R: A Language and Environment for Statistical Computing
... To classify the AUC measured in the EcoPlate as the presence (1) or absence (0) of carbon substrate metabolism, we used a quantile-thresholding method. [20,21] A matrix of MF values was obtained for each sample (treatment + BAC concentration on EcoPlate) and threshold (0.1-0.9). ...
... All the statistical analyses were performed in R. [21] Initially, the MF indexes of control and BAC per threshold were compared using the Kruskal-Wallis (KW) test. Then, samples (treatment + BAC concentration on EcoPlate) were compared by KW, and multiple comparisons with Dunn's test at alpha = 0.05 were conducted for thresholds 0.1, 0.5, and 0.9). ...
... Reads without any or weak classifications, where the function (% sequence identity + % alignment coverage)/2 did not exceed the value of 93, remained unclassified, and were assigned to the meta-group "No Relative" as recommended by previous studies. [29,31] The data were analyzed with R version 3.6.1 [21] using RStudio (Version 1.2.1335 © 2009-2019 RStudio). We used the relative abundance to observe qualitative differences in the taxonomic composition of the EcoPlates microbial communities between each treatment (BAC dosage in exposed and nonexposed AS). ...
Benzalkonium chloride (BAC) is a quaternary ammonium compound (QAC) widely used as the active ingredient of disinfectants. Its excessive discharge into wastewater is constant and in high concentrations, likely affecting the physiology of microbial communities. We compared the physiological community profile of activated sludge (AS) bacteria with and without prior in vitro exposure to a high concentration of BAC (10 mg L −1). We measured the community functional diversity, carbon substrate mul-tifunctionality, and the median effective concentration that inhibits carbon respiration (EC 50) using Biolog EcoPlates supplemented with a gradient of 0-50 mg L −1 of BAC. Surprisingly, we did not find significant differences in the physiological parameters among treatments. Certain abundant bacteria, including Pseudomonas, could explain the community's tolerance to high concentrations of BAC. We suggest that bacterial communities in wastewater treatment plants' AS are "naturally" adapted to BAC due to frequent and high-dose exposure. We highlight the need to understand better the effects of QACs in wastewater, their impact on the selection of tolerant groups, and the alteration in community metabolic profiles.
... All statistical analyses were conducted using R version 4.0.2 [33], with additional R packages meta (v.4.16-2 [34]) and dmetar (v.0.0.9000 [35]). Results were presented as forest plots, and the significance level was set at p ≤ 0.05. ...
Background
Surgical site infections (SSIs) represent ~ 20% of all hospital-acquired infections in surgical patients and are associated with prolonged hospital stay, admission to intensive care, and mortality. We conducted a systematic review with economic and environmental models to assess whether triclosan-coated sutures (Plus Sutures) provide benefits over non-coated sutures in the reduction of SSI risk.
Methods
Searches were conducted in fifteen databases. A total of 1,991 records were retrieved. Following deduplication and screening by two independent reviewers, 31 randomized controlled trials in adults and children were included in the review.
Similarity of the studies was assessed by narrative review and confirmed by quantitative assessment. A fixed effects meta-analysis of SSI incidence model including all groups of patients estimated a risk ratio of 0.71 (95% confidence interval: 0.64 to 0.79) indicating those in the Plus Sutures group had a 29% reduction in the risk of developing an SSI compared with those in the control group (p < 0.001). Safety outcomes were analysed qualitatively.
Results
The economic model estimated the use of Plus Sutures to result in average cost savings of £13.63 per patient. Plus Sutures remained cost-saving in all subgroup analyses with cost-savings ranging between £11 (clean wounds) and £140 (non-clean wounds).
The environmental impact of SSI is substantial, and the model suggests that the introduction of Plus Sutures could result in potential environmental benefits.
Conclusions
The evidence suggests that Plus Sutures are associated with a reduced incidence of SSI across all surgery types alongside cost savings when compared with standard sutures.
... The statistical software R, version 3.4.2, was used for all calculations [23]. The R-packages 'logicFS' and 'LogicReg' were used for the interaction analysis [24,25]. ...
Light-at-night triggers the decline of pineal gland melatonin biosynthesis and secretion and is an IARC-classified probable breast-cancer risk factor. We applied a large-scale molecular epidemiology approach to shed light on the putative role of melatonin in breast cancer. We investigated associations between breast-cancer risk and polymorphisms at genes of melatonin biosynthesis/signaling using a study population of 44,405 women from the Breast Cancer Association Consortium (22,992 cases, 21,413 population-based controls). Genotype data of 97 candidate single nucleotide polymorphisms (SNPs) at 18 defined gene regions were investigated for breast-cancer risk effects. We calculated adjusted odds ratios (ORs) and 95% confidence intervals (CI) by logistic regression for the main-effect analysis as well as stratified analyses by estrogen- and progesterone-receptor (ER, PR) status. SNP-SNP interactions were analyzed via a two-step procedure based on logic regression. The Bayesian false-discovery probability (BFDP) was used for all analyses to account for multiple testing. Noteworthy associations (BFDP < 0.8) included 10 linked SNPs in tryptophan hydroxylase 2 (TPH2) (e.g. rs1386492: OR = 1.07, 95% CI 1.02–1.12), and a SNP in the mitogen-activated protein kinase 8 (MAPK8) (rs10857561: OR = 1.11, 95% CI 1.04–1.18). The SNP-SNP interaction analysis revealed noteworthy interaction terms with TPH2- and MAPK-related SNPs (e.g. rs1386483R ∧ rs1473473D ∧ rs3729931D: OR = 1.20, 95% CI 1.09–1.32). In line with the light-at-night hypothesis that links shift work with elevated breast-cancer risks our results point to SNPs in TPH2 and MAPK-genes that may impact the intricate network of circadian regulation.
... Two-sided p-values less than 0.05 were considered statistically significant. Statistical analyses were performed using R version 4.1 [28] with packages survival [29], rms [23], and survminer [30]. ...
Background and aims
Although treatment of ischemia-causing epicardial stenoses may improve symptoms of ischemia, current evidence does not suggest that revascularization improves survival. Conventional myocardial ischemia imaging does not uniquely identify diffuse atherosclerosis, microvascular dysfunction, or nonobstructive epicardial stenoses. We sought to evaluate the prognostic value of integrated myocardial flow reserve (iMFR), a novel noninvasive approach to distinguish the perfusion impact of focal atherosclerosis from diffuse coronary disease.
Methods
This study analyzed a large single-center registry of consecutive patients clinically referred for rest-stress myocardial perfusion positron emission tomography. Cox proportional hazards modeling was used to assess the association of two previously reported and two novel perfusion measures with mortality risk: global stress myocardial blood flow (MBF); global myocardial flow reserve (MFR); and two metrics derived from iMFR analysis: the extents of focal and diffusely impaired perfusion.
Results
In total, 6867 patients were included with a median follow-up of 3.4 years [1st–3rd quartiles, 1.9–5.0] and 1444 deaths (21%). Although all evaluated perfusion measures were independently associated with death, diffusely impaired perfusion extent (hazard ratio 2.65, 95%C.I. [2.37–2.97]) and global MFR (HR 2.29, 95%C.I. [2.08–2.52]) were consistently stronger predictors than stress MBF (HR 1.62, 95%C.I. [1.46–1.79]). Focally impaired perfusion extent (HR 1.09, 95%C.I. [1.03–1.16]) was only moderately related to mortality. Diffusely impaired perfusion extent remained a significant independent predictor of death when combined with global MFR (p < 0.0001), providing improved risk stratification (overall net reclassification improvement 0.246, 95%C.I. [0.183–0.310]).
Conclusions
The extent of diffusely impaired perfusion is a strong independent and additive marker of mortality risk beyond traditional risk factors, standard perfusion imaging, and global MFR, while focally impaired perfusion is only moderately related to mortality.
... 18 All analyses were run on R version 4.2 (R Core Team, 2022). 19 Package "coxme" for the 1-stage IPD and packages "survival" and "metafor" were used for the 2-stage IPD meta-analysis. Package "ipw" was also used for the inverse probability of treatment weighted analysis. ...
IMPORTANCE The effect of continuous positive airway pressure (CPAP) on secondary cardiovascular disease prevention is highly debated. OBJECTIVE To assess the effect of CPAP treatment for obstructive sleep apnea (OSA) on the risk of adverse cardiovascular events in randomized clinical trials. DATA SOURCES PubMed (MEDLINE), EMBASE, Current Controlled Trials: metaRegister of Controlled Trials, ISRCTN Registry, European Union clinical trials database, CENTRAL (Cochrane Central Register of Controlled Trials), and ClinicalTrials.gov databases were systematically searched through June 22, 2023. STUDY SELECTION For qualitative and individual participant data (IPD) meta-analysis, randomized clinical trials addressing the therapeutic effect of CPAP on cardiovascular outcomes and mortality in adults with cardiovascular disease and OSA were included. DATA EXTRACTION AND SYNTHESIS Two reviewers independently screened records, evaluated potentially eligible primary studies in full text, extracted data, and cross-checked errors. IPD were requested from authors of the selected studies (SAVE [NCT00738179], ISAACC [NCT01335087], and RICCADSA [NCT00519597]). MAIN OUTCOMES AND MEASURES One-stage and 2-stage IPD meta-analyses were completed to estimate the effect of CPAP treatment on risk of recurrent major adverse cardiac and cerebrovascular events (MACCEs) using mixed-effect Cox regression models. Additionally, an on-treatment analysis with marginal structural Cox models using inverse probability of treatment weighting was fitted to assess the effect of good adherence to CPAP (Ն4 hours per day). RESULTS A total of 4186 individual participants were evaluated (82.1% men; mean [SD] body mass index, 28.9 [4.5]; mean [SD] age, 61.2 [8.7] years; mean [SD] apnea-hypopnea index, 31.2 [17] events per hour; 71% with hypertension; 50.1% receiving CPAP [mean {SD} adherence, 3.1 {2.4} hours per day]; 49.9% not receiving CPAP [usual care], mean [SD] follow-up, 3.25 [1.8] years). The main outcome was defined as the first MACCE, which was similar for the CPAP and no CPAP groups (hazard ratio, 1.01 [95% CI, 0.87-1.17]). However, an on-treatment analysis by marginal structural model revealed a reduced risk of MACCEs associated with good adherence to CPAP (hazard ratio, 0.69 [95% CI, 0.52-0.92]). CONCLUSIONS AND RELEVANCE Adherence to CPAP was associated with a reduced MACCE recurrence risk, suggesting that treatment adherence is a key factor in secondary cardiovascular prevention in patients with OSA.
... All the analyses were conducted with Metafor package 41 in R version 4.0.2. 42 Data Synthesis. Effects of biochar additions to GI substrates were summarized based on meta-analysis and qualitative synthesis using a vote-counting method. ...
Urbanization has degraded ecosystem services on a global scale, and cities are vulnerable to long-term stresses and risks exacerbated by climate change. Green infrastructure (GI) has been increasingly implemented in cities to improve ecosystem functions and enhance city resilience, yet GI degradation or failure is common. Biochar has been recently suggested as an ideal substrate additive for a range of GI types due to its favorable properties; however, the generality of biochar benefits the GI ecosystem function, and the underlying mechanisms remain unclear. Here, we present a global meta-analysis and synthesis and demonstrate that biochar additions pervasively benefit a wide range of ecosystem functions on GI. Biochar applications were found to improve substrate water retention capacity by 23% and enhance substrate nutrients by 12−31%, contributing to a 33% increase in plant total biomass. Improved substrate physicochemical properties and plant growth together reduce discharge water volume and improve discharge water quality from GI. In addition, biochar increases microbial biomass on GI by ∼150% due to the presence of biochar pores and enhanced microbial growth conditions, while also reducing CO 2 and N 2 O emissions. Overall results suggest that biochar has great potential to enhance GI ecosystem functions as well as urban sustainability and resilience.
... P-values were adjusted for multiple testing using the Benjamini-Hochberg correction in order to control the false discovery rate. All analyses were performed with statistical software R 3.6 [16]. Visualization of functional enrichment in networks was carried out using the Cytoscape plug-in EnrichmentMap [17]. ...
MYC-driven Group 3 medulloblastoma (MB) (subtype II) is a highly aggressive childhood brain tumor. Sensitivity of MYC-driven MB to class I histone deacetylase inhibitors (HDACi) has been previously demonstrated in vitro and in vivo. In this study we characterize the transcriptional effects of class I HDACi in MYC-driven MB and explore beneficial drug combinations.
MYC-amplified Group 3 MB cells (HD-MB03) were treated with class I HDACi entinostat. Changes in the gene expression profile were quantified on a microarray. Bioinformatic assessment led to the identification of pathways affected by entinostat treatment. Five drugs interfering with these pathways (olaparib, idasanutlin, ribociclib, selinexor, vinblastine) were tested for synergy with entinostat in WST-8 metabolic activity assays in a 5 × 5 combination matrix design. Synergy was validated in cell count and flow cytometry experiments. The effect of entinostat and olaparib on DNA damage was evaluated by γH2A.X quantification in immunoblotting, fluorescence microscopy and flow cytometry.
Entinostat treatment changed the expression of genes involved in 22 pathways, including downregulation of DNA damage response. The PARP1 inhibitors olaparib and pamiparib showed synergy with entinostat selectively in MYC-amplified MB cells, leading to increased cell death, decreased viability and increased formation of double strand breaks, as well as increased sensitivity to additional induction of DNA damage by doxorubicin. Non-MYC-amplified MB cells and normal human fibroblasts were not susceptible to this triple treatment.
Our study identifies the combination of entinostat with olaparib as a new potential therapeutic approach for MYC-driven Group 3 MB.
... Statistical analyses were performed with R software [16] version 4.2.1 using the packages base, lsmeans [17] version 2.30-0 and multcomp [18] version 1.4-20. Chisquare tests of homogeneity and hypothesis tests in the linear models were performed at a 5% statistical significance level. ...
Background
In the current context of global warming, thermal manipulation of avian embryos has received increasing attention as a strategy to promote heat tolerance in avian species by simply increasing the egg incubation temperature. However, because of their likely epigenetic origin, thermal manipulation effects may last more than one generation with consequences for the poultry industry. In this work, a multigenerational and transgenerational analysis of thermal manipulation during embryogenesis was performed to uncover the long-term effects of such procedure.
Results
Thermal manipulation repeated during 4 generations had an effect on hatchability, body weight, and weight of eggs laid in Japanese quails, with some effects increasing in importance over generations. Moreover, the effects on body weight and egg weight could be transmitted transgenerationally, suggesting non-genetic inheritance mechanisms. This hypothesis is reinforced by the observed reversion of the effect on growth after five unexposed generations. Interestingly, a beneficial effect of thermal manipulation on heat tolerance was observed a few days after hatching, but this effect was not transgenerational.
Conclusions
Our multigenerational study showed that thermal conditioning of quail embryos has a beneficial effect on post-hatch heat tolerance hampered by transgenerational but reversible defects on growth. Assuming that no genetic variability underlies these changes, this study provides the first demonstration of epigenetic inheritance of traits induced by environmental temperature modification associated with long-term impacts in an avian species.
... Analogous to the data management steps, analyses are performed on a secure server using R (version ≥ 4.1 ) [32]. ...
Background
Osteoporosis poses a growing healthcare challenge owing to its rising prevalence and a significant treatment gap, as patients are widely underdiagnosed and consequently undertreated, leaving them at high risk of osteoporotic fracture. Several tools aim to improve case-finding in osteoporosis. One such tool is the Fracture Risk Evaluation Model (FREM), which in contrast to other tools focuses on imminent fracture risk and holds potential for automation as it relies solely on data that is routinely collected via the Danish healthcare registers. The present article is an analysis protocol for a prediction model that is to be used as a modified version of FREM, with the intention of improving the identification of subjects at high imminent risk of fracture by including pharmacological exposures and using more advanced statistical methods compared to the original FREM. Its main purposes are to document and motivate various aspects and choices of data management and statistical analyses.
Methods
The model will be developed by employing logistic regression with grouped LASSO regularization as the primary statistical approach and gradient-boosted classification trees as a secondary statistical modality. Hyperparameter choices as well as computational considerations on these two approaches are investigated by an unsupervised data review (i.e., blinded to the outcome), which also investigates and handles multicollinarity among the included exposures. Further, we present an unsupervised review of the data and testing of analysis code with respect to speed and robustness on a remote analysis environment. The data review and code tests are used to adjust the analysis plans in a blinded manner, so as not to increase the risk of overfitting in the proposed methods.
Discussion
This protocol specifies the planned tool development to ensure transparency in the modeling approach, hence improving the validity of the enhanced tool to be developed. Through an unsupervised data review, it is further documented that the planned statistical approaches are feasible and compatible with the data employed.
... We used Mplus 8.7 [52] to compute the multilevel reliability coefficients, estimate the models for our hypothesis tests, and for sensitivity and additional analyses. Preliminary analyses and all other reliability estimates were computed using R version 4.2.1 [59]. ...
Background
Instability in self-esteem and instability in affect are core features of borderline personality disorder (BPD). For decades, researchers and theorists have been interested in the temporal dynamics between these constructs. Some hypothesize that changes in affective states should precede changes in self-esteem (Linehan, Cognitive-behavioral treatment of borderline personality disorder. Diagnosis and treatment of mental disorders, 1993), while others suggest that changes in self-esteem should precede changes in affective states (Kernberg, Borderline conditions and pathological narcissism, 1975).
Methods
In this study, we investigated the temporal relations between negative affective arousal states and current self-esteem in daily life. Patients with BPD (n = 42) or depressive disorders (DD; n = 40), and non-clinical controls (NCC; n = 40) were assessed every 15 min for 13 h.
Results
As expected, dynamic structural equation modeling showed higher levels of average daily negative affective arousal and lower levels of average daily self-esteem in the BPD group compared with the NCC group, and scores in the DD group were in-between the BPD and the NCC groups. In line with predictions based on Linehan’s (Cognitive-behavioral treatment of borderline personality disorder. Diagnosis and treatment of mental disorders, 1993) model of affective dysregulation in BPD, negative affective arousal (t) and subsequent self-esteem (t+ 1) were significantly linked only in the BPD group, implying that higher negative affective arousal is followed by lower current self-esteem in the next measurement (ca. 15 min later). Importantly, self-esteem (t) and subsequent negative affective arousal (t + 1) were not significantly related (Kernberg, Borderline conditions and pathological narcissism, 1975).
Conclusions
Our findings suggest close dynamic temporal relations between affective instability and self-esteem instability in BPD, which highlights the importance of providing patients with means to effectively modulate high negative affective arousal states.
... (Variance Component Estimation Method) in agricolae package of R 3.4.3 [11] which is applicable for families of partially balanced designs like lattice and alpha designs. The model used in analysis of variance was: ...
The existence of genetic variability is a prerequisite in crop improvement programs. Thus, the experiment was conducted to assess genetic variability among sesame accessions collected from different regions of Ethiopia based on their qualitative and quantitative traits. A total of forty-nine sesame genotypes were evaluated at Kamashi research sub-station during 2017/18 cropping season. The experimental design used was 7 x 7 simple lattice design. Each experimental material was planted on a plot consisted of 5 rows with 4 m length, and 10 cm and 40 cm intra and inter row spacing, respectively. Data was recorded on 10 qualitative and 14 quantitative traits. Statistical analysis was computed using R and SAS University Edition. In the present study, genetic variation was exhibited among sesame genotypes for eight qualitative traits such as leaves hairiness, stem hairiness, capsule hairiness, number of flower/leaf axil, number of capsules/leaf axil, number of carpels/capsule, number of locules/capsule and seed coat color. In addition, analysis of variance on quantitative traits revealed the presence of genetic variability among sesame genotypes for days to flowering, bacterial blight disease resistance, days to maturity, plant height to first branching, length of capsule bearing zone, internode length, capsule length, number of capsules/plant, 1000 seeds weight and seed yield. Factor analysis confirmed that bacterial blight disease resistance, plant height, length of capsule bearing zone, number of branches/plant, number of capsules/plant and seed yield were the most important traits those highly contributed to an observed genetic variation. Further, cluster analysis based on 14 quantitative traits grouped the 49 sesame genotypes into seven groups, indicating the presence of genetic potential which could be exploited in sesame breeding.
... All data were processed using the software RStudio R 3.0.1 [37] and SPSS version 22. The Confirmatory Factor Analysis (CFA) was conducted through the robust weighted least squares-means and variance adjusted (WLSMV) estimator and followed the same procedure used by Cerolini and colleagues [28] to test the best factor structure of the model. ...
Background
It remains unclear among clinicians and researchers whether orthorexia nervosa (ON) is a part of the obsessive–compulsive disorder spectrum or eating disorders. Disgust seems to be a shared psychopathological factor in these clinical presentations, indicating a potentially crucial role in ON. On the other hand, numerous psychometric tools have been developed to evaluate ON. The Dusseldorf Orthorexia Scale (DOS) was recently validated in an Italian sample. However, the study's primary limitation was that the scale was only administered to undergraduate university students. This study aimed to investigate the psychometric properties (including factorial structure, reliability, and measurement invariance conditional on sex) of the Italian version of the DOS (I-DOS) on a sample from the general population. Additionally, the study sought to determine the nomological validity of the I-DOS by examining its relationship with disgust sensitivity.
Methods
A sample of 521 participants took part in this study and completed a battery that assessed ON and disgust sensitivity. To assess the I-DOS structure, reliability, and measurement invariance we respectively conducted confirmatory factor analysis (CFA), computed McDonalds’s omega, and performed hierarchical series of multigroup CFAs. Then, we tested the relationship between ON and disgust sensitivity.
Results
CFA confirmed the unifactorial model of I-DOS and it respected the configural, metric, and strict invariance while a partial scalar invariance was achieved. It also showed good reliability with an omega of 0.87. In addition, we found a positive relationship between ON and disgust sensitivity, thus confirming the nomological validity of I-DOS.
Conclusions
Our findings suggest that the Italian version of the Dusseldorf orthorexia scale (I-DOS) exhibits strong psychometric properties and can be an effective instrument for assessing ON in a general population sample. Notably, the most significant and innovative outcome was the positive correlation between ON and disgust sensitivity. As disgust has been linked to other clinical presentations, this preliminary result could serve as a foundation for future research exploring this phenomenon in greater detail.
... The visual 2D-3D interactions of the best-analysed conformation with the lowest binding energy value (kcal/mol) were further used to understand the characteristic bonds (i.e. Hydrogen, polar groups, pi-cation, pi-pi stack) exhibited between the docked protein-ligand structure using PyMol software and the Schrodinger plugin ( This research methodology created a scatter plot using the R programming language [33] and the ggplot2 library [34]. The data consisted of two variables, namely MMGBSA (ΔGbind) and Docking Scores (kcal/mol), which were used to create a data frame. ...
Beyond the pains of pregnancy, miscarriages and other child-bearing risks associated with the pride of motherhood, Uterine fibroids (UFs) are another significant reproductive age detriment in women’s health. These tumours are often challenging to detect in the early stage until they become large outgrowth which always requires surgical removal to mitigate risks. However, with the understanding of alteration in the complex signalling pathways, specific proteins connected in this rapid outgrown have been identified, and some studies have been reported on dietary phytochemicals’ potency to halt the growth. Consequently, this computer-aided study explores this class of phytochemicals as inhibitors of five specific UFs targets (estrogen receptor protein (ESR), epidermal growth factor receptor protein (EGFR), insulin-like growth factor 1 receptor (IGF-1R), progesterone receptor (PGR), and Yes1 Associated protein (YAP1)). During the screening, the gene-disease association revealed a correlation between these proteins to six reproductive conditions including UFs with a 0 to 1 evidence index. The molecular docking and molecular mechanics’ free energy combined with Generalized Born and surface area showed comparable close points in the regression line supporting the binding affinity of dietary phytochemicals to the mapped proteins’ active site. Overall, more than 50% of the phytochemicals exhibit good pharmacokinetic, drug-likeness and ADMET profiles as compared to the standard drugs and co-ligands. Hence, their PASS bioactivity supports anti-cancer potential with a good Pa > Pi ratio, and they have stable and less reactivity from the quantum mechanical calculation. Ultimately, these phytochemicals are proposed for further experimental evaluation for efficacy in managing and treating UFs.
... Measured parameters were analysed in R Version 4.0.2 [28] by fitting linear models and using an analysis of variance (ANOVA) with 'species' and 'P treatment' as predictor variables. Linear mixed-effects models were fitted to the root traits that were measured in each soil layer (i.e., topsoil, band, and subsoil) (R package: nlme) [29]. ...
The root traits of many warm-season pasture species have not been characterised thoroughly. Depending on the nature of legume root architecture, alternative phosphorus (P) application strategies may improve the success of legume establishment and persistence, particularly if legumes exhibit a spatially responsive root system. The purpose of the present experiment was to investigate the root morphology of several warm-season pasture species and to determine the response of these species to a subsurface application of P fertiliser. Monocultures of two grasses (Panicum coloratum and Digitaria eriantha) and two legumes (Medicago sativa and Desmanthus spp.) were established in pots to investigate root morphology and P acquisition in response to three soil-P distribution treatments. The P fertiliser that was applied to the subsurface ‘band’ layer was labelled with 32P-radioisotope to determine P recovery. There were significant differences in shoot yield and root morphology among the species. The largest shoot yields were usually produced by plants grown in the uniform high-P treatment, while the grasses generally produced longer roots more efficiently than the legumes across the three soil-P distribution treatments. Nevertheless, each species responded to the banded high-P treatment by acquiring more P from the zone of P enrichment (banded high-P = 31% cf., uniform low-P = 3%, and uniform high-P = 9%). This result suggests that a subsurface application of P fertiliser at the planting stage will benefit warm-season pasture species, particularly grasses that are highly responsive to fertiliser placement. Nevertheless, preferential placement of fertiliser below legumes may improve the productivity of this component if their root systems have more time to respond spatially.
... A data analysis was performed in the R 4.2.1 environment for statistical analysis [10]. The normality of the data and the homogeneity of variances were evaluated using the Shapiro-Wilk and Bartlett tests, respectively. ...
Physical exercise generates a systemic response in the immune system. It has been observed that cell populations respond to exercise stimuli, especially Natural Killer cells, whose number increase within minutes of starting physical exertion. This study aimed to evaluate the acute effect of moderate- and high-intensity exercise on immunological markers in healthy women. As specific objectives, the percentages of CD3-CD56+ Natural Killer total cells, CD56brightCD16dim effector subpopulation, CD56dimCD16bright cytotoxic subpopulation, NKG2A inhibition receptor, NKG2D activation receptor, and NKT cells were analyzed. In addition, the levels of the cytokines IL-1β, IL-6, IL-8, IL-10, IL-12p70, and TNF and the chemokines CCL5/RANTES, CXCL9/MIG, CCL2/MCP-1, and CXCL10/IP-10 were also analyzed. Natural Killer total cells showed an increase in their percentage in both exercise protocols (p = 0.001 for the moderate-intensity group and p = 0.023 for the high-intensity group); however, only in the high-intensity exercise session was there an increase in the CD56dimCD16bright cytotoxic subpopulation (p = 0.014), as well as a decrease in CD56brightCD16dim effector subpopulation (p = 0.001) and their NKG2A inhibition receptor (p = 0.043). An increase in IL-6 was observed after the high-intensity exercise session (p = 0.025). Conclusions. Physical exercise influences immunological markers and shows an acute response to moderate- or high-intensity exercise.
... Once the best model is selected, the values of parameters related to the disease dynamics were inferred by re-running the ABC-SMC algorithm separately for the model. The disease simulations were implemented in the C programming language and the ABC-SMC algorithm was run in R [16]. ...
In December 2014, a novel foot and mouth disease (FMD) virus was introduced to a pig farm in South Korea, despite the animals being vaccinated. A marginal antigenic matching between the novel and vaccine strains potentially led to the infection of the vaccinated animals. To understand the impact of using an FMD vaccine on the transmission dynamics of an unmatched field strain, simulation models were employed using daily reported data on clinical cases from the farm. The results of this study indicated that immunisation with the FMD vaccine reduced the shedding of the novel FMD virus in pigs. However, there was no evidence to suggest that the immunisation had a significant effect in reducing the development of clinical signs. These findings highlight that the use of an unmatched FMD vaccine can confound the outbreak by altering the disease dynamics of the novel virus. Based on this study, we emphasise the importance of continuous testing to ensure antigenic matching between the circulating strains and the vaccine pool.
We use granular information on securities holdings from 2008 to 2021 to estimate the market risk of Italian bank securities portfolios. The market risk is measured by the value-at-risk and the expected shortfall. The main advantages of our approach are the following: (1) profits and losses are computed through simple operations and without the need of complex calibration algorithms; (2) we are able to incorporate all market data available in Refinitiv; and (3) the risk measures can be estimated for all banks located in Italy, irrespective if the bank has validated internal models for market risk or not. Finally, we conduct an econometric analysis to identify the main drivers of market risk and to perform a forecasting exercise.
Accumulating evidence suggests that substance addictive behaviors are associated with traumatic experiences, emotion dysregulation, and psychopathological symptoms. Emotion dysregulation may contribute to initiating and sustaining addictive behaviors, as a way to cope with interpersonal trauma. However, the interplay between interpersonal trauma, emotion dysregulation, and substance addictive behaviors is still understudied. An online survey was disseminated via snowball sampling. One thousand four hundred and forty-six individuals from the Italian general population were assessed for substance addictive behaviors, interpersonal trauma, emotion dysregulation, and psychopathological symptoms. A correlation network approach was used to examine the associations among these variables. Positive relationships were found between interpersonal trauma, emotion dysregulation, and substance addictive behaviors. Emotional neglect bridged the other types of trauma with substance use and psychopathology. Among psychopathological variables, depression, anxiety, and impaired personality functioning symptoms had the highest strength. Emotion dysregulation had the highest bridging. The findings suggest that psychopathological symptoms, emotion dysregulation, and emotionally traumatic experiences play a significant role in the activation of the addictive behavior network. Promoting emotion regulation strategies might be part of preventative actions and early intervention programs for substance addictive behaviors.
Individuals across various animal species communicate their presence to conspecifics. Especially phytophagous and parasitoid insects with their brood developing on limited resources rely on chemical cues, such as host-marking pheromones, to reduce intraspecific competition. Bark beetles are phytophagous insects with some species being economically and ecologically relevant forest pests. Several of them use the volatile compound verbenone to inhibit attraction and reduce intraspecific competition. However, in the Eurasian spruce bark beetle, Ips typographus (L.), temporal emission patterns did so far not quite support the putative function of verbenone as an indicator of densely colonised host trees. More importantly, it is currently unclear how well verbenone emission is actually related to colonisation density and thus intraspecific competition. Here, we inoculated Norway spruce logs with I. typographus at two defined colonisation densities in the greenhouse and measured the emission of verbenone and its precursors α-pinene and verbenol over time. Verbenone emission was 3–7 times greater from colonised logs compared to decaying logs without beetles during the major part of larval development. Furthermore, our data supports the quantitative hypothesis, that the termination of attack on a tree is mediated by a cessation of the release of verbenol and continuous emission of verbenone. The latter is most likely a passively produced host-marking cue reflecting the actual density of conspecifics since per-beetle emission was unaffected by colonisation density. These findings shed new light on the regulation of bark beetle mass aggregations, which are currently causing previously unseen economic damages in temperate forests.
Primary production in freshwater ecosystems is largely a function of light and nutrient availability, both of which have been changing in many lakes and reservoirs in response to anthropogenic pressures. Recent studies focusing on natural lakes have found a hump-shaped response of primary production (sometimes measured as chlorophyll-a) to dissolved organic matter (DOM, measured as dissolved organic carbon, DOC), which has both light-absorbing chromophoric properties and DOM-bound nutrients. We used the United States National Lakes Assessment dataset to integrate reservoirs into this paradigm in comparison with natural lakes and assessed the relative differences in the predicted response’s model structure, regression parameter values, and drivers of the chlorophyll-a residuals. We found that chlorophyll-a in reservoirs exhibited a hump-shaped response to DOC, while natural lakes from this dataset were better fit with a linear response, differing from previous studies focused on boreal lakes. Despite this, reservoirs had a greater maximum chlorophyll-a response compared to natural lakes in this study (45.5 versus 33.8 μg L⁻¹), which occurred at a lower DOC concentration threshold (18.3 versus 26.4 mg L⁻¹) when compared using quadratic models. Reservoirs had lower median light:nutrient values compared to natural lakes, and greater median surface area and total phosphorus (TP), that can all influence the light environment and the peak chlorophyll-a responses. In both reservoirs and natural lakes, chlorophyll-a residuals were most strongly influenced by TP, where TP < 25–30 µg L⁻¹ suppressed chlorophyll-a residuals and higher TP amplified them. Light:nutrient values were somewhat important predictors, and patterns with chlorophyll-a residuals supported previous work showing low light:nutrient values amplified chlorophyll-a responses and higher values suppressed them. Quantifying the shape of the response of primary production to DOM quantity and quality as well as the drivers of the residuals, namely TP for lakes and reservoirs in this dataset, will be important for understanding the effects that changes in water quality may have on primary production and freshwater ecosystem processes.
Wetland restoration has received increasing attention to compensate for the continuing loss of natural wetlands and revive biodiversity and associated ecological functions. The development of methods for assessing the effectiveness of restoration measures is important for wetland management. However, most studies assessing restoration success in freshwater ecosystems are based on taxonomic biodiversity; trait-based approaches remain limited, particularly in wetland ecosystems. Here, we assess the effectiveness of wetland restoration in the Sanjiang Plain, Northeast China, based on the trait composition and functional diversity of aquatic insect assemblages. We found that functional richness in restored wetlands was significantly higher than impacted wetlands but lower than natural wetlands. Compared to natural wetlands, functional beta diversity of impacted wetlands was higher. In terms of dissimilarity between wetland types, trait composition of aquatic insects in restored wetlands showed a higher similarity to natural wetlands compared to those in impacted wetlands. Trait compositions of aquatic insect assemblages in restored wetlands were more similar to impacted wetlands in May but showed a greater similarity to natural wetlands in October. Our study shows that restoration measures have facilitated the partial recovery of functional diversity and trait composition of aquatic insect assemblages in the Sanjiang Plain wetlands. Our study confirms the potential of using trait-based approach to assess the effectiveness of wetland restoration. Given that assessments based on taxonomic and trait data can provide complementary information, we recommend incorporating both taxonomic and functional metrics and considering seasonal dynamics of wetlands in post-restoration monitoring and assessment in wetlands.
_Introduction_ People in low- to middle-income countries, such as Bangladesh, have less access to healthcare than those in wealthier nations. In Bangladesh, households spend an average of Tk 103.46 billion (US $1.49 billion) on out-of-pocket medical costs each year, which accounts for 64.3% of total health expenditures. The informal sector, which employs 85.1% of the total workforce, has limited or no health insurance (HI). Less than 1% of Bangladesh’s population has access to social health protection, which is mostly limited to those who work in the formal sector (14.9% of all jobs). This comparative study will use the contingent valuation method to determine the willingness-to-pay (WTP) for health insurance and associated factors between formal and informal health workers. _Methods and analysis_ This is the study protocol for a comparative study of the willingness-to-pay (WTP) for health insurance and associated factors between formal and informal health workers using the contingent valuation method (CVM), which will be conducted over a 12-month period, from September 2022 to September 2023. A total of 250 health workers will be selected by a convenience sampling technique from various formal and informal work stations in Dhaka City. Of the 250 participants, 125 will be from the formal sector and 125 will be from the informal sector. To collect data, a semi-structured questionnaire will be used via face-to-face interviews. Data will be processed and analyzed using R (version 4.3.0), RStudio (2023.03.1 Build 446). WTP for social health insurance will be estimated using the DCchoice package. _Ethics and dissemination_ Ethical clearance was obtained from the Institutional Review Board (IRB) of the National Institute of Preventive and Social Medicine (NIPSOM) on December 29, 2022. The memo number is NIPSOM/IRB/2022/14 (1). Informed consent will be taken from each participant before data collection. Privacy and confidentiality of data will be maintained strictly. Participants will have full freedom to refuse to participate at any point in the study. The results of the study will be published in scientific, peer-reviewed journals. _Strengths and limitations of this study_ 1. The contingent valuation method is a well-established method of eliciting WTP for health insurance. 2. The current study will be among the first of its nature as it will focus on formal and informal healthcare workers. 3. Starting point bias may affect the result as this type of bias comes with the Double bounded dichotomous choice (DBDC) method used in this study.
This paper addresses knowledge gaps in the biomass, productivity and value of livestock for the pastoral, mixed crop-livestock and specialized dairy systems in Ethiopia. Population size, reproductive performance, mortality, offtake and productivity of cattle were calculated from official statistics and a meta-analysis of data available in the published literature. This information was then used to estimate biomass and output value for 2020 using a herd dynamics model. The mixed-crop livestock system dominates the Ethiopian cattle sector, with 55 million cattle (78% total population) and contributing 8.52 billion USD to the economy through the provision of meat, milk, hides and draft power in 2021. By comparison, the pastoral (13.4 million head) and specialized dairy (1.8 million head) systems are much smaller. Productivity varied between different production systems, with differences in live body weight, productivity and prices from different sources. The estimated total cattle biomass was 14.8 billion kg in 2021, i.e., 11.3 billion kg in the mixed crop-livestock system, 2.60 billion kg in the pastoral system and 0.87 billion kg in the specialized dairy system. The total economic asset values of cattle in the mixed crop-livestock, pastoral and specialized dairy systems were estimated as 24.8, 5.28 and 1.37 billion USD, respectively. The total combined output value (e.g., beef, milk and draft power) of cattle production was 11.9 billion USD, which was 11.2% of the GDP in Ethiopia in 2021. This work quantifies the importance of cattle in the Ethiopian economy. These estimates of herd structure, reproductive performance, productivity, biomass, and economic value for cattle production systems in Ethiopia can be used to inform high-level policy, revealing under-performance and areas to prioritize and provide a basis for further technical analysis, such as disease burden.
Most of the empirical evidence that lays the ground for research on recognition of printed morphologically complex words comes from experimental paradigms employing morphological priming, e.g., exposure to morphologically related forms. Furthermore, most of these paradigms rely on context-less presentation of isolated words. We examined whether well-established morphological priming effects (i.e., faster recognition of a word preceded by a morphologically related word) are observable under more natural conditions of fluent text reading. Using the GECO database of eye-movements recorded during the reading of a novel, we examined the long-lag morphological and identity priming in one's first language (L1, English and Dutch) or second language (L2, English). While the effects of identity priming were ubiquitous, no evidence of morphological priming was observed in the L1 or L2 eye-movement record. We discuss implications of these findings for ecological validity and generalizability of select current theories of morphological processing.
Species distributions are conventionally modelled using coarse‐grained macroclimate data measured in open areas, potentially leading to biased predictions since most terrestrial species reside in the shade of trees. For forest plant species across Europe, we compared conventional macroclimate‐based species distribution models (SDMs) with models corrected for forest microclimate buffering. We show that microclimate‐based SDMs at high spatial resolution outperformed models using macroclimate and microclimate data at coarser resolution. Additionally, macroclimate‐based models introduced a systematic bias in modelled species response curves, which could result in erroneous range shift predictions. Critically important for conservation science, these models were unable to identify warm and cold refugia at the range edges of species distributions. Our study emphasizes the crucial role of microclimate data when SDMs are used to gain insights into biodiversity conservation in the face of climate change, particularly given the growing policy and management focus on the conservation of refugia worldwide.
This longitudinal study of low-income families tested neighborhood-, family-, and child-centered promotive factors in early childhood, responses to an early family intervention, and their interactions as predictors of school-entry levels of and early school-age gains in academic skills. Using a racially-diverse, low-income sample (n = 527) from a randomized controlled trial of the Family Check-Up (FCU) intervention and Bayesian multilevel regression modeling, we tested whether neighborhood cohesion, positive mother-child engagement, and child self-regulation in early childhood (ages 2-5 years) and their interactions with FCU group assignment predicted the intercept and slope of academic skills across child age 5, 7.5, and 8.5 years. Higher positive mother-child engagement and child self-regulation predicted higher academic skills at school entry. An interaction between the FCU intervention and positive mother-child engagement predicted gains in academic skills compared to national norms. The findings suggest the FCU intervention leveraged positive mother-child engagement in early childhood to promote academic skills, offering a potential avenue from which to prevent income achievement gaps before school entry.
A fundamental question in invasive plant ecology is whether invasive and native plants have different ecological roles. Differences in functional traits have been explored, but we lack a comparison of the factors affecting the spread of co-occurring natives and invasives. Some have proposed that to succeed, invasives would colonize a wider variety of sites, would disperse farther, or would be better at colonizing sites with more available light and soil nutrients than natives. We examined patterns of spread over 70 years in a regenerating forest in Connecticut, USA where both native and invasive species acted as colonizers. We compared seven invasive and 19 native species in the characteristics of colonized plots, variation in these characteristics, and the importance of site variables for colonization. We found little support for the hypotheses that invasive plants succeed by dispersing farther than native plants or by having a broader range of site tolerances. Colonization by invasives was also not more dependent on light than colonization by natives. Like native understory species, invasive plants spread into closed-canopy forest and species-rich communities despite earlier predictions that these communities would resist invasion. The biggest differences were that soil nitrate and the initial land cover being open field increased the odds of colonization for most invasives but only for some natives. In large part, though, the spread of native and invasive plants was affected by similar factors.
Widespread decline in underwater forests, formed by kelps and other macroalgae, is occurring in all oceans. Loss
of the vulnerable surface canopy typically leads to alternate rocky reef states dominated by substrate-near,
understory vegetation, or reefs without any large fleshy macroalgae such as sea urchin barrens. Such alternate
reef states represent a major shift in food availability and quality, and may impact kelp-preferring grazers forced
to rely on less nutritious foods. Here we investigate the physiological responses of grazers to changes in food
quality and quantity. We quantify the mass-independent oxygen consumption (ṀO2), as a proxy of wholeorganism physiology, of four grazing invertebrate species (two sea urchins: Mesocentrotus franciscanus and
Strongylocentrotus purpuratus; and two gastropods: Pomaulax gibberosus and Tegula pulligo) provisioned with one
of three diet treatments over seven weeks: 1) higher quality, canopy kelp, 2) lower quality, substrate-near kelp,
or 3) restricted: no kelp. We further test for differences in the heat resistance of four grazers using an acute, nearlethal heat exposure after completion of the provisioning period. Food restrictions had the strongest influence on
oxygen consumption in the two urchins (mass-independent ṀO2 was reduced by 26–78%). By contrast, the two
gastropod grazers did not display metabolic depression under food restrictions. Although kelp restrictions had
clear physiological consequences in sea urchins, overall, the type of kelp provisioned (Macrocystis and Saccharina) did not relate to oxygen consumption after seven weeks. While heat resistance was also similar across food
treatments, unfed individuals showed a slight tendency for lower heat tolerance compared to fed individuals.
These results suggest a weak coupling between heat resistance and food quality and quantity, at least for these
species and at short time spans. Our work highlights the importance of diet diversity and metabolic depression as
strategies to cope with the energetic costs of warming.
Urbanisation and its associated habitat loss and fragmentation are considered a major
threat to wildlife. In this study, we assessed the predictors of bird species abundance,
richness and composition within 70 cells of 500 m by 500 m spread across the five
urban areas constituting Ibadan metropolis. A total of 4167 individuals of 55 species
belonging to 30 families were recorded. We report that Laughing dove Streptopelia
senegalensis, Speckled pigeon Columba guinea and Yellow-billed
kite Milvus aegyptius
contributed to a greater proportion of bird abundance across sites and Columbidae
was the most abundant bird family. Bird species richness increased significantly with
tree abundance but decreased significantly with the number of pedestrians. Similarly,
foraging guild richness declined significantly with the number of pedestrians.
Granivores and scavengers constituted the most abundant foraging guilds. Areas with
high pedestrians' traffic were associated with fewer trees and were dominated by
fewer numbers of species belonging to a few foraging guilds. This is likely because
such areas offer limited foraging opportunities or cover from potential predators.
We conclude that improving urban landscape characteristics through revegetation,
establishment of green spaces and buffering from human disturbance will improve the
composition and richness of avian species in the Ibadan metropolis.
As mudanças climáticas globais têm sido frequentemente apontadas como principal impacto futuro nas populações animais, afetando suas taxas de crescimento e elevando seu risco de extinção. Contudo, ainda não se sabe como as populações de pequenos vertebrados tetrápodes (anfíbios, répteis e pequenos mamíferos) de ecossistemas tropicais sujeitos ao estresse hídrico – como as restingas do litoral Norte Fluminense – responderiam a tais variações. Os pequenos mamíferos (roedores e marsupiais), anfíbios e répteis das formações florestais e abertas arbustivas do Parque Nacional da Restinga de Jurubatiba (PNRJ) têm sido alvo de estudos populacionais dentro do programa de Pesquisas Ecológicas de Longa Duração (PELD), permitindo avaliar possíveis mudanças em suas flutuações populacionais em função das variações climáticas abrangidas pelo período de estudo. A partir de séries temporais de dados climáticos e de abundância de tetrápodes (mamíferos: 2011-2018; anfíbios e répteis: 2013-2018) em formações abertas arbustivas de Clusia (FAC) e formações florestais de restinga (FFR), foi avaliado se a flutuação populacional das espécies foi sincrônica ou assincrônica
antes e depois de uma estiagem prolongada em 2014, e qual fator climático influenciou as variações populacionais. Os resultados evidenciaram um grau muito limitado de sincronia populacional entre as espécies ao longo de todo o período de estudo, embora tenha sido observada alguma sincronia entre espécies dos três grupos em escalas temporais menores. As flutuações populacionais da maioria
dos táxons exibiram uma forte regulação densidade-dependente negativa e uma influência menor dos fatores climáticos. Dentre os fatores climáticos, a temperatura máxima e a umidade se destacaram como os preditores mais influentes das taxas de crescimento populacional, especialmente em populações da FAC, possivelmente por regularem a disponibilidade de recursos e a fisiologia das espécies em um ambiente mais árido do que a FFR. A longa estiagem registrada em 2014 aparentemente teve um impacto nas populações, gerando maior sincronia entre as flutuações de mamíferos, répteis e anfíbios, nos anos seguintes à seca, e também promovendo uma posterior redução na amplitude de oscilação das populações de mamíferos. A fauna de tetrápodos não voadores da restinga provavelmente apresenta táxons com grande tolerância às variações dos parâmetros climáticos no período de estudo, mas que ainda são sensíveis a períodos prolongados de estiagem.
Os pequenos mamíferos não voadores constituem um grupo diverso de espécies de marsupiais e pequenos roedores que exercem importantes funções ecológicas nos ecossistemas neotropicais. O Parque Nacional da Restinga de Jurubatiba (PNRJ) tem sido alvo de numerosos estudos com pequenos mamíferos, abordando desde a ecologia populacional das espécies até a sua taxonomia, evolução e conservação. A partir dos dados acumulados entre 2001 e 2018 por diferentes grupos de pesquisa,
o presente capítulo apresenta uma síntese sobre a composição e a riqueza de espécies de pequenos mamíferos do PNRJ e avalia a influência de fatores climáticos e bióticos na variação temporal de abundância das espécies. O monitoramento da comunidade, combinado com registros publicados na literatura, indica que o PNRJ está entre as dez áreas de proteção da Mata Atlântica mais ricas em espécies de pequenos mamíferos não voadores, abrigando 19 espécies (11 de roedores e oito de marsupiais), dentre as quais os roedores Cerradomys goytaca e Trinomys eliasi encontram-se ameaçados de extinção. A série de dados compreendeu três fases climáticas com diferentes regimes de pluviosidade e sazonalidade de chuvas, e apenas as abundâncias dos marsupiais Didelphis aurita e Philander quica responderam aos fatores climáticos e bióticos avaliados. O incremento populacional contínuo de D. aurita na fisionomia florestal do PNRJ foi influenciado pelo aumento da temperatura ao longo da série de anos mais secos, e afetou direta e negativamente a abundância de P. quica, cujo declínio teve influência também da menor pluviosidade ao longo da última fase climática do monitoramento.
As abundâncias de outras espécies de pequenos mamíferos monitoradas não apresentaram relações perceptíveis com fatores climáticos, embora tenham apresentado tendências lineares de declínio ou incremento populacional ao longo do tempo. Os resultados sugerem que as respostas das espécies de pequenos mamíferos às mudanças ambientais de longo prazo são idiossincráticas e, portanto, dependem da espécie monitorada.
Using the visual world paradigm with printed words, this study investigated the flexibility and representational nature of phonological prediction in real-time speech processing. Native speakers of Mandarin Chinese listened to spoken sentences containing highly predictable target words and viewed a visual array with a critical word and a distractor word on the screen. The critical word was manipulated in four ways: a highly predictable target word, a homophone competitor, a tonal competitor, or an unrelated word. Participants showed a preference for fixating on the homophone competitors before hearing the highly predictable target word. The predicted phonological information waned shortly but was re-activated later around the acoustic onset of the target word. Importantly, this homophone bias was observed only when participants were completing a ‘pronunciation judgement’ task, but not when they were completing a ‘word judgement’ task. No effect was found for the tonal competitors. The task modulation effect, combined with the temporal pattern of phonological pre-activation, indicates that phonological prediction can be flexibly generated by top-down mechanisms. The lack of tonal competitor effect suggests that phonological features such as lexical tone are not independently predicted for anticipatory speech processing.
The seeds of Morinda citrifolia L. present unevenness and delay in germination in relation to other fruit trees. Knowledge about the physiological quality of seeds is extremely relevant for the production of seedlings and propagation of the species. Thus, the objective was to study maturation indices and the physiological quality of seeds and fruits of M. citrifolia. Seeds from freshly picked fruits, fruits harvested after seven days of maturation and freshly dropped fruits were used. The extracted and processed seeds were submitted to the following pre-germination treatments: GA3, KNO3 and H2O. The following were analyzed: fruit length and diameter, seed length, width and thickness, number of seeds per fruit, average number of seeds per kg, weight of 1000 seeds, germination, germination speed index, shoot and root length, seedling dry mass and percentage of normal seedlings. The experimental design used was completely randomized, with three stages of fruit maturation and six treatments, with four replications of 25 seeds. M. citrifolia seeds do not show tegumentary dormancy. The seeds of freshly harvested fruits and fruits harvested after seven days of maturation do not need pre-germination treatments. GA3 promotes greater germination in seeds of fruits harvested from the ground. Fruits that have just fallen to the ground have a higher content of soluble solids and a higher content of acidity. The storage of fruit in a refrigerator for a week provides the maintenance of texture characteristics, such as hardness, adhesiveness, elasticity and gumminess. Fruits with greater hardness have higher physiological seed quality.
Statistical learning – the ability to extract distributional regularities from input – is suggested to be key to language acquisition. Yet, evidence for the human capacity for statistical learning comes mainly from studies conducted in carefully controlled settings without auditory distraction. While such conditions permit careful examination of learning, they do not reflect the naturalistic language learning experience, which is replete with auditory distraction – including competing talkers. Here, we examine how statistical language learning proceeds in a virtual cocktail party environment , where the to-be-learned input is presented alongside a competing speech stream with its own distributional regularities. During exposure, participants in the Dual Talker group concurrently heard two novel languages, one produced by a female talker and one by a male talker, with each talker virtually positioned at opposite sides of the listener (left/right) using binaural acoustic manipulations. Selective attention was manipulated by instructing participants to attend to only one of the two talkers. At test, participants were asked to distinguish words from part-words for both the attended and the unattended languages. Results indicated that participants’ accuracy was significantly higher for trials from the attended vs. unattended language. Further, the performance of this Dual Talker group was no different compared to a control group who heard only one language from a single talker (Single Talker group). We thus conclude that statistical learning is modulated by selective attention, being relatively robust against the additional cognitive load provided by competing speech, emphasizing its efficiency in naturalistic language learning situations.
The environment experienced by one generation has the potential to affect the subsequent one through non-genetic inheritance of parental effects. Since both mothers and fathers can influence their offspring, questions arise regarding how the maternal, paternal and offspring experiences integrate into the resulting phenotype. We aimed to disentangle the maternal and paternal contributions to transgenerational thermal acclimation in a reef fish, Acanthochromis polyacanthus, by exposing two generations to elevated temperature (+1.5°C) in a full factorial design and analyzing the F2 hepatic gene expression. Paternal and maternal effects showed common but also parent-specific components, with the father having the largest influence in shaping the offspring transcriptomic profile. Fathers contributed to transgenerational response to warming through transfer of epigenetically controlled stress-response mechanisms while mothers influenced increased lipid metabolism regulation. However, the key to acclimation potential was matching thermal experiences of the parents. When both parents were exposed to the same condition, offspring showed increased structural RNA production and transcriptional regulation, whereas environmental mismatch in parents resulted in maladaptive parental condition-transfer, revealed by translation suppression and endoplasmic reticulum stress. Interestingly, the offspring's own environmental experience had the smallest influence on their hepatic transcription profiles. Taken together, our results show the complex nature of the interplay between paternal, maternal and offspring cue integration, and reveal that acclimation potential to ocean warming depends not only on maternal and paternal contributions, but importantly on congruent parental thermal experiences.
Harbour porpoises are visually inconspicuous but highly soniferous echolocating marine predators that are regularly studied using passive acoustic monitoring (PAM). PAM can provide quality data on animal abundance, human impact, habitat use, and behaviour. The probability of detecting porpoise clicks within a given area (P̂) is a key metric when interpreting PAM data. Estimates of P̂ can be used to determine the number of clicks per porpoise encounter that may have been missed on a PAM device, which, in turn, allows for the calculation of abundance and ideally non-biased comparison of acoustic data between habitats and time periods. However, P̂ is influenced by several factors, including the behaviour of the vocalising animal. Here, the common implicit assumption that changes in animal behaviour have a negligible effect on P̂ between different monitoring stations or across time is tested. Using a simulation-based approach informed by acoustic biologging data from 22 tagged harbour porpoises, it is demonstrated that porpoise behavioural states can have significant (up to 3× difference) effects on P̂. Consequently, the behavioural state of the animals must be considered in analysis of animal abundance to avoid substantial over- or underestimation of the true abundance, habitat use, or effects of human disturbance.
Elucidating the interaction between lexical processing and word learning is essential for a complete understanding of the underlying mechanisms of each of them. Long-term priming for words reflects an interplay between lexical processing and word learning. Although robust long-term priming effects have been found between two occurrences of the same word and between semantically similar words, it remains unclear whether long-term priming between orthographically similar words (i.e., long-term form priming) is a reliable effect. Following the theoretical analysis based on the connectionist framework, we articulated the possibility that long-term form priming might be modulated by the phonological congruency between the prime and target words, and that if this modulator was under control, reliable effects of long-term form priming would emerge. However, this hypothesis has not been adequately tested empirically. The present study tested this hypothesis by using Chinese phonograms and the phonetic radicals embedded in them as the prime and target items. In three experiments that varied in the types of stimuli and testing tasks, we consistently found that when the prime and target had the same phonology, naming the prime facilitated later processing of the target, while when they had different phonologies, the priming effect was inhibitory. These observations were consistent with the connectionist account of long-term priming for words. Our findings help confirm the reliability, generalizability, and robustness of long-term form priming and elucidate its underlying mechanisms, and suggesting promising future directions on the interactions between lexical processing and word learning.
Natural history museums comprise a unique and important component of biological infrastructure worldwide, and underlie diverse research, education, and outreach in the natural sciences. Each museum is built around one or more biological collections that serve as a repository of important materials for study, which have contributed to scientific research in increasingly important areas ranging from understanding global climate change to developing new biotechnological applications. However, despite centuries of existence, global collections sizes have only been recently estimated, and aside from analyses of certain institutions or well-studied clades, little is known about how patterns of collecting activity across institutions, geographic regions, or taxonomic clades, or how these patterns vary across time. To address this important gap in our understanding of critical life sciences infrastructure, I gathered and analyzed zoological records associated with preserved specimens collected between 1900 and 2015 and housed in worldwide natural history collections using data from the Global Biodiversity Information Facility. My analysis indicated that global, museum-associated collecting activity focused on animals has varied greatly over time, peaking around 2000 and declining significantly since. By stratifying data by institution, nation, and taxonomic phylum and class, I also illuminated how individual data series contribute to these global patterns. Institutions and nations had either concentrated or dispersed periods of relatively high collecting activity that occurred over different time periods, although most growth occurred in the second half of the 20th century for both many individual institutions and globally. Certain taxonomic clades comprise the largest proportions of collections records over this time period, namely arthropods (especially insects) and chordates (especially vertebrates), underscoring the taxonomically biased collecting histories of many institutions. Altogether, my analyses provide a critical, early view of historical zoological collecting activity and, to help other museum stakeholders to explore the data and results in more depth, I also describe and release NHMinformatics, an interactive dashboard built using R Shiny. These resources, when combined with recommendations I have made for sustainable collections growth, will be helpful for establishing policy goals, provisioning museum infrastructure, and training curatorial personnel.
Dense congregations of shorebirds forage on tidal flats during long-distance migration, and their abundance is presumed to mirror the underlying ecological conditions. We quantified the nutritional content of intertidal biofilm (a thin layer of microalgae, bacteria, and other microorganisms embedded in a mucilaginous matrix that sits on the surface of tidal flats) to assess whether biofilm biomass, macronutrient content (lipid, protein, and carbohydrate), or both, provide a measure of habitat quality for migrating shorebirds. We compared shorebird use, biofilm biomass, macronutrient content, and stable isotope signatures at two mudflats on the Fraser River estuary, British Columbia, Canada, during summer 2020 (southward migration) and spring 2021 (northward migration). The abundances of Western Sandpiper ( Calidris mauri ) and Dunlin ( Calidris alpina ) were consistently higher (6–100×) at Brunswick Point relative to the Iona Foreshore site during both migration periods. Biofilm biomass (chlorophyll a ) was 2× higher at Brunswick Point than Iona Foreshore during southward migration, and was similar between sites during northward migration, suggesting biofilm biomass alone was not a main determinant of shorebird use of these sites. Macronutrient content (lipid, protein, and carbohydrate) in intertidal biofilm was 1.4× to 3.8× higher at Brunswick Point than Iona Foreshore during both migration periods, indicating an association between macronutrient content and shorebird use. Carbohydrate content was higher during southward migration at both tidal flats, whereas protein and lipid content at Iona Foreshore did not show significant differences between years or migration periods. Carbon and nitrogen stable isotope signatures during spring 2021 did not differ between the two sites, suggesting that nutrients had similar relative inputs from marine and freshwater sources. While our comparative study does not eliminate alternative explanations that might act concomitantly (e.g., invertebrate abundance, predation risk, and disturbance), our results are consistent with the hypothesis that small-bodied shorebirds are more abundant at sites where intertidal biofilm has high macronutrient content. The latter can vary in complex ways depending on the taxonomic composition and physiological state of the microphytobenthos. Thus, the nutritional “quality” of intertidal biofilm can serve as a useful measure for determining restoration goals for tidal flats or assessing coastal areas for development projects.
Objective
To explore differences between published reviews and their respective protocols in a sample of 97 non-Cochrane Systematic Reviews (non-CSRs) and 97 Cochrane Systematic Reviews (CSRs) in terms of PICOS (Patients/Population, Intervention, Comparison/Control, Outcome, Study type) elements and the extent to which they were reported.
Study Design and Setting
We searched PubMed and Cochrane databases to identify non-CSRs and CSRs that were published in 2018. We then searched for their corresponding Cochrane or PROSPERO protocols. The published reviews were compared to their protocols. The primary outcome was changes from protocol to review in terms of PICOS elements.
Results
We identified a total of 227 changes from protocol to review in PICOS elements, 1.11 (Standard Deviation (SD), 1.22) changes per review for CSRs and 1.23 (SD, 1.12) for non-CSRs per review. More than half of each sub-sample (54.6% of CSRs and 67.0% of non-CSRs) (Absolute Risk Reduction (ARR) 12.4% [−1.3%; 26.0%]) had changes in PICOS elements. For both subsamples, approximately a third of all changes corresponded to changes related to primary outcomes. Marked differences were found between the sub-samples for the reporting of changes. 95.8% of the changes in PICOS items were not reported in the non-CSRs compared to 42.6% in the CSRs (ARR 53.2% [43.2%; 63.2%]).
Conclusion
CSRs showed better results than non-CSRs in terms of the reporting of changes. Reporting of changes from protocol needs to be promoted and requires general improvement. The limitations of this study lie in its observational design. Registration: https://osf.io/6j8gd/ .
Background
Histopathological growth patterns (HGPs) are a prognostic biomarker in colorectal liver metastases (CRLM). Desmoplastic HGP (dHGP) is associated with liver-only recurrence and superior overall survival (OS), while non-dHGP is associated with multi-organ recurrence and inferior OS. This study investigated the predictive value of HGPs for adjuvant hepatic arterial infusion pump (HAIP) chemotherapy in CRLM.
Methods
Patients undergoing resection of CRLM and perioperative systemic chemotherapy in two centers were included. Survival outcomes and the predictive value of HAIP versus no HAIP per HGP group were evaluated through Kaplan–Meier and Cox regression methods, respectively.
Results
We included 1233 patients. In the dHGP group ( n = 291, 24%), HAIP chemotherapy was administered in 75 patients (26%). In the non-dHGP group ( n = 942, 76%), HAIP chemotherapy was administered in 247 patients (26%). dHGP was associated with improved overall survival (OS, HR 0.49, 95% CI 0.32–0.73, p < 0.001). HAIP chemotherapy was associated with improved OS (HR 0.61, 95% CI 0.45–0.82, p < 0.001). No interaction could be demonstrated between HGP and HAIP on OS (HR 1.29, 95% CI 0.72–2.32, p = 0.40).
Conclusions
There is no evidence that HGPs of CRLM modify the survival benefit of adjuvant HAIP chemotherapy in patients with resected CRLM.
Mildawati, Sobir, Sulistijorini, Chikmawati T. 2023. Phylogeny of Davallia (Davalliaceae) from Sumatra and Mentawai Islands, Indonesia: evidence from trnL-F Intergenic Spacer. Biodiversitas 24: 4589-4596. Davallia is a member of the family Davalliaceae, which has a wide distribution in the Malesia region. The classification of this genus based on morphological and molecular data shows differences that cause the relationship among species to be debated until now. This study aimed to examine the phylogeny of Davallia from Sumatra and Mentawai Islands, Indonesia based on trnL-F intergenic spacer (IGS) sequence data. A total of 26 accessions representing 10 Davallia species were selected as ingroup and Oleandra articulata (Sw.) C.Presl as an outgroup was downloaded from Gen-Bank (accession number KF667613.1). Data analysis using the Maximum Parsimony (MP) method confirmed Davallia into 2 clades with divided into 7 subclades. Results showed that trnL-F IGS sequence as a non-coding gene explains the grouping species in Davallia. trnL-F IGS sequence can estimate species identity caused by changes in nucleotide bases from mutation. The MP analysis showed each species was resolved as monophyletic. Based on the phylogenetic tree, the longest branching was found in D. corniculata, suggesting that this species is the most primitive in the genus of Davallia in this region. Thus, the trnL-F marker effectively showed the relationship among species in Davallia in Sumatra and Mentawai Islands.
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