R: A Language and Environment for Statistical Computing
... In the study, soil salinity classes are the outcome variables. In the process of data import in R core environment software [75], the categories of salinity classes were coded alphabetically as 1 (None), 2 (Moderate), and 3 (Strong). Specifically, two logit functions are needed in the three-outcome category model. ...
... Using R Core Environment software (Version 4.2.1) [75] and RStudio IDE [79], soil salinity classes at 3 different depths in the reference study area and CLNR, FNR, NDVI, AVG_HH_dB, AVG_HV_dB, Elevation, Slope, and Salinity Index 1 were selected and estimated using these environmental covariates. Descriptive statistical parameters were computed for the values of the eight chosen digital covariates within both the reference and target regions. ...
A comprehensive understanding of soil salinity distribution in arid regions is essential for making informed decisions regarding agricultural suitability, water resource management, and land use planning. A methodology was developed to identify soil salinity in Sudan by utilizing optical and radar-based satellite data as well as variables obtained from digital elevation models that are known to indicate variations in soil salinity. The methodology includes the transfer of models to areas where similar conditions prevail. A geographically coordinated database was established, incorporating a variety of environmental variables based on Google Earth Engine (GEE) and Electrical Conductivity (EC) measurements from the saturation extract of soil samples collected at three different depths (0–30, 30–60, and 60–90 cm). Thereafter, Multinomial Logistic Regression (MNLR) and Gradient Boosting Algorithm (GBM), were utilized to spatially classify the salinity levels in the region. To determine the applicability of the model trained at the reference site to the target area, a Multivariate Environmental Similarity Surface (MESS) analysis was conducted. The producer’s accuracy, user’s accuracy, and Tau index parameters were used to evaluate the model’s accuracy, and spatial confusion indices were computed to assess uncertainty. At different soil depths, Tau index values for the reference area ranged from 0.38 to 0.77, whereas values for target area samples ranged from 0.66 to 0.88, decreasing as the depth increased. Clay normalized ratio (CLNR), Salinity Index 1, and SAR data were important variables in the modeling. It was found that the subsoils in the middle and northwest regions of both the reference and target areas had a higher salinity level compared to the topsoil. This study highlighted the effectiveness of model transfer as a means of identifying and evaluating the management of regions facing significant salinity-related challenges. This approach can be instrumental in identifying alternative areas suitable for agricultural activities at a regional level.
... Gene expression data were normalized with DESeq2 [40], and PAL values were calculated for gene-centric pathways using R [41]. PALs for classical pathways were calculated using the python package oncoboxlib [20]. ...
... Statistical analysis was carried out using R [41] with the following packages: pROC [42], Stats, survival [43,44], survminer [45], and survcomp [46,47]. Results were visualized in Python 3 using seaborn [48] and matplotlib [49], as well as in R using ggplot2 [50]. ...
Individual gene expression and molecular pathway activation profiles were shown to be effective biomarkers in many cancers. Here, we used the human interactome model to algorithmically build 7470 molecular pathways centered around individual gene products. We assessed their associations with tumor type and survival in comparison with the previous generation of molecular pathway biomarkers (3022 “classical” pathways) and with the RNA transcripts or proteomic profiles of individual genes, for 8141 and 1117 samples, respectively. For all analytes in RNA and proteomic data, respectively, we found a total of 7441 and 7343 potential biomarker associations for gene-centric pathways, 3020 and 2950 for classical pathways, and 24,349 and 6742 for individual genes. Overall, the percentage of RNA biomarkers was statistically significantly higher for both types of pathways than for individual genes (p < 0.05). In turn, both types of pathways showed comparable performance. The percentage of cancer-type-specific biomarkers was comparable between proteomic and transcriptomic levels, but the proportion of survival biomarkers was dramatically lower for proteomic data. Thus, we conclude that pathway activation level is the advanced type of biomarker for RNA and proteomic data, and momentary algorithmic computer building of pathways is a new credible alternative to time-consuming hypothesis-driven manual pathway curation and reconstruction.
... The matched dataset was then analysed to describe a set of quantitative indicators of surveillance system performance for signals originating from each of the four surveillance components (20, 21) ( Table 2). All quantitative analyses of data from the community indicator-and event-based and other event-based surveillance systems were conducted using R software (22). ...
Background
This study evaluated an early warning, alert and response system for a crisis-affected population in Doolo zone, Somali Region, Ethiopia, in 2019–2021. To adequately cover an area populated by semi-nomadic pastoralist population with sparse access to healthcare facilities, the surveillance system included four components: health facility indicator-based surveillance, community indicator- and event-based surveillance, and alerts from other actors in the area. This evaluation described the usefulness, acceptability, completeness, timeliness, positive predictive value, and representativeness across each of these components.
Methods
We carried out a mixed-methods study retrospectively analysing data from the surveillance system February 2019 - January 2021 along with key informant interviews with system implementers, and focus group discussions with local communities. Transcripts were analyzed using a mixed deductive and inductive approach, with surveillance attributes used as deductive themes.
Results
1010 signals were analysed; these resulted in 168 verified events, 58 alerts, and 29 responses. Most of the alerts (46/58) and responses (22/29) were initiated through the community event-based branch of the surveillance system. In comparison, one alert and one response was initiated via the community indicator-based branch and no alerts or responses via the health-facility indicator-based branch. Positive predictive value of signals received was about 6%. About 80% of signals were verified within 24 hours of reports, and 40% were risk assessed within 48 hours. System responses included new mobile clinic sites, measles vaccination catch-ups, and water and sanitation-related interventions. Focus group discussions emphasized that responses generated were an expected return by participant communities for their role in data collection and reporting. Participant communities found the system acceptable when it led to the responses they expected. Some event types, such as those around animal health, led to the community’s response expectations not being met. Community event-based surveillance was designed to be representative of both settled and semi-nomadic communities.
Conclusions
Event-based surveillance can produce useful data for localized public health action for pastoralist populations. This approach may be better suited to public health surveillance of pastoralist populations than community indicator-based methods. Improvements could include greater community involvement in the system design and potentially incorporating One Health approaches.
... All reliability analyses were performed using R v.4.0.2. 33 The statistical significance threshold was set at p < 0.05. ...
Purpose
Laboratory tests are commonly performed by cross‐country (XC) skiers due to the challenges of obtaining reliable performance indicators on snow. However, only a few studies have reported reliability data for ski‐specific test protocols. Therefore, this study examined the test–retest reliability of ski‐specific aerobic, sprint, and neuromuscular performance tests.
Methods
Thirty‐nine highly trained XC skiers (26 men and 13 women, age: 22 ± 4 years, V̇O2max: 70.1 ± 4.5 and 58.8 ± 4.4 mL·kg⁻¹·min⁻¹, respectively) performed two test trials within 6 days of a diagonal V̇O2max test, n = 27; skating graded exercise test to assess the second lactate threshold (LT2), n = 27; 24‐min double poling time trial (24‐min DP, n = 25), double poling sprint test (SprintDP1, n = 27), and 1‐min self‐paced skating sprint test (Sprint1‐min, n = 26) using roller skis on a treadmill, and an upper‐body strength test (UB‐ST, n = 27) to assess peak power (Ppeak) with light, medium, and heavy loads. For each test, the coefficient of variation (CV), intraclass correlation coefficient (ICC), and minimal detectable change (MDC) were calculated.
Results
V̇O2max demonstrated good‐to‐excellent reliability (CV = 1.4%; ICC = 0.99; MDC = 112 mL·min⁻¹), whereas moderate‐to‐excellent reliability was found for LT2 (CV = 3.1%; ICC = 0.95). Performance during 24‐min DP, SprintDP1, and Sprint1‐min showed good‐to‐excellent reliability (CV = 1.0%–2.3%; ICC = 0.96–0.99). Absolute reliability for UB‐ST Ppeak was poor (CV = 4.9%–7.8%), while relative reliability was excellent (ICC = 0.93–0.97) across the loads.
Conclusion
In highly trained XC skiers, sport‐specific aerobic and sprint performance tests demonstrated high test–retest reliability, while neuromuscular performance for the upper body was less reliable. Using the presented protocols, practitioners can assess within‐ and between‐season changes in relevant performance indicators.
... All data analyses were conducted using R version 4.2.1. 38 A total of 786 of the 1294 participants who participated in the NDIT study had complete data on all study variables at Cycle 21. Of the 786, 16 participants reported more than 20 h per day in a single movement behavior (e.g., sleep) and were excluded because these values are highly improbable. ...
Background
Movement behaviors (i.e., physical activity [PA], sedentary behaviors [SB], sleep) relate to mental health. Although movement behaviors are often analyzed as distinct entities, they are in fact highly inter‐dependent (e.g., if an individual increases sleep, then PA and/or SB must be reduced) and these dependencies should be accounted for in the analysis. We tested whether perceptions of time spent in movement behaviors (i.e., moderate‐to‐vigorous intensity PA [MVPA], light physical activity [LPA], SB, and sleep) related to depressive symptoms and self‐report mental health in young adults using a compositional analysis. We then estimated change in depressive symptoms with reallocation of time across movement behaviors using compositional time‐reallocation models.
Methods
Data were drawn from the longitudinal NDIT dataset. Complete data were available for 770 young adults (Mage = 20.3, 55% females).
Results
The proportion of time spent in MVPA relative to other movement behaviors related to depressive symptoms non‐significantly and to mental health significantly. Reallocating 15 min from MVPA to SB resulted in a significant (0.46 unit) increase in depressive symptoms, and reallocating 15 min of MVPA to LPA was associated with a (0.57) increase in depressive symptoms.
Conclusion
These results indicate the importance of relative time spent in each movement behavior to mental health. Further research should examine these associations over time.
... We implemented our proposed approach in an R [44] package available at https:// github. com/ xthch en/ haplo test. ...
Background
The identification of genomic regions affected by selection is one of the most important goals in population genetics. If temporal data are available, allele frequency changes at SNP positions are often used for this purpose. Here we provide a new testing approach that uses haplotype frequencies instead of allele frequencies.
Results
Using simulated data, we show that compared to SNP based test, our approach has higher power, especially when the number of candidate haplotypes is small or moderate. To improve power when the number of haplotypes is large, we investigate methods to combine them with a moderate number of haplotype subsets. Haplotype frequencies can often be recovered with less noise than SNP frequencies, especially under pool sequencing, giving our test an additional advantage. Furthermore, spurious outlier SNPs may lead to false positives, a problem usually not encountered when working with haplotypes. Post hoc tests for the number of selected haplotypes and for differences between their selection coefficients are also provided for a better understanding of the underlying selection dynamics. An application on a real data set further illustrates the performance benefits.
Conclusions
Due to less multiple testing correction and noise reduction, haplotype based testing is able to outperform SNP based tests in terms of power in most scenarios.
... Using protein files exported from the Prokka annotations in FASTA format, a maximum likelihood tree was computed via the RaxML program (v8.2.12) [42], applied inside Phy-loPhlAn (v3.0.60) pipeline using the PhyloPhlAn protein markers database and with the default diversity parameter for genus/family level phylogenies [43]. The tree was visualized using the ggtree package (v3.4.4) of R (v4.2.1) [44,45]. ...
Bacteriocins are antimicrobial peptides produced by bacteria. This study aimed to in silico analyze the presence of bacteriocin gene clusters (BGCs) among the genomes of 22 commensal Staphylococcus isolates from different origins (environment/human/food/pet/wild animals) previously identified as bacteriocin producers. The resistome and plasmidome were studied in all isolates. Five types of BGC were detected in 18 genomes of the 22 bacteriocin-producing staphylococci included in this study: class I (Lanthipeptides), class II, circular bacteriocins, the non-ribosomal-peptide lugdunin and the thiopeptide micrococcin P1 (MP1). A high frequency of lanthipeptides was detected in this collection: BGC variants of BSA, bacCH91, and epilancin15X were identified in two Staphylococcus aureus and one Staphylococcus warneri isolates from food and wild animals. Moreover, two potentially new lanthipeptide-like BGCs with no identity to database entries were found in Staphylococcus epidermidis and Staphylococcus simulans from food and wild animal, respectively. Interestingly, four isolates (one S. aureus and one Staphylococcus hominis , environmental origin; two Staphylococcus sciuri , food) carried the MP1 BGC with differences to those previously described. On the other hand, seven of the 22 genomes (~32%) lacked known genes related with antibiotic or disinfectant-acquired resistance mechanisms. Moreover, the potential carriage of plasmids was evaluated, and several Rep-proteins were identified (~73% of strains). In conclusion, a wide variety of BGCs has been observed among the 22 genomes, and an interesting relationship between related Staphylococcus species and the type of bacteriocin has been revealed. Therefore, bacteriocin-producing Staphylococcus and especially coagulase-negative staphylococci (CoNS) can be considered good candidates as a source of novel bacteriocins.
... A q value < 0.05 was used to determine the significance of the gene-wide and GWAS-informed analysis using the Benjamini and Hochberg method to adjust for the false discovery rate (FDR) [63]. All analyses were performed by using R [64]. ...
Introduction
The onset of puberty is associated with a shift in the circadian timing of sleep, leading to delayed sleep initiation [i.e., later sleep onset time (SOT)] due to later bedtimes and/or longer sleep onset latency (SOL). Several genome-wide association studies (GWAS) have identified genes that may be involved in the etiology of sleep phenotypes. However, circadian rhythms are also epigenetically regulated; therefore, epigenetic biomarkers may provide insight into the physiology of the pubertal sleep onset shift and the pathophysiology of prolonged or delayed sleep initiation.
Results
The gene-wide analysis indicated differential methylation within or around 1818 unique genes across the sleep initiation measurements using self-report, actigraphy (ACT), and polysomnography (PSG), while GWAS-informed analysis yielded 67 genes. Gene hits were identified for bedtime (PSG), SOL (subjective, ACT and PSG) and SOT (subjective and PSG). DNA methylation within 12 genes was associated with both subjective and PSG-measured SOL, 31 with both ACT- and PSG-measured SOL, 19 with both subjective and ACT-measured SOL, and one gene ( SMG1P2 ) had methylation sites associated with subjective, ACT- and PSG-measured SOL.
Conclusions
Objective and subjective sleep initiation in adolescents is associated with altered DNA methylation in genes previously identified in adult GWAS of sleep and circadian phenotypes. Additionally, our data provide evidence for a potential epigenetic link between habitual (subjective and ACT) SOL and in-lab SOT and DNA methylation in and around genes involved in circadian regulation (i.e., RASD1 , RAI1 ), cardiometabolic disorders (i.e., FADS1 , WNK1 , SLC5A6 ), and neuropsychiatric disorders (i.e., PRR7 , SDK1 , FAM172A ). If validated, these sites may provide valuable targets for early detection and prevention of disorders involving prolonged or delayed SOT, such as insomnia, delayed sleep phase, and their comorbidity.
... Excluding non-native species, the final matrix consisted of 5244 records belonging to 1131 genera and 170 families. The names of all species were standardized using the R [80] software package 'plantlist' [81], with the order of families based on the nomenclature of Angiosperm Phylogeny Group IV [82]. ...
Floristic regions, conventionally established using species distribution patterns, have often overlooked the phylogenetic relationships among taxa. However, how phylogenetic relationships influence the historical interconnections within and among biogeographic regions remains inadequately understood. In this research, we compiled distribution data for seed plants in Gansu, a region of significant biogeographic diversity located in northwestern China.We proposed a novel framework for floristic regions within Gansu, integrating distribution data and phylogenetic relationships of genera-level native seed plants, aiming to explore the relationship between phylogenetic relatedness, taxonomic composition, and regional phylogenetic delineation. We found that (1) phylogenetic relatedness was strongly correlated with the taxonomic composition among floras in Gansu. (2) The southeastern Gansu region showed the lowest level of spatial turnover in both phylogenetic relationships and the taxonomic composition of floristic assemblages across the Gansu region. (3) Null model analyses indicated nonrandom phylogenetic structure across the region, where most areas showed higher phylogenetic turnover than expected given the underlying taxonomic composition between sites. (4) Our results demonstrated a consistent pattern across various regionalization schemes and highlighted the preference for employing the phylogenetic dissimilarity approach in biogeographical regionalization investigations. (5) Employing the phylogenetic dissimilarity approach, we identified nine distinct floristic regions in Gansu that are categorized into two broader geographical units, namely the northwest and southeast. (6) Based on the phylogenetic graphic regions of China across this area.
... To create the map of coalmine fire-related PM2.5 distribution in Figure 1, we used geospatial data of national, state/territory, and Statistical Area Boundaries from the Australian Bureau of Statistics, 21 coalmine boundaries from the Victorian Department of Primary Industries 22 and Department of Energy, Environment and Climate Action's DataShare platform, 23 and modelled PM2.5 distribution estimates. 24 The map was created using the following R packages: rmapshaper 25 to simplify map boundaries, sf 26,27 to read and write shapefiles, and tmap 28 to draw and save maps. ...
Background
Extreme but discrete fine particle <2.5μm (PM2.5) exposure is associated with higher prevalence of respiratory symptoms. It is unknown whether these effects abate, persist, or worsen over time, nor whether COVID-19 exacerbates PM2.5 effects.
Methods
We analysed longitudinal survey data from a cohort residing near a 2014 coalmine fire in regional Australia. A 2016/2017 survey included n=4,056 participants, of whom n=612 were followed-up in 2022. Items include questions about 7 respiratory symptoms, history of COVID-19, and time-location diaries that were combined with geospatial models of fire-related PM2.5. Associations were examined using logistic and mixed-effects logistic regressions.
Results
PM2.5 exposure predicted higher prevalence of chronic cough and current wheeze 2-3 years post-fire. At the 2022 follow-up, PM2.5 exposure was associated with worsening prevalence of chronic cough and possibly current wheeze. While were no detectable interaction effects between PM2.5 and COVID-19, participants with a history of COVID-19 exhibited more significant associations between PM2.5 exposure and respiratory symptoms.
Discussion
Short-term but extreme PM2.5 may increase the long-term prevalence of chronic cough, while COVID-19 may exacerbate the effect on other respiratory symptoms.
... The data were analysed using R version 4.2.2 [58]. The confirmatory factor analyses (CFAs) and structural equation modelling (SEM) were performed using the lavaan package [59]. ...
Background:
The increasing demand for outpatient care is associated with a higher risk of infection transmission in these settings. However, there is limited research on infection prevention and control practices in ambulatory clinics, and none focuses on patients.
Aim:
This study aims to examine outpatients' hand hygiene behaviours, their determinants, and their associations with other infection prevention measures during the COVID-19 pandemic.
Methods:
We observed the hand hygiene behaviour of one cohort of patients in one outpatient clinic and surveyed a separate sample in five clinics about their hand hygiene practice in outpatient facilities. A questionnaire based on the Theoretical Domains Framework (TDF) was used to examine predictors of the behaviour. Moreover, patients indicated their compliance with COVID-19 infection prevention measures, vaccination status, disease risk perception, and vaccine hesitancy.
Findings:
Observed hand hygiene rates among 618 patients were low (12.8%), while 67.3% of the 300 surveyed patients indicated sanitising their hands upon entering the clinic. The TDF domains memory, attention, and decision processes, and emotions significantly predicted both current (today's) and general hand hygiene behaviour in outpatient clinics. Hand hygiene behaviour and compliance with COVID-19 infection prevention showed a positive association; however, no significant connection was found with patients' vaccination status, suggesting different behavioural motivators.
Conclusion:
Hand hygiene among outpatients should be improved through interventions focusing on helping patients remember to clean their hands. More research on infection prevention in outpatient facilities is needed to ensure patient safety.
... Next, for comparability with prior research, we performed correlations between versions. Additionally, we completed the two one-sided test (TOST) procedure using the TOSTER package (Caldwell, 2022) in R (R Core Team, 2021) to statistically test for comparability between the two versions of the EIT (full code provided in Supplementary Materials; see Lakens, 2017 for a tutorial and Zimmerman et al., 2022 for an application of this procedure in language assessment research). The first step in the TOST procedure is to identify a range of scores deemed equivalent to the absence of an effect (referred to as an equivalence range). ...
Assessing proficiency in a standardized way is fundamental to second language acquisition research methodology and theory building. Ortega and colleagues' (2002) Elicited Imitation Task (EIT), developed to measure global oral proficiency across various languages, has been supported by a body of methodological research that provides evidence that the task yields scores that are internally reliable and externally valid. However, where only one EIT has been validated for a given language, as in Spanish, the EIT's usefulness for longitudinal or repeated-measures research is limited due to possible test effects. The present study tests the parallel forms reliability of a minimally modified version of the Ortega et al. (2002) Spanish EIT (version A) and a second version (version B) designed to provide a parallel option for longitudinal research. Both versions were administered to participants (n = 96), from whom self-ratings of proficiency were also collected. Parallel forms reliability was supported by a wide variety of metrics, including comparability between the versions in terms of overall scores, internal reliability, item-level statistics, and correlations with an external measure (self-ratings of proficiency). These results provide evidence for the two versions' parallel forms equivalence, which in our view supports their utility for longitudinal research. A primary goal for second language acquisition (SLA) researchers is to better understand second language (L2) proficiency, including how L2 proficiency develops over time, under what conditions it is most likely to improve, and how it affects L2 processing and future learning (see Hulstijn, 2012 for discussion). The availability of assessments that produce valid and reliable estimates of L2 proficiency is paramount in addressing these questions in research. Such assessments can aid in providing a more methodologically ☆ The first three authors contributed equally to this research. All materials used in this research are openly available on the IRIS Database. We have no conflicts of interest to disclose. We gratefully acknowledge the contributions of research assistants and colleagues from the Cognition of Second Language Acquisition Laboratory at University of Illinois Chicago, including Luz Orozco and Sergio Ramos; research assistants at Northern Illinois University, including Jennifer Kinney, Alberto Fernández, and Michelle Rauch; and research assistants at University of Tennessee, Knoxville. We also wish to thank the special issue editors, Todd McKay, and an anonymous reviewer for their insightful comments and constructive recommendations .
Background. Estimation of animal body weight (BW) is a fundamental tool in herd management for the development of reproductive, nutritional and health programmes. Objective. To compare the actual BW and its estimation by visual method and measurement of the heart girth (HG) or hip width (HW) for estimating BW in crossbred beef heifers reared under humid tropical conditions in Mexico. Methodology. Data on GH, HW, BW estimated by the visual method (MV) and actual BW were recorded in 105 crossbred replacement heifers (Bos taurus × Bos indicus) Swiss American, Beef Master, Simmental, and Brahman with different degrees of crossbreeding. Heifers ranged in age from three to 20 months and were grazed on star grass (Cynodon nlemfuensis) and humidicola grass (Brachiaria humidicola) pastures without supplementation. BW was recorded using a digital scale, HG was measured using a flexible fibreglass tape and HW was measured using a 65 cm forceps. BW by visual estimation was considered as the average of three observations made by three observers, HG and HW methods using the formula 1) BW (kg): 202.68-4.39 × HG + 0.03 × HG 2 ; 2) BW (kg): 0.26 × HW 1.90. The Pearson coefficient and the distribution (density) of each variable, were assessed using a correlation matrix graph. Also, a comparison the measures obtained by each of the different estimation methods with the observed weights, by inspecting the paired Bland-Altman plots, prior to logarithmic transformation. Results. Correlations between observed BW and predicted BW for the HG, HW and visual methods showed a positive and significant relationship (P<0.001), with r values of 0.95, 0.89 and 0.92, respectively. The HG method tended to overestimate the real BW, whereas, in the visual and HW methods, the values are evenly and randomly distributed around the line, indicating that these methods neither underestimated nor overestimated the BW. Implications. Although the HG method showed the highest correlation coefficient between observed and predicted BW, the result of the present study showed that visual assessment highlights the ability of observers
Context.
Conservation of endangered species necessitates an in-depth understanding of their ecological requirements. Particularly in landscape ecology, the behavioural tendencies of threatened butterfly species in Gotland, a biodiversity-rich island in the Baltic Sea, become crucial.
Objectives.
The primary aim of this study was to elucidate the movement patterns of three threatened butterfly species—Euphydryas aurinia, Parnassius apollo, and Phengaris arion—in Gotland and to identify the influence of specific land characteristics on these patterns.
Methods.
The study was conducted from 2017 to 2020 within a 60 km² area in Gotland. Data collection involved 29,584 captures, encompassing 16,223 distinct individuals. Variables such as open vegetated land, ground moisture index, and forest cover were assessed.
Results.
Among the 4821 arrivals and 5083 departures documented, the species exhibited differential responses to the evaluated habitat features. Both E. aurinia and P. apollo displayed a positive density-dependent dispersal, while P. arion's movements were not significantly associated with any habitat features examined. Landscape properties like open vegetated land and ground moisture index statistically influenced the likelihood of arrival and departure.
Conclusions.
The study accentuates the intricate relationship between land cover and the behavioural tendencies of the subject butterfly species. It has broader implications for the targeted habitat management strategies that would benefit threatened butterfly populations in Gotland.
Este Informe Final cumple con los requerimientos técnicos del proyecto GEFSEC ID:9766 “Promoviendo la conservación y el manejo sostenible de los humedales costeros y sus cuencas aportantes, a través de la mejora en la gestión y planificación de los ecosistemas de borde costero de la zona centro sur de Chile, hotspot de biodiversidad”, quien solicitó realizar el estudio de “Diagnóstico ambiental actual y fuentes emisoras del Humedal Costero del Río Elqui, Región de Coquimbo”. El presente Informe Final es de autoría de Gesnat Group SpA y su equipo de profesionales.
Reporte y anexos disponibles en: https://gefhumedales.mma.gob.cl/diagnostico-de-las-fuentes-emisoras-puntuales-y-difusas-de-contaminacion-del-humedal-rio-elqui/
The proportion of adult males to females in the adult population, the adult sex ratio (ASR), is an important demographic parameter that has implications in sexual selection, ecology and conservation. ASR variation can be multifactorial but specific variables including sex roles –sex differences in courtship, mate competition, social pair-bonds and parental care– and sex-specific mortality have been suggested as important ASR determinants in birds. However, these relationships have not yet been comprehensively tested in specific avian groups. Here, we used phylogenetic comparative methods to study drivers of ASR variation across shorebirds (Charadrii and Scolopaci; n = 205 species), a charismatic bird group characterised by displaying extreme variations in ecology, sex roles and sexual selection traits. We found that ASR variation is associated with most sex role components but not with their sex-specific mortality. Although sex role and life history variables showed no significant sex bias, we found a trend towards reversed size dimorphism and sex role reversal across shorebirds. Sex roles components also showed correlations among each other that were surprisingly strong and in unexpected directions. Our results confirm that sex roles are important drivers of ASR variation and suggest that shorebirds may have alternative means of sex-specific mortality, possibly linked to their ecology.
Global warming may have a significant negative impact on insects in the tropics due to an increase in the frequency and intensity of heat waves. Heat waves may have a particularly harsh impact on the relatively sessile juvenile stages of holometabolous insects, such as larvae and pupae. The honey bee (Apis mellifera L.) is an important tropical holometabolous insect whose queens and drones may also be negatively impacted by heat waves during their development, leading to reduced reproductive capacity. However, we have little information on the thermal tolerance of honey bee subspecies in tropical regions. To address this knowledge gap, we evaluated the effect of simulated heat waves during development on drones and queens of Africanized A. mellifera in terms of the size, shape, and symmetry of their forewings, as well as their reproductive traits such as sperm concentration and viability in drones, and ovariole number and spermatheca volume in queens. Drones raised at high temperatures were more asymmetric in forewing size but not in shape, and had a smaller body size and reduced sperm concentration and viability compared to those raised at normal hive temperatures. In contrast, no effect of an elevated temperature regime during development was seen in queens in terms of the size and symmetry of the forewing, the number of ovarioles, and the volume of the spermatheca. Our results support the notion that males of insects are more susceptible to high temperatures compared to females. We discuss the implications of our findings for the reproductive fitness of honey bee colonies in tropical regions.
We aimed to tackle a common problem in post-fire tree mortality where the number of trees that survived surpasses the number of dead trees. Here, we investigated the factors that affect Korean red pine ( Pinus densiflora Siebold & Zucc.) tree mortality following fires and assessed the statistical effects of class-balancing methods when fitting logistic regression models for predicting tree mortality using empirical bootstrapping ( B = 100,000). We found that Slope , Aspect , Height , and Crown Ratio potentially impacted tree mortality, whereas the bark scorch index ( BSI ) and diameter at breast height ( DBH ) significantly affected tree mortality when fitting a logistic regression with the original dataset. The same variables included in the fitted logistic regression model were observed using the class-balancing regimes. Unlike the imbalanced scenario, lower variabilities of the estimated parameters in the logistic models were found in balanced data. In addition, class-balancing scenarios increased the prediction capabilities, showing reduced root mean squared error (RMSE) and improved model accuracy. However, we observed various levels of effectiveness of the class-balancing scenarios on our post-fire tree mortality data. We still suggest a thorough investigation of the minority class, but class-balancing scenarios, especially oversampling strategies, are appropriate for developing parsimonious models to predict tree mortality following fires.
Studies of the role of bird song in avian communication have revealed numerous functions across many species, including its critical importance in female mate choice (intersexual selection) and male-male competition (intrasexual selection). A first step in understanding the role of song in different contexts is to describe the note, syllable, and song-types that occur, as well as their patterns of production within a population. Here, we do so for a north-central Illinois, USA, population of Northern House Wrens (Troglodytes aedon). As has been described in other populations, most songs (≈ 1–3 s in duration) contain an introductory section of soft, broadband notes followed by a terminal section of loud, frequency-modulated syllables that tend to be trilled. In characterizing the contents of 3.919 songs produced by 32 males throughout the breeding season, we identified 62 distinct notes, from which 76 syllables were produced. These syllables were organized in patterns largely unique to the individual—most notes and syllables were shared across the population, but almost no song-types were produced by more than one male. Singing declined over the course of the nesting cycle, and throughout the breeding season. Song production was at its minimum while fertile females were egg-laying, suggesting that males may change singing behaviour to guard against extra-pair copulations, which tend to occur at this time.
The best ideotypes are under mounting pressure due to increased aridity in many parts of the world. Understanding the conserved molecular mechanisms that evolve in wild plant species adapted to harsh environments is crucial in developing new strategies for sustainable agriculture. Yet our knowledge of such mechanisms in wild species is scant, particularly in extreme environments. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama plant species and phylogenetically related plant species that do not live in Atacama (Sister species). We analyzed pathway and reaction enrichment to understand the biochemical commonalities and differences of wild Atacama plant species. To gain insights into the mechanisms that ensure plant survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and Sister species. We found significant biochemical convergences in primary and secondary metabolism characterized by reactions enriched in at least 50% of the Atacama species across major plant phylogenetic lineages. Analysis of the annotation indicated potential advantages against drought, salinity, high solar irradiance, and nitrogen starvation. These findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh environmental conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses in these Atacama species. Hence, genes underlying these adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.
Plant translocation can increase the chances of long-term survival of threatened plant species; nevertheless, can be costly and challenging, with unknowns in the pre- and post-release phases, limiting success. Methodological advances have been made in the pre-release phase but long-term monitoring and post-release site management (i.e., “aftercare”) are not always applied and almost neglected in the literature despite being frequently effective for identifying and mitigating unexpected threats (e.g., interspecific competition, herbivory) to outplant survival.
Aiming to fill this gap, we reviewed published and gray literature on 296 translocations to shed light on the importance of aftercare on translocation outcome. We identified the most common aftercare techniques, then we performed a meta-analysis on a subset of studies that were specifically designed to test the effect of aftercare against a control (i.e., no aftercare).
The most common aftercare techniques were competition reduction, water irrigation and plant protection. Aftercare significantly increased the percentage of survival of plants when herbivory reduction and other understorey species were enhanced. Aftercare reported also a positive trend toward improved qualitative outcome when plants were protected or competition was mitigated. Nevertheless, more evidence is needed on the importance and effectiveness of aftercare techniques.
Long-term monitoring and post-release site management should be the post-translocation standard in plant translocations when ethical and possible, with plant protection, competition limitation and water irrigation being applied when needed to reduce transplant mortality. To provide statistically supported data on the effect of aftercare on translocation outcome, aftercare should be tested against a control when feasible.
OBJECTIVE
Pediatric achondroplasia is often associated with conditions requiring neurosurgical intervention, including CSF diversion and multilevel spinal decompression. However, there is a lack of clinical guidelines and reliable estimates of the benefits and risks of these interventions. This study aimed to summarize the literature on the neurosurgical management of pediatric achondroplasia patients in order to aid in determining optimal treatment and standardization of care.
METHODS
A systematic review of peer-reviewed studies with an objective diagnosis of achondroplasia, patient demographic information, and available data on neurosurgical interventions performed before 18 years of age for cervicomedullary compression, spinal stenosis, and hydrocephalus was performed. Study quality and risks of bias were assessed using standardized scores. Independent patient data on surgical indications, outcomes, reoperations, and complication risks were aggregated using means and percentages.
RESULTS
Of 204 records, 25 studies with 287 pediatric achondroplasia patients (mean age 25 ± 36 months) treated for cervicomedullary compression (n = 153), spinal stenosis (n = 100), and obstructive hydrocephalus (n = 34) were evaluated. Symptomatic cervicomedullary compression occurred early in life (mean age 31 ± 25 months), with apnea (48%), T2-weighted MRI cord signal (28%), myelopathy (27%), and delayed motor skills (15%) requiring foramen magnum decompression observed in 99% of patients, as well as cervical laminectomy in 65% of patients. Although 91% of treated patients had resolution of symptoms, 2% mortality, 9% reoperation, and 21% complication rates were reported. Spinal stenosis was treated in relatively older children (mean age 13 ± 3 years) with laminectomy (23%), as well as with instrumented fusion (73%) for neurogenic claudication (59%), back pain (15%), and sciatica (8%). Although 95% of patients had symptom resolution after surgery, 17% reported complications and 18% required reoperation. Of the hydrocephalus patients (mean age 56 ± 103 months), half were treated with endoscopic third ventriculostomy (ETV) and half had a shunt placed for progressive ventriculomegaly (66%), headaches (32%), and delayed cognitive development (4%). The shunted patients had a 3% mortality rate and an average of 1.5 shunt revisions per patient. None of the patients who underwent ETV as the primary procedure required a revision.
CONCLUSIONS
Neurosurgical intervention for pediatric achondroplasia conditions, including cervicomedullary compression, spinal stenosis, and hydrocephalus, is associated with high recovery rates and good outcomes. However, complications and reoperations are common. Further studies with follow-up into adulthood are needed to evaluate the long-term outcomes.
Deciduous forests form the dominant natural vegetation of Europe today, but were restricted to small refugia during Pleistocene cold stages, implying an evolutionary past shaped by recurrent range contractions and expansions. Cold‐stage forest refugia were probably widespread in southern and central Europe, with the northwestern Balkan Peninsula being of particular importance. However, the actual number and location of deciduous forest refugia, as well as the connections between them, remain disputed. Here, we address the evolutionary dynamics of the deciduous forest understorey species Euphorbia carniolica as a proxy for past forest dynamics. To do so, we obtained genomic and morphometric data from populations representing the species' entire range, investigated phylogenetic position and intraspecific genetic variation, tested explicit demographic scenarios and applied species distribution models. Our data support two disjoint groups linked to separate refugia on the northwestern and central Balkan Peninsula. We find that genetic differentiation between groups started in the early Pleistocene via vicariance, suggesting a larger distribution in the past. Both refugia acted as sources for founder events to the southeastern Alps and the Carpathians; the latter were likely colonised before the last cold stage. In line with traditional views on the pre‐Pleistocene origin of many southeastern European deciduous forest species, the origin of E . carniolica was dated to the late Pliocene. The fact that E . carniolica evolved at a time when a period of continuous forestation was ending in much of Eurasia provides an interesting biogeographical perspective on the past links between Eurasian deciduous forests and their biota.
A cross-sectional study was conducted on bovine brucellosis in a sample of 173 medium/small-scale cattle farmers in a tropical region of Ecuador. A total of 173 milk tank samples were collected and analyzed through an indirect ELISA. A survey was also applied to each farm to collect information on herd management, evaluate the level of knowledge about the disease and estimate the risk that bovine brucellosis on those farms could represent for public health. The apparent prevalence among farms was 11.5% (95% CI: 6.7%–16.2%). The medium farms had a prevalence significantly higher (23.8%, 95% CI: 10.9%–36.6%, p < 0.0001 ) than the small farms (7.6%, 95% CI: 4.5%–9%). Two multivariable analysis were conducted to identify risk factors associated with bovine brucellosis or reproductive disorders. Medium farms had 3.7 more odds to be infected than the small farms (OR: 3.7, 95% CI: 1.39–9.84, p = 0.008 ). Incineration/burial of abortion material was identified as a protective factor (OR: 0.4, 95% CI: 0.14–0.98, p = 0.04 ). Farm size and brucellosis were identified as risk factors for the occurrence of reproductive disorders. Only 25% of the farmers were aware of bovine brucellosis. Unpasteurized curdled milk was regularly consumed and marketed on 112 farms of which 14 were positive for bovine brucellosis. Highly at-risk practices, such as manipulation of aborted fetuses were also reported. These results indicate that there is a need to develop public health education programs targeted at medium/small-scale farmers in Ecuador.
This study describes a dataset containing urban fire events that took place in mainland Portugal between 2013 and 2022. The Regulation n.º3317-A/2018, established by the Portuguese National Emergency and Civil Protection Authority ( Autoridade Nacional de Emergência e Proteção Civil , ANEPC), defines the Operations Management System ( Sistema de Gestão de Operações , SGO). Among other attributions, this system allows to manage the lyfe-cycle of the urban fire events, from ignition to extinction, through the Operations Decision Support System ( Sistema de Apoio à Decisão Operacional , SADO). This system supports the systematic collection of a minimum set of data on each event. All instances included in the dataset were retrieved from SADO. To make the data suitable for analytic purposes, several pre-processing actions were taken, including the steps of data transformation and cleaning. The dataset was further validated by a set of technical procedures aiming to verify both data correctness and utility. The final dataset provides the most recent multi-year record of Portuguese urban fires including 27 variables on 72641 events.
Key message
A generalized performance equation is proposed to fit the Lorenz curve of the leaf size distribution of an individual plant and is validated using 12 individual bamboo plants.
Abstract
The goal of this study is to provide a rigorous tool to quantify the inequality of the leaf size distribution of an individual plant, thereby serving as a reference trait for quantifying plant adaptations to local environmental conditions. The tool to be presented and tested employs three components: (1) a performance equation (PE), which can produce flexible asymmetrical and symmetrical bell-shaped curves, (2) the Lorenz curve (i.e., the cumulative proportion of leaf size vs. the cumulative proportion of number of leaves), which is the basis for calculating, and (3) the Gini index, which measures the inequality of leaf size distribution. We sampled 12 individual plants of a dwarf bamboo and measured the area and dry mass of each leaf of each plant. We then developed a generalized performance equation (GPE) of which the PE is a special case and fitted the Lorenz curve to leaf size distribution using the GPE and PE. The GPE performed better than the PE in fitting the Lorenz curve. We compared the Gini index of leaf area distribution with that of leaf dry mass distribution and found that there was a significant difference between the two indices that might emerge from the scaling relationship between leaf dry mass and area. Nevertheless, there was a strong correlation between the two Gini indices (r² = 0.9846). This study provides a promising tool based on the GPE for quantifying the inequality of leaf size distributions across individual plants and can be used to quantify plant adaptations to local environmental conditions.
Aside from the personal and health difficulties brought about by the COVID-19 pandemic, teachers also faced tremendous work-related challenges that led to increased stress levels and poorer well-being. This is especially true for resource-constrained schools in an Eastern context. The present study aimed to examine the moderating role of principal autonomy-support on the relationship between stress and teacher well-being during the early stages of the pandemic. Data was collected from 1150 K-12 teachers in the Philippines and hierarchical multiple regression was used to assess the moderating effect of principal autonomy-support on the relationship between stress and well-being. Findings show that stress was negatively associated with emotional, psychological, and social well-being and principal autonomy-support moderated the link between stress and psychological well-being. Johnson-Neyman plots and simple slopes analyses demonstrated that the negative relationship between stress and psychological well-being is more pronounced for teachers who reported lower autonomy-support from principals and weaker for those who reported higher principal autonomy-support. The study highlights the crucial role of autonomy-supportive school leadership in mitigating the adverse effects of stress on teachers’ well-being, particularly in the challenging backdrop of a pandemic. The findings further corroborate the relevance of autonomy-support on well-being not only in the Western perspective but specifically within an Eastern, lower-middle-income context. Key discussions and research implications for improving teacher well-being are discussed.
Purpose
Soil microbial communities and related key ecological processes play critical roles in timberline delineation and soil carbon balance in alpine ecosystems, which are highly vulnerable to climate change. Accordingly, understanding their geographical differentiation will facilitate recognition of ecosystem functions and improve soil carbon models. In this study, we explored the biogeographic patterns of soil bacterial communities and their mechanisms in maintaining soil carbon balance in an alpine timberline ecosystem of the Sygera Mountains, Southeast Tibet.
Materials and methods
Soil samples were collected from typical forest belts above and below the timberline. The abundance and composition of bacterial communities, as well as functional genes, were assessed using the gene chip technology. The relationship of key microbial taxa, functional genes, and soil carbon maintenance was investigated using random forest analysis, multi-model inference, and structural equation modeling.
Results and discussion
The shrubland soil bacterial community exhibited greater diversity compared with the coniferous forest community, with higher Shannon Index and more functional genes at the taxonomic and functional levels, respectively. Bacterial community composition differed between the two forest types, with copiotrophic bacteria more abundant in shrubland, and oligotrophic bacteria more abundant in coniferous forest. The shrubland community was also more efficient at utilizing labile organic carbon, while the coniferous forest community utilized recalcitrant organic carbon more efficiently. Genes related to labile carbon degradation were more intense in shrubland, while genes related to recalcitrant carbon degradation were more concentrated in the coniferous forest. Soil temperature and C:N ratio were dominant drivers of bacterial community composition and function. Besides key soil-environment and microbial properties, certain bacterial taxa and functional genes also exerted unique roles in soil carbon variation.
Conclusions
Significant differences exist in soil bacterial community composition and functions between the two forest types above and below the timberline of the Sygera Mountains. These differences may be attributed to soil temperature and soil C:N ratio. Coupling these microbial variables into the earth system model can improve the predictive power of the carbon feedback process in terrestrial ecosystems.
Psoriasis is a dermatologic disease that affects 2% of the world population. Psoriasis is characterized by chronic inflammation and aberrant behavior of keratinocytes, which display increased levels of proliferation, and decreased differentiation and apoptosis. Stimulation of keratinocytes by psoriatic cytokines leads to the increased production of immunostimulatory ligands that further attract immune cells and amplify inflammatory responses. Psoriasis can have severe, moderate, or mild outcomes and while these severity levels demand custom medical treatment schemes, assigning an effective treatment to patients with moderate or severe disease is a demanding task. The varied responses of patients to treatments highlight a large disease complexity, demanding that new ways to analyze and integrate patients' molecular profiles are developed to design patient-specific therapies. We have used gene expression values from psoriasis biopsies to separate patients into two clusters, each with distinct expression profiles, but nevertheless not correlating with any of the available clinical data, such as disease severity. When using these gene expression levels in logical model simulations these data became highly descriptive of patient-specific phenotype characteristics. Starting from a psoriatic keratinocyte model that we published recently, we added additional pathways highlighted by a differential gene expression analysis between the subgroups. This included components from the Interleukin-1 family, IFN-alpha/beta and IL-6 signaling pathways. Model personalization was performed by using patient gene expression levels in model configurations, exploiting the PROFILE pipeline. Personalized simulations revealed that the two patient clusters represent more innate immunity-driven, highly inflammatory phenotypes and adaptive immunity-driven, chronic phenotypes, respectively. The model was also able to finely capture differences between responses in patients with a known disease severity. A treatment response analysis among the patient cohort predicted differential responses to the inhibition of psoriatic stimuli, with IL-17, TNFalpha, and PGE2 inhibition reducing proliferation and inflammatory phenotypes. Alternative treatment with PGE2 or TNFalpha inhibition instead of IL-17 was suggested for patients with high NF-kappaB activity and prosurvival factors, such as CREB1. With this project, we aim to highlight the value of combining omics data with logical modeling for the detection of "emergent" phenotypes and for gaining disease knowledge on the individual patient level.
Study objectives:
Sleep and affect are closely related. Whether modifiable cognitive factors moderate this association is unclear. This study examined whether Dysfunctional Beliefs and Attitudes about Sleep moderate the impact of sleep on next-day affect in young people.
Methods:
Four hundred and sixty-eight young people (205 adolescents, 54.1% female, M ± SDage=16.92 ± 0.87; 263 emerging adults, 71.9% female, M±SDage=21.29 ± 1.73) self-reported sleep and affect, and wore an actigraph for 7-28 days, providing >5000 daily observations. Linear mixed-effects models tested whether Dysfunctional Beliefs and Attitudes about Sleep moderated daily associations between self-reported and actigraphic sleep duration, sleep efficiency, and next-day affect on between- and within-person levels. Both valence (positive/negative) and arousal (high/low) dimensions of affect were examined. Covariates included age, sex, race/ethnicity, day of week, and previous-day affect.
Results:
Dysfunctional Beliefs and Attitudes about Sleep significantly moderated sleep and high arousal positive affect associations on between- but not within-person levels. Individuals with higher Dysfunctional Beliefs and Attitudes about Sleep (+1 SD) and lower average sleep duration (actigraphic: p = .020; self-reported: p = .047) and efficiency (actigraphic: p = .047) had significantly lower levels of high arousal positive affect. After adjusting for multiple comparisons, Dysfunctional Beliefs and Attitudes about Sleep did not moderate relationships between sleep duration and low arousal positive affect (p ≥ .340).
Conclusions:
Young people with more unhelpful beliefs about sleep and shorter, or poorer, sleep may experience dampened levels of high arousal positive affect. DBAS may constitute a modifiable factor increasing affective vulnerability on a global but not day-to-day level. Intervention studies are needed to determine if changing Dysfunctional Beliefs and Attitudes about Sleep may reduce sleep-related affect disturbances in young people.
Sucrose concentration in soy-derived foods is becoming a seminal trait for the production of food-grade soybeans. However, limited scientific knowledge is reported on this increasingly important breeding objective. In this study, 473 genetically diverse soybean germplasm accessions and 8477 high-quality single nucleotide polymorphisms (SNPs) were utilized to pinpoint genomic regions associated with seed sucrose contents through a genome-wide association study (GWAS). A total of 75 significant SNPs (LOD ≥ 6.0) were identified across GLM, FarmCPU and BLINK models, including four stable and novel SNPs (Gm03_45385087_ss715586641, Gm06_10919443_ss715592728, Gm09_45335932_ ss715604570 and Gm14_10470463_ss715617454). Gene mining near 20 kb flanking genomic regions of the four stable SNP markers identified 23 candidate genes with the majority of them highly expressed in soybean seeds and pod shells. A sugar transporter encoding major facilitator superfamily gene (Glyma.06G132500) showing the highest expression in pod shells was also identified. Moreover, selection accuracy, efficiency and favorable alleles of 75 significantly associated SNPs were estimated for their utilization in soybean breeding programs. Furthermore, genomic predictions with three different scenarios revealed better feasibility of GWAS-derived SNPs for selection and improvement of seed sucrose concentration. These results could facilitate plant breeders in marker-assisted breeding and genomic selection of sucrose-enriched food-grade soybean cultivars for the global soy-food industry.
This manuscript presents a novel geofencing method in behavioral research. Geofencing, built upon geolocation technology, constitutes virtual fences around specific locations. Every time a participant crosses the virtual border around the geofenced area, an event can be triggered on a smartphone, e.g., the participant may be asked to complete a survey. The geofencing method can alleviate the problems of constant location tracking, such as recording sensitive geolocation information and battery drain. In scenarios where locations for geofencing are determined by participants (e.g., home, workplace), no location data need to be transferred to the researcher, so this method can ensure privacy and anonymity. Given the widespread use of smartphones and mobile Internet, geofencing has become a feasible tool in studying human behavior and cognition outside of the laboratory. The method can help advance theoretical and applied psychological science at a new frontier of context-aware research. At the same time, there is a lack of guidance on how and when geofencing can be applied in research. This manuscript aims to fill the gap and ease the adoption of the geofencing method. We describe the current challenges and implementations in geofencing and present three empirical studies in which we evaluated the geofencing method using the Samply application, a tool for mobile experience sampling research. The studies show that sensitivity and precision of geofencing were affected by the type of event, location radius, environment, operating system, and user behavior. Potential implications and recommendations for behavioral research are discussed.
A fishery-independent survey with a commercial bottom otter trawl was conducted in the Pagasitikos Gulf, a semi-enclosed, trawl-restricted gulf in Greece. The study aimed to ecologically assess the fishery communities that are experiencing a decline in fishery landings. Twelve hauls of 30 min duration each were conducted in the eastern, western, and central parts of the gulf at depths between 62 and 97 m. In total, 57 species were captured, with the highest species number recorded in the west (35 species), followed by the center (32 species) and east (29 species). The highest numerical abundance was recorded at the center, followed by the east and west, with an opposing trend exhibited for biomass; however, GLM detected no significant spatial differences (in area or depth) or interaction. Ecological indices exhibited significantly lower values in the west–east area comparison. Linear Discriminant Analysis, mMDS, and hierarchical clustering indicated the presence of two main groups (east and west), with PERMANOVA showing a significant difference in the demersal communities among the identified groups. The results indicated moderately disturbed demersal communities and an increasing level of disturbance from east to west. Considering the economic value of Pagasitikos to the local fishing community, additional fishery management measures are deemed necessary to protect the fishery resources and mitigate the potential risks of overexploitation.
Recent studies suggest that eco-anxiety motivates pro-environmental behaviors. However, these studies are all cross-sectional in nature, and they frequently neglect possible important confounding variables (e.g., ecological identity). The present study was designed to deepen our understanding of the effect of eco-anxiety on pro-environmental behaviors by addressing the abovementioned limitations of recent research. The present study consisted of a 2-wave longitudinal study in which eco-anxiety and pro-environmental behaviors as well as possible confounding variables (i.e., ecological identity and personality) were assessed among French adults. As hypothesized, individuals’ experience of eco-anxiety at t1 was positively and significantly related to individuals’ engagement in pro-environmental behaviors at t2. This significant positive relationship was observed even when ecological identity, the Big Five domains of personality, and pro-environmental behaviors at t1 were controlled for. It thus appeared that compared with individuals with low levels of eco-anxiety at a given time, individuals with higher levels of eco-anxiety at a given time displayed a greater likelihood of experiencing increases in their subsequent engagement in pro-environmental behaviors. The results are discussed in light of current knowledge about the function of anxiety.
The measurement of the blood insulin concentration, and comparison to cut-offs, is essential in diagnosing insulin dysregulation, a common equine endocrinopathy. However, different insulin assays provide disparate results. We aimed to ease comparison between assays by compiling original and published data into a web app to convert insulin measurements from one assay to another. Data were available for ADVIA Centaur insulin chemiluminescent immunoassay (CLIA), Beckman Coulter insulin radioimmunoassay (RIA), Immulite 1000 CLIA, Immulite 2000 CLIA, Immulite 2000 XPi CLIA, Mercodia equine insulin enzyme-linked immunosorbent assay (ELISA), and Millipore porcine insulin RIA. Linear models were fitted for 13 assay pairs using non-decreasing splines, and integrated into this app. Assay comparisons including data from several studies showed a lower performance. This indicates technical variation between laboratories, which has not been described before, but is relevant when diagnostic measurements and cut-offs are provided by different laboratories. Nevertheless, the models’ overall high performance (median r2 = 0.94; range 0.57–1.00) supports their use to interpret results from diagnostic insulin measurements when the reference assay is unavailable, and to compare values obtained from different assays.
Dementia is on the rise in the world population and has been defined by the World Health Organization as a global public health priority. In Italy, according to demographic projections, in 2051 there will be 280 elderly people for every 100 young people, with an increase in all age-related chronic diseases, including dementia. Currently the total number of patients with dementia is estimated to be over 1 million (mainly with Alzheimer’s disease (AD) and Parkinson’s disease (PD)). In-depth studies of the etiology and physiology of dementia are complicated due to the complexity of these diseases and their long duration. In this work we present a dataset on mortality rates (in the form of Standardized Mortality Ratios, SMR) for AD e PD in Italy at provincial level over a period of 8 years (2012–2019). Access to long-term, spatially detailed and ready-to-use data could favor both health monitoring and the research of new treatments and new drugs as well as innovative methodologies for early diagnosis of dementia.
Ceratocystis wilt, caused by Ceratocystis fimbriata , is the primary disease affecting kiwifruit ( Actinidia spp. ) and a major constraint for its cultivation and expansion in Brazil. Additionally, it poses a potential threat to other major kiwifruit-producing countries, such as China, New Zealand and Italy, where the disease has not reported on kiwifruit yet. In kiwifruit vines, the infection generally initiates through the roots, but pruning wounds can also serve as an entry point for the pathogen. Currently, there is a dearth of proven effective strategies for controlling this disease, and there is no information on the effectiveness of fungicides for preventing the disease. In the present study, we evaluated the efficacy of four fungicides: metalaxyl + mancozeb, boscalide + cresoxim-methyl, pyraclostrobin, and copper hydroxide, against C. fimbriata isolates. We found that metalaxyl + mancozeb and pyraclostrobin were the most effective in inhibiting mycelial growth in vitro. However, when evaluated as wound pruning protectors in two kiwifruit cultivars, these fungicides were not effective. The results found in the in vitro assays can serve as guides for the development of chemical control of Ceratocystis wilt in kiwifruit. Furthermore, as none of the fungicides tested here were effective in protecting pruning wounds against C. fimbriata infection in kiwifruit vines, it is interesting that other active ingredients or application methods are evaluated in further studies.
Previous studies suggested that past changes in carbon sources and pathways in pelagic food webs can be investigated using carbon isotopic analysis (δ13C) of ephippia, resting-eggs produced by Daphnia. However, ephippia are known to be produced by Daphnia within a relatively short time window. Moreover, δ13CDaphnia value may vary considerably over the annual cycle of lakes due to seasonal variations in the availability of the different carbon sources for pelagic consumers, such as phytoplankton or methanogenic carbon, under the effect of stratification and turnover mechanisms. As a result, the information provided by δ13Cephippia can mainly depend on the timing of ephippia production with respect to the timing of lake autumnal turnover. Nevertheless, there is still limited information in the literature about the timing of ephippia production in relation to the seasonal variability of δ13CDaphnia. However, it may have important implications for the use of carbon isotopic signature of ephippia as a paleoecological proxy of pelagic carbon transfers in stratified lakes. In this study, we combine a limnological survey on nine French lakes with a paleolimnological approach on three sediment cores to identify the factors controlling the integration period of δ13Cephippia and to assess the relevance of using δ13Cephippia as a proxy for pelagic carbon transfers in paleolimnological studies. Our limnological survey of nine lakes suggests that δ13Cephippia depends mainly on the timing of autumnal turnover. Lakes with the earliest turnover had lower ephippia δ13C due to methanogenic carbon transfer in the pelagic food web after autumnal turnover, whereas lakes with later autumnal turnover had higher δ13Cephippia, mainly reflecting phytoplankton consumption by Daphnia during stratification period. Consequently, potential shifts over time in lake turnover timing relative to ephippia production period may lead to the misinterpretation of δ13Cephippia variations in sediment records. Our paleolimnological study on three lakes shows that complementary δ13C analysis of other Daphnia remains like claws, reflecting a time-integrated average isotopic signature of the Daphnia source population, can help to identify potential changes in the integration period of δ13Cephippia and avoid misinterpretation of stratigraphic and temporal δ13Cephippia trends regarding carbon sources fuelling pelagic consumers.
Background and aims:
Several different scoring systems for early risk stratification after out-of-hospital cardiac arrest have been developed, but few have been validated in large datasets. The aim of the present study was to compare the well-validated Out-of-hospital Cardiac Arrest (OHCA) and Cardiac Arrest Hospital Prognosis (CAHP)-scores to the less complex MIRACLE2- and Target Temperature Management (TTM)-scores.
Methods:
This was a post-hoc analysis of the Targeted Hypothermia versus Targeted Normothermia after Out-of-Hospital Cardiac Arrest (TTM2) trial. Missing data were handled by multiple imputation. The primary outcome was discriminatory performance assessed as the area under the receiver operating characteristics-curve (AUROC), with the outcome of interest being poor functional outcome or death (modified Rankin Scale 4-6) at 6 months after OHCA.
Results:
Data on functional outcome at 6 months were available for 1829 cases, which constituted the study population. The pooled AUROC for the MIRACLE2-score was 0.810 (95% CI 0.790 - 0.828), 0.835 (95% CI 0.816 - 0.852) for the TTM-score, 0.820 (95% CI 0.800 - 0.839) for the CAHP-score and 0.770 (95% CI 0.748 - 0.791) for the OHCA-score. At the cut-offs needed to achieve specificities >95%, sensitivities were <40 % for all four scoring systems.
Conclusions:
The TTM-, MIRACLE2- and CAHP-scores are all capable of providing objective risk estimates accurate enough to be used as part of a holistic patient assessment after OHCA of a suspected cardiac origin. Due to its simplicity, the MIRACLE2-score could be a practical solution for both clinical application and risk stratification within trials.
Background: Although the Bhanja bandavirus (BHAV) is widely distributed in some European countries, human infections are rarely reported. This study analyzed the prevalence of BHAV antibodies in patients with neuroinvasive diseases of unsolved etiology. Methods: A total of 254 Croatian patients who developed neurological symptoms during the four consecutive arbovirus transmission seasons (April 2017–October 2021) were tested. Cerebrospinal fluid (CSF) and urine samples were tested using RT-qPCR. In addition, CSF and serum samples were tested using a virus neutralization test. Results: BHAV RNA was not detected in any samples, while neutralizing (NT) antibodies were detected in serum samples of 53/20.8% of patients (95% CI = 16.0–26.3). In two patients, BHAV NT antibodies were detected in the CSF, indicating a recent infection. Both patients were inhabitants of rural areas in continental Croatia, and one reported a tick bite two weeks before symptoms onset. The seropositivity was high in all age groups (15.2–29.1%). The majority of seropositive patients (94.3%) resided at altitudes less than 200 m above sea level. The prevalence rates correlated positively with population density and negatively with certain climate parameters (temperature, number of hot/warm days). Conclusions: The presented results indicate that BHAV is distributed in Croatia. Further studies are needed to determine the clinical significance of this neglected arbovirus.
Previous research has provided evidence for cross-language phonological activation during visual word recognition. However, such findings mainly came from alphabetic languages, and readers’ familiarity with the two scripts might differ. The present study aimed to test whether such cross-language phonological activation can be observed in Chinese, a logographic script, without the confounding factor of script familiarity as readers read the same script in different languages. Cantonese–Mandarin bilinguals were tested in an eye-tracking experiment in which they were instructed to read sentences silently. A target word in the sentence was replaced by either a homophone in both Cantonese and Mandarin, a homophone in Cantonese or in Mandarin only, or an unrelated character. The results showed that native Cantonese readers could activate phonological representations of L1 and L2 while reading Chinese sentences silently. However, the degree to which they relied on phonological decoding in L1 and L2 varied in the two languages.
A total of 320 pigs (Line 241 × 600, DNA, Columbus, NE; initially 11.9 ± 0.22 kg) were used in a 21-d growth study to determine the available P (aP) release curve for Smizyme TS G5 2,500 (Barentz, Woodbury, MN). At approximately 19 d of age, pigs were weaned, randomly allotted to pens, and fed common starter diets. Pigs were blocked by average pen body weight (BW) and randomly allotted to one of eight dietary treatments on day 18 postweaning, considered day 0 of the study. Dietary treatments were derived from a single basal diet and ingredients including phytase, monocalcium P, limestone, and sand were added to create the treatment diets. Treatments included three diets containing increasing inorganic P from monocalcium P (0.11%, 0.20%, and 0.28% aP), or five diets with increasing phytase (500, 1,000, 1,500, 2,000, or 2,500 FTU/kg) added to the diet containing 0.11% aP. All diets were corn–soybean meal–canola meal-based and were formulated to contain 1.24% standardized ileal digestibility Lys, 0.30% phytate P, and an analyzed Ca:P ratio of 1.10:1. Prior to the beginning of the study, all pigs were fed a diet containing 0.11% aP for a 2-d period (days 16 to 18 postweaning). At the conclusion of the study, one pig, closest to the mean weight of each pen, was euthanized and the right fibula, rib, and metacarpal were collected to determine bone ash, density, and total bone P. Bones were weighed while suspended in a vessel of water and the weights used to calculate bone density (Archimedes’ principle). For bone ash, bones were processed using the non-defatted method. For the overall experimental period, pigs fed increasing inorganic P had increased (quadratic, P ≤ 0.033) average daily gain (ADG), average daily feed intake (ADFI), and final BW and a tendency for increased (quadratic, P ≤ 0.090) gain:feed ratio (G:F). Pigs fed increasing phytase had increased (quadratic, P ≤ 0.004) ADG, G:F, and final BW and increased (linear, P = 0.019) ADFI. For fibula, rib, and metacarpal characteristics, pigs fed increasing aP from inorganic P had increased (linear, P < 0.001) bone ash weight, percentage bone ash, bone density, and bone P concentration. Additionally, pigs fed increasing phytase had increased (linear or quadratic, P < 0.05) bone ash weight, percentage bone ash, bone density, and bone P. TheaP release curve generated for Smizyme TS G5 2,500 for percentage bone ash using data generated from all three bones is aP = (0.228 × FTU/kg) ÷ (998.065 + FTU/kg).
Mexico’s topographic and environmental heterogeneity, in combination with environmental fluctuations of the Neogene- Quaternary, has uniquely influenced the evolutionary history and distribution patterns of the region’s flora and fauna, sometimes causing closely related species to exhibit distinct climatic niches. Our study aimed to characterize the climatic niches of Thamnophis scalaris and Thamnophis scaliger, as well as evaluate the impact of the Pleistocene-Holocene transition on their paleodistributions. We generated 357 models per species, each with three sets of distinct combinations of climatic variables, based on 108 occurrence records for T. scalaris and 62 for T. scaliger. We evaluated the niche overlap, equivalency, and similarity between both species and transferred the present-day models to eight distinct historical periods, with the goal of encompassing the distinctive climatic variation of the Pleistocene-Holocene (P-H) transition. Both species showed significant differences in their respective climatic regimes and did not display climatic niche conservatism (the tendency of species to retain ancestral ecological characteristics), despite their previously reported ecological, morphological, and biogeographic similarities. Likewise, they seem to have responded similarly to the environmental changes in the P-H, with both paleodistributions experiencing expansion phases during glacial periods and contraction phases during interglacial periods. Possible areas of refugia that remained climatically stable and viable for both species throughout this period were identified. These refugia could potentially harbor a greater genetic diversity with respect to regions that recently acquired suitable conditions for the establishment of these populations. As such, this work offers a methodological procedure that may be used as an early inference for identifying specific regions of interest in phylogeographic studies and conservation planning.
The forest–savanna transition is the most widespread ecotone in the tropics, with important ecological, climatic, and biogeochemical implications at local to global scales. However, the factors and mechanisms that control this transition vary among continents and regions. Here, we analyzed which factors best explain the transition in northern South America (Llanos ecoregion and northwestern Amazon), where common thresholds on typical environmental factors (for example, mean annual precipitation (MAP), wet season precipitation) fail to predict it. For instance, savannas in the Llanos occur at MAP levels (> 1500 mm) which are typical of forests in other tropical regions. We examined the transition’s climate features, soils, and disturbance (fire frequency) spaces using remotely sensed data. We used logistic generalized linear models to assess the effect of seasonal (season length) and intra-seasonal (daily precipitation frequency and intensity) precipitation metrics during the dry season, soil silt content, and fire frequency, on the transition using canopy cover, tree cover, and the maximum Plant Area Volume Density as vegetation structure descriptor variables. Fire frequency and precipitation frequency were the most important variables explaining the transition. Although most fires occur in savannas, we found that a significant percentage of savanna pixels (46%) had no fires. This study indicates that the transition should be characterized regionally in response to biogeographic differences (for example, climatic space) among regions and continents. Our results highlight the importance of fire frequency and intra-seasonal precipitation in determining the transition in northern South America. Furthermore, future studies should consider regional differences in the climatic space of forest and savanna to improve projections of global change impacts on these highly diverse ecosystems.
El oeste de la Península Antártica (PA) es una de las regiones más productivas del Océano Austral, siendo las zonas costeras los lugares con mayor acumulación de fitoplancton. Particularmente, la región costera al oeste de la PA entre los 63° y 67° S encierra varios fiordos y bahías con glaciares que descargan directamente en el mar, caletas, pasajes y estrechos entre islas. Los procesos ecológicos y biogeoquímicos de estos ecosistemas costeros están fuertemente influenciados por la formación de hielo marino y la entrada de agua dulce procedente del deshielo de los glaciares y el hielo marino. Recientemente, la PA ha sufrido un rápido calentamiento climático con un aumento de 2°C de la temperatura media anual desde 1950, generando una disminución de la extensión y duración del hielo marino y el retroceso de los glaciares.
Las zonas costeras de la PA son un refugio para los mamíferos y aves marinos que llegan principalmente atraídos por su fuente de alimento, el krill antártico. El rol fundamental que cumple el fitoplancton como la base de la cadena trófica y sustento del krill, implica que cambios en su composición pueden tener efecto en cadena en todo el ecosistema. Por ejemplo, el reemplazo en esta comunidad de diatomeas microplanctónicas (>20 μm) por flagelados nanoplanctónicos (2-20 μm) podría significar una pérdida de entre el 40% y el 60% de energía en la red trófica, debido a que el krill se alimenta selectivamente de diatomeas microplanctónicas. Las altas congregaciones de krill en estas zonas costeras sugieren una alta productividad primaria asociada a floraciones de diatomeas microplanctónicas, aunque no existen estudios que lo confirmen. Tampoco estudios que describan la composición fitoplanctónica ni muestreos plurianuales que permitan captar la estacionalidad, sobre todo durante la temporada productiva (primavera-verano).
La evaluación de la estructura y dinámica de los ecosistemas en las zonas costeras al oeste de la PA es esencial para dilucidar los patrones existentes de productividad y biodiversidad y comprender la sensibilidad de dichos ecosistemas al cambio climático. En este contexto, el presente trabajo de tesis tiene como objetivo general caracterizar la composición, dinámica espacial y temporal y productividad de la comunidad fitoplanctónica de estas zonas costeras poco exploradas ubicadas en la costa oeste de la PA entre los 63° y 67° S, con el fin de proveer información de base sobre el estado actual que sirva para evaluar los posibles efectos del cambio climático sobre estas comunidades y los ecosistemas asociados. Para tal fin se colectaron muestras de agua para análisis microscópicos provenientes de distintas zonas costeras y en distintas estaciones del año (primavera, verano y otoño) entre los años 2015 y 2019, en el marco de dos proyectos colaborativos internacionales.
En este trabajo de tesis se registraron cinco grupos fitoplanctónicos principales (criptofitas, diatomeas, dinoflagelados, pequeños flagelados y prasinofitas), pertenecientes a la fracción nano y microplanctónica. Dentro de estos cinco grupos, las diatomeas fueron el grupo más común y diverso, con 50 géneros y numerosos taxones endémicos. Los organismos nanoplanctónicos (ej. criptofitas, prasinofitas y pequeños dinoflagelados) fueron difícilmente identificados microscópicamente debido a la necesidad de emplear otras técnicas o a que los organismos no coincidían con citas previas para la PA ni para Antártida. Esto sugiere que en aguas Antárticas todavía queda una diversidad inexplorada de organismos fitoplanctónicos.
Se analizó la abundancia y biomasa de los componentes del fitoplancton en las distintas estaciones del año en diferentes zonas costeras al oeste de la PA con el fin de comparar y contextualizar los resultados con investigaciones previas llevadas a cabo en otras zonas mejor conocidas de la PA. Los valores más altos de abundancia y biomasa se registraron durante los meses de primavera y verano cuando se registraron varias floraciones (≥1,5 x 106 células L-1 y ≥97,5 μgC L-1), entre ellas la primera floración de dinoflagelados desnudos al oeste de la PA. Se destaca la elevada abundancia de los nanoflagelados en estas aguas y el aporte de biomasa de las diatomeas microplanctónicas.
Asimismo, se analizó particularmente el fitoplancton de primavera (2015) y otoño (2016) en un fiordo (bahía Andvord) ubicado en la zona media de la PA, en relación con la productividad primaria y las tasas de crecimiento, medidas con incubaciones de 14C. Se destaca la alta productividad de la bahía en primavera (151,2 ± 62,5 mgC m-3 d-1), particularmente en muestras dominadas por un ensamble de diatomeas microplanctónicas (ej. Odontella weissflogii, Neomoelleria antarctica, Proboscia spp.). El ensamble dominado por criptofitas tuvo una productividad intermedia (63,1 ± 32 mgC m-3 d-1) y la productividad más baja se encontró en un ensamble dominado por pequeños dinoflagelados gymnodinioides (6,9 ± 5,1 mgC m-3 d-1). Los resultados de este análisis apoyan hipótesis previas de que el cambio climático podría afectar los ecosistemas costeros de la PA al favorecer ensambles de fitoplancton menos productivos (criptofitas) sobre ensambles de fitoplancton más productivos (diatomeas). Las estimaciones de productividad, asimilación de carbono y crecimiento del fitoplancton presentadas en esta tesis contribuyen a comprender el ciclo del carbono en estos ecosistemas.
Conjuntamente, se analizó el fitoplancton de seis zonas costeras conectadas al estrecho de Gerlache entre los 64° y 65° S durante tres veranos consecutivos (2016-2019) a lo largo de los meses de primavera-verano (de noviembre a marzo). Los patrones sucesionales detectados se ponen en contexto con procesos oceanográficos a pequeña escala, particularmente con la ocurrencia de un frente térmico que se forma en el medio del estrecho de Gerlache (~64,5°S) durante los meses de verano, separando aguas más cálidas al norte y más frías al sur. En los dos primeros veranos se encontraron diferencias significativas en la composición de la comunidad fitoplanctónica y en los patrones sucesionales al norte y al sur del área de muestreo, principalmente en los meses de alta biomasa: diciembre y enero. Durante diciembre, las criptofitas formaron floraciones al norte, mientras que las diatomeas microplanctónicas dominaron al sur, y durante enero, pequeñas diatomeas centrales dominaron al norte, mientras que las prasinofitas formaron floraciones al sur. Esta distinción espacial en las comunidades de fitoplancton se asoció a la presencia del frente térmico en el estrecho de Gerlache, que fue confirmado por el análisis de 10 años de datos de teledetección.
Esta tesis representa una línea de base a partir de la cual futuras investigaciones en zonas costeras al oeste de la PA podrán evaluar cambios en la comunidad fitoplanctónica asociados al calentamiento global. La identidad de los organismos nanoplanctónicos formadores de floraciones no pudo ser dilucidada mediante análisis ultraestructurales con microscopía electrónica, por lo cual estudios futuros deberán incluir el establecimiento de cultivos celulares y combinar análisis microscópicos y genéticos a fin de brindar una caracterización más completa de la diversidad fitoplanctónica en estas aguas. Durante el período abarcado en esta tesis no se encontraron floraciones de diatomeas microplanctónicas probablemente debido al retroceso temprano del hielo marino durante los años muestreados. Se considera también la posibilidad de que el krill antártico ejerza una importante presión de pastoreo sobre las diatomeas microplanctónicas en las zonas costeras analizadas, favoreciendo así el predominio de la fracción nanoplanctónica. Sin embargo, se necesitan análisis comparativos complementarios de fitoplancton y zooplancton para probar esta hipótesis, así como el análisis de otros factores ambientales. Estudios a futuro permitirán comprobar el poder predictivo de los patrones sucesionales aquí propuestos y seguir aprendiendo sobre la composición del fitoplancton en estas zonas costeras.
Anxiety disorders are among the most common disorders in early childhood. Although many older children and adolescents with anxiety disorders recover and remain well, little is known about the continuity of early childhood anxiety and the factors that predict persistence/recurrence in later childhood and adolescence. We followed 129 children who met anxiety disorder criteria at age 3 and/or 6 and determined how many continued to experience an anxiety disorder between age 7 and 15, as well as the continuity of specific anxiety disorders. We explored whether biological sex, number of anxiety disorders, early childhood persistence (i.e., anxiety diagnosis at both age 3 and 6), childhood comorbidities, temperamental behavioral inhibition, a maternal history of anxiety, and authoritarian and overprotective parenting predicted persistence/recurrence of an anxiety disorder from age 7 to 15. Sixty-five (50.4%) of the adolescents with an early childhood anxiety disorder met anxiety disorder criteria during the age 7–15 interval. Homotypic continuity from early childhood to school-age/mid-adolescence was observed for social anxiety disorder, separation anxiety disorder, and generalized anxiety disorder (GAD). Early childhood agoraphobia predicted school-age/mid-adolescent GAD and early childhood GAD predicted school-age/mid-adolescent specific phobia. In bivariate analyses, number of anxiety disorders, persistence of anxiety from age 3 to 6, and having a mother with a history of anxiety predicted the persistence/recurrence of anxiety disorders from age 7 to 15. Only early childhood persistence of anxiety uniquely predicted the persistence/recurrence of an anxiety disorder over and above the other predictors. Early intervention efforts should focus on identifying and intervening with young children who demonstrate a protracted course of anxiety.
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