proximity to nest sites were significant predictors of nut-cracking occurrence. This suggests that the spatial distribution of nut-cracking sites is mediated by the broader behavioural landscape and is influenced by non-extractive foraging of perennial resources and non-foraging activities. Additionally, the number of functional tools was greater at sites with higher nut-cracking frequency, and was negatively correlated with site inactivity. Our research indicates that the technological landscape of Bossou chimpanzees shares affinities with the ‘favoured places’ model of hominin site formation, providing a comparative framework for reconstructing landscape-scale patterns of ancient human behaviour. A French translation of this abstract is provided in theelectronic supplementary information: EMS 2.
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Large-effect loci---those discovered by genome-wide association studies or linkage mapping---associated with key traits segregate amidst a background of minor, often undetectable genetic effects in both wild and domesticated plants and animals. Accurately attributing mean differences and variance explained to the correct components in the linear mixed model (LMM) analysis is important for both selecting superior progeny and parents in plant and animal breeding, but also for gene therapy and medical genetics in humans. Marker-assisted prediction (MAP) and its successor, genomic prediction (GP), have many advantages for selecting superior individuals and understanding disease risk. However, these two approaches are less often integrated to simultaneously study the modes of inheritance of complex traits. This simulation study demonstrates that the average semivariance can be applied to models incorporating Mendelian, oligogenic, and polygenic terms, simultaneously, and yields accurate estimates of the variance explained for all relevant terms. Our previous research focused on large-effect loci and polygenic variance exclusively, and in this work we want to synthesize and expand the average semivariance framework to a multitude of different genetic architectures and the corresponding mixed models. This framework independently accounts for the effects of large-effect loci and the polygenic genetic background and is universally applicable to genetics studies in humans, plants, animals, and microbes.
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Background The cardiovascular system is strongly dependent on the gravitational environment. Gravitational changes cause mechanical fluid shifts and, in turn, autonomic effectors influence systemic circulation and cardiac control. We implemented a tilt paradigm to (1) investigate the acute hemodynamic response across a range of directions of the gravitational vector, and (2) to generate specific dose‐response relationships of this gravitational dependency. Methods and Results Twelve male subjects were tilted from 45° head‐up tilt to 45° head‐down tilt in 15° increments, in both supine and prone postures. We measured the steady‐state hemodynamic response in a range of variables including heart rate, stroke volume, cardiac output, oxygen consumption, total peripheral resistance, blood pressure, and autonomic indices derived from heart rate variability analysis. There is a strong gravitational dependence in almost all variables considered, with the exception of oxygen consumption, whereas systolic blood pressure remained controlled to within ≈3% across the tilt range. Hemodynamic responses are primarily driven by differential loading on the baroreflex receptors, combined with differences in venous return to the heart. Thorax compression in the prone position leads to reduced venous return and increased sympathetic nervous activity, raising heart rate, and systemic vascular resistance while lowering cardiac output and stroke volume. Conclusions Gravitational dose‐response curves generated from these data provide a comprehensive baseline from which to assess the efficacy of potential spaceflight countermeasures. Results also assist clinical management of terrestrial surgery in prone posture or head‐down tilt positions.
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Gapping in embedded environments may occur in two configurations: (i) the whole coordination containing both conjuncts is embedded (= embedded gapping, EG), (ii) the second (i.e. elliptical) clause is embedded within its own conjunct (= single conjunct embedded gapping, SCEG). Languages seem to differ in their restrictions on these two structures: EG in some languages does not allow for a complementizer in the elliptical conjunct, while it does in other languages. SCEG is outright unacceptable in some languages but acceptable in other languages. Overall, languages seem to fall into two groups such that one group allows a complementizer in the elliptical conjunct of EG and generally allows SCEG, whereas the other group allows neither. We present four experiments in Spanish on the acceptability of the complementizer que ‘that’ in the elliptical conjunct in EG. Our results suggest that que in Spanish EG is overall subject to similar restrictions as SCEG gapping: There are different degrees of degradation depending on the (type of) embedding verb without outright unacceptability. While the relevant property has been argued to be factivity for SCEG, we argue that it is not the factivity of the embedding verb as such that drives acceptability, but assertion embedding. We outline a theoretical proposal building on existing accounts of structural ambiguity in gapping, the truncation of complement CPs under some verbs including factives, and the general flexibility of the semantic/pragmatic categories factivity and assertion.
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In previous observational studies, the association between coffee intake and risk of cardiovascular disease has reversed from positive to negative over time. This long-term international ecological study examined whether the association between coffee intake and mortality and incidence rates of ischemic heart disease (IHD) changed between 1990 and 2018 using multiple coherent data. We obtained data on coffee intake per capita, IHD mortality and incidence rates per 100,000 population, and socioeconomic and lifestyle indicators for each country from various publicly available databases. We integrated and analyzed data from 147 countries with populations of ≥ 1 million. We employed a linear mixed model analysis to assess the association between coffee intake and IHD mortality and incidence rates by year. The mean global coffee intake increased (p < 0.001), whereas IHD mortality (p < 0.001) and incidence (p = 0.073) decreased. In all models, the interaction between coffee intake and year showed a significant inverse association for IHD mortality and incidence rates (p < 0.001 for all). The country-level association between coffee intake and IHD mortality and incidence rates between 1990 and 2018 was stronger in the negative direction.
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This longitudinal study investigated bidirectional associations between pupils’ social competence and their interpersonal relationships and classroom climate in segregated special education schools for pupils with Emotional and Behavioral Disorders in the Netherlands. Participants were in Grade 4 and 5 in school year 1 (N = 441) and Grade 5 and 6 in school year 2 (N = 504) (Mage Time1 = 10.82, SD = 0.86). Digital surveys were administered to pupils and teachers twice each school year to gather information about pupils’ relationships with teachers and peers, classroom climate (structure, atmosphere), and social competence. Structural path models were estimated separately for each school year. Altogether, classroom structure and peer relations were inconsistently linked with teacher and self-reported social competence. Peer relationships (first school year) and structure (second school year) predicted teacher-reported social competence. Self-reported social competence predicted peer relationships, while teacher-reported social competence predicted structure (second school year). Explanations and implications of the findings are discussed.
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The contribution of genes towards T2D development varies among different population groups across the world. It has been reported that a number of loci involved in T2D susceptibility are common across certain population groups, but ethnicity specific variants are also observed. The population of Mizoram has an independent ethnic identity and there are no scientific records about the history of the Mizo people; which makes this ethnic group unique and interesting to study. The aim of the study focuses on the identification of the gene variants which may contribute to T2D susceptibility in Mizo-Mongloid ethnic tribe of North east India through whole exome sequencing. The variants like 328G > C (KRT18), 997G > T (CYP4A11), 2368 T > C (SLC4A3), 508G > A (SLC26A5), 1659C > T (KCNS1), 650C > A (ABCD1) 821A > T (YTHDC2), 931G > T (PINX1), 3280C > A (TNRC6A), 48C > A(TACO1), 6035A > T(LAMA1), 805C > A(ACP7) and 806A > G(ACP7) variants were not reported for any disease in the database and were found to be pathogenic in different insilico analysis softwares. The changes in protein stability upon mutation has been predicted where 35.71% increases the stability of the protein, while 64.28% of the variants decrease the stability of the protein. These findings present the population specific variants which might involve in the susceptibility to T2D in Mizo population. Further, in this study some gene variants have contribution as a possible diagnostic or prognostic marker for other diseases as well, which suggests the need for performing association analysis for different disease manifestations in Mizo population in the near future.
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Empirical evidence has shown that introduced honeybees, Apis mellifera L., can change the structural organization of ecological networks involving pollinators and flowering plants. In this case, studies have shown that A. mellifera is highly connected within networks (i.e., high interactive role) mainly due to its high abundances, long colony lifetime, generalist diet, and great capacity of spread and adaptation to new environments. However, there is little knowledge on how the interactive role of A. mellifera in these flower-visitor networks changes spatially and the potential correlates of such variation across ecological and geographical gradients worldwide. In this study, we evaluated how native and exotic distribution ranges, local climate, human influence (i.e., anthropogenic disturbance), and latitude shape the interactive role of the honeybee in plant-floral visitor networks globally. To achieve that, we compiled 95 weighted plant-floral visitor networks encompassing ca. 87 degrees of latitude and 227 degrees of longitude across the globe. We found that the interactive role of A. mellifera is higher in its exotic range than in the native distributional range and positively associated with mean annual temperature and precipitation. Further, the interactive role of A. mellifera was high at intermediate values of global human influence and increased with latitude. Our findings help us to understand how different drivers related to rapid global change could affect the capacity of A. mellifera to colonize and increase its impact on other pollinator species in different environments.
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The present research compared internalizing problems of adolescents who experienced parental divorce with those of adolescents who remained in intact families. Furthermore, this research investigated the association of teacher autonomy support with adolescents’ internalizing problems for the whole sample and further ascertained whether this association was moderated by distinctive personality profiles using a person-centered approach and family structures (divorced vs. intact families). A sample of 2756 Chinese adolescents (8.5% from divorced families), aged 13–18 years, participated in the present research. They completed a set of self-reported questionnaires during school hours. Results based on ANCOVA showed that adolescents who experienced parental divorce reported higher internalizing problems than did those who remained in intact families. Moreover, latent profile analysis revealed three personality profiles: psychopathic (22.7%), normative (56.4%), and resilient (20.9%). In addition, teacher autonomy support was negatively related to adolescents’ internalizing problems in the overall sample. However, interaction analyses further exhibited that this association was insignificant for psychopathic adolescents who experienced parental divorce. The current findings indicate that although teacher autonomy support may protect adolescents from internalizing problems, psychopathic adolescents whose parents got divorced should be paid exceptional attention by mental health professionals and school counselors.
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RESEARCH QUESTION : Are paired samples of endometrium and ovarian endometriomas synchronous with each other throughout the menstrual cycle? DESIGN : The expression levels of 57 endometrial receptivity associated genes were determined from the matched endometrial and endometrioma samples (n=31) collected from women with endometriosis throughout the menstrual cycle. RESULTS : The expression profile of endometrial receptivity genes divided endometrial samples according to their menstrual cycle phase. Endometrioma samples grouped together irrespective of the menstrual cycle phase and formed a distinct cluster from endometrial samples. Pairwise comparison showed 21, 16, 33 and 23 differentially expressed genes (adjusted p<0.05) between the lesions and endometria collected in proliferative, early-secretory, mid-secretory and late-secretory menstrual cycle phases, respectively, confirming the distinct expression profiles of endometrium and endometrioma.
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Background Arboviruses transmitted by Aedes aegypti including dengue, Zika, and chikungunya are a major global health problem, with over 2.5 billion at risk for dengue alone. There are no licensed antivirals for these infections, and safe and effective vaccines are not yet widely available. Thus, prevention of arbovirus transmission by vector modification is a novel approach being pursued by multiple researchers. However, the field needs high-quality evidence derived from randomized, controlled trials upon which to base the implementation and maintenance of vector control programs. Here, we report the EVITA Dengue trial design (DMID 17-0111), which assesses the efficacy in decreasing arbovirus transmission of an innovative approach developed by the World Mosquito Program for vector modification of Aedes mosquitoes by Wolbachia pipientis . Methods DMID 17-0111 is a cluster-randomized trial in Belo Horizonte, Brazil, with clusters defined by primary school catchment areas. Clusters ( n = 58) will be randomized 1:1 to intervention (release of Wolbachia -infected Aedes aegypti mosquitoes) vs. control (no release). Standard vector control activities (i.e., insecticides and education campaigns for reduction of mosquito breeding sites) will continue as per current practice in the municipality. Participants ( n = 3480, 60 per cluster) are children aged 6–11 years enrolled in the cluster-defining school and living within the cluster boundaries who will undergo annual serologic surveillance for arboviral infection. The primary objective is to compare sero-incidence of arboviral infection between arms. Discussion DMID 17-0111 aims to determine the efficacy of Wolbachia -infected mosquito releases in reducing human infections by arboviruses transmitted by Aedes aegypti and will complement the mounting evidence for this method from large-scale field releases and ongoing trials. The trial also represents a critical step towards robustness and rigor for how vector control methods are assessed, including the simultaneous measurement and correlation of entomologic and epidemiologic outcomes. Data from this trial will inform further the development of novel vector control methods. Trial registration ClinicalTrials.gov NCT04514107 . Registered on 17 August 2020 Primary sponsor: National Institute of Health, National Institute of Allergy and Infectious Diseases
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