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Team RDC.R: A Language And Environment For Statistical Computing. R Foundation for Statistical Computing: Vienna, Austria

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... All statistical analyses were conducted with R Version 4.03 [97]. We used generalized linear models (GLMs) with a binomial distribution and a log link function to assess the yard-and landscape-level features associated with the probability of nymph presence in yards, for each of the tick species collected. ...
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Background The incidence of tick-borne disease has increased dramatically in recent decades, with urban areas increasingly recognized as high-risk environments for exposure to infected ticks. Green spaces may play a key role in facilitating the invasion of ticks, hosts and pathogens into residential areas, particularly where they connect residential yards with larger natural areas (e.g. parks). However, the factors mediating tick distribution across heterogeneous urban landscapes remain poorly characterized. Methods Using generalized linear models in a multimodel inference framework, we determined the residential yard- and local landscape-level features associated with the presence of three tick species of current and growing public health importance in residential yards across Staten Island, a borough of New York City, in the state of New York, USA. Results The amount and configuration of canopy cover immediately surrounding residential yards was found to strongly predict the presence of Ixodes scapularis and Amblyomma americanum, but not that of Haemaphysalis longicornis. Within yards, we found a protective effect of fencing against I. scapularis and A. americanum, but not against H. longicornis. For all species, the presence of log and brush piles strongly increased the odds of finding ticks in yards. Conclusions The results highlight a considerable risk of tick exposure in residential yards in Staten Island and identify both yard- and landscape-level features associated with their distribution. In particular, the significance of log and brush piles for all three species supports recommendations for yard management as a means of reducing contact with ticks. Graphical Abstract
... As in the previous analyses, males and females were analysed separately. All calculations were performed in the statistical programming language R [19]. ...
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Introduction and hypothesis In women, the risk of pelvic floor prolapse is known to be associated with age and parity. Different studies suggested that it is also related to pelvic dimensions, e.g. biomechanical modelling showed that a larger pelvic canal results in higher values of displacement, stress and strain in the pelvic floor muscles, which can increase the risk of pelvic floor disorders. To better understand the multiple factors contributing to pelvic floor disorders, we assessed how age, body weight, body height, parity (in women), pelvic canal size and overall muscle development affected pelvic floor geometry. Methods A comprehensive geometric morphometric analysis of variation in pelvic floor muscle shape was conducted based on a dense set of 3D landmarks measured on CT scans in a cohort of 49 deceased men and 52 deceased women. The multivariate association between biological variables (parity, dimensions of the true pelvis, age, body weight, height) and pelvic floor muscle morphology was explored by reduced rank regression in both sexes. Results In women, advanced age, high body weight relative to body height and a large pelvic canal were associated with a deeper pelvic floor. Surprisingly, parity did not have any strong association with overall pelvic floor shape. In men, high body weight was associated with a deep pelvic floor. Age had little effect on male pelvic floor shape, except for the thickness of the ischiocavernosus muscle, which reduced with age. Conclusion These results suggest that age, relative body weight and the size of the pelvic canal contribute to the risk of female pelvic floor disorders via their effect on pelvic floor shape, independently of birth-related factors such as injury and avulsion of pelvic floor muscles.
... All simulations and analyses have been conducted in R software version 4.1.1 [73] 2 . ...
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Background Anchored covariate-adjusted indirect comparisons inform reimbursement decisions where there are no head-to-head trials between the treatments of interest, there is a common comparator arm shared by the studies, and there are patient-level data limitations. Matching-adjusted indirect comparison (MAIC), based on propensity score weighting, is the most widely used covariate-adjusted indirect comparison method in health technology assessment. MAIC has poor precision and is inefficient when the effective sample size after weighting is small. Methods A modular extension to MAIC, termed two-stage matching-adjusted indirect comparison (2SMAIC), is proposed. This uses two parametric models. One estimates the treatment assignment mechanism in the study with individual patient data (IPD), the other estimates the trial assignment mechanism. The first model produces inverse probability weights that are combined with the odds weights produced by the second model. The resulting weights seek to balance covariates between treatment arms and across studies. A simulation study provides proof-of-principle in an indirect comparison performed across two randomized trials. Nevertheless, 2SMAIC can be applied in situations where the IPD trial is observational, by including potential confounders in the treatment assignment model. The simulation study also explores the use of weight truncation in combination with MAIC for the first time. Results Despite enforcing randomization and knowing the true treatment assignment mechanism in the IPD trial, 2SMAIC yields improved precision and efficiency with respect to MAIC in all scenarios, while maintaining similarly low levels of bias. The two-stage approach is effective when sample sizes in the IPD trial are low, as it controls for chance imbalances in prognostic baseline covariates between study arms. It is not as effective when overlap between the trials’ target populations is poor and the extremity of the weights is high. In these scenarios, truncation leads to substantial precision and efficiency gains but induces considerable bias. The combination of a two-stage approach with truncation produces the highest precision and efficiency improvements. Conclusions Two-stage approaches to MAIC can increase precision and efficiency with respect to the standard approach by adjusting for empirical imbalances in prognostic covariates in the IPD trial. Further modules could be incorporated for additional variance reduction or to account for missingness and non-compliance in the IPD trial.
... The study cohort was extracted from a larger register linkage, using SAS (v9.4). Statistical analyses were performed in R (v4.0.2) [29]. Tetrachoric correlations were computed using the "polycor" package (v0.7-10) ...
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Objectives To assess whether persistence to treatment with methotrexate (MTX) in early rheumatoid arthritis (RA) is shared among first-degree relatives with RA and to estimate any underlying heritability. Methods First-degree relative pairs diagnosed with RA 1999–2018 and starting MTX (in monotherapy) as their first disease-modifying anti-rheumatic drug (DMARD) treatment were identified by linking the Swedish Rheumatology Quality Register to national registers. Short- and long-term persistence to MTX was defined as remaining on treatment at 1 and 3 years, respectively, with no additional DMARDs added. We assessed familial aggregation through relative risks (RR) using log-binomial regression with robust standard errors and estimated heritability using tetrachoric correlations. We also explored the familial aggregation of EULAR treatment response after 3 and 6 months. To mimic the clinical setting, we also tested the association between having a family history of MTX persistence and persistence within the index patient. Results Familial persistence was not associated with persistence at 1 (RR=1.02, 95% CI 0.87–1.20), only at 3 (RR=1.41, 95% CI 1.14–1.74) years. Heritability at 1 and 3 years was estimated to be 0.08 (95% CI 0–0.43) and 0.58 (95% CI 0.27–0.89), respectively. No significant associations were found between family history and EULAR response at 3 and 6 months, neither overall nor in the clinical setting analysis. Conclusions Our findings imply a familial component, including a possible genetic element, within the long-term persistence to MTX following RA diagnosis. Whether this component is reflective of characteristics of the underlying RA disease or determinants for sustained response to MTX in itself will require further investigation.
... The expected counts of each gene in the RSEM outputs were used with R (version 3.4.2) [62] in the following analysis. The R script used in this study was deposited in https:// github. ...
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Background Quantification of gene expression such as RNA-Seq is a popular approach to study various biological phenomena. Despite the development of RNA-Seq library preparation methods and sequencing platforms in the last decade, RNA extraction remains the most laborious and costly step in RNA-Seq of tissue samples of various organisms. Thus, it is still difficult to examine gene expression in thousands of samples. Results Here, we developed Direct-RT buffer in which homogenization of tissue samples and direct-lysate reverse transcription can be conducted without RNA purification. The DTT concentration in Direct-RT buffer prevented RNA degradation but not RT in the lysates of several plant tissues, yeast, and zebrafish larvae. Direct reverse transcription on these lysates in Direct-RT buffer produced comparable amounts of cDNA to those synthesized from purified RNA. To maximize the advantage of the Direct-RT buffer, we integrated Direct-RT and targeted RNA-Seq to develop a cost-effective, high-throughput quantification method for the expressions of hundreds of genes: DeLTa-Seq (Direct-Lysate reverse transcription and Targeted RNA-Seq). The DeLTa-Seq method could drastically improve the efficiency and accuracy of gene expression analysis. DeLTa-Seq analysis of 1056 samples revealed the temperature-dependent effects of jasmonic acid and salicylic acid in Arabidopsis thaliana . Conclusions The DeLTa-Seq method can realize large-scale studies using thousands of animal, plant, and microorganism samples, such as chemical screening, field experiments, and studies focusing on individual variability. In addition, Direct-RT is also beneficial for gene expression analysis in small tissues from which it is difficult to purify enough RNA for the experiments.
... All of the statistical analyses were performed using R software [33]. The average number of reads (i.e., the concentration of species-specific eDNA particles) was calculated for each site and each OTU (species) as a mean of the two replicates and was used as a proxy of abundance per species and per site. ...
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The Mekong River is one of the largest rivers in the world and hosts the second greatest fish diversity in the world after the Amazon. However, despite the importance of this diversity and its associated biomass for human food security and the economy, different anthropogenic pressures threaten the sustainability of the Mekong River and fish diversity, including the intense damming of the main river. Both the increase in salt-water penetration into the Mekong Delta and the disrupted connectivity of the river may have serious impacts on the numerous freshwater and migratory species. To evaluate the potential of an eDNA approach for monitoring fish diversity, water was sampled at 15 sites along the salinity gradient in the Mekong Delta and along 1500 km of the main stream, from Vietnam to Thailand and Laos. A total of 287 OTUs were recovered, of which 158 were identified to the species level using both reference sequences available in GenBank and references obtained locally. Agglomerative hierarchical clustering and PCA identified up to three main species assemblages in our samples. If the transition from brackish to freshwater conditions represents the main barrier between two of these assemblages, more surprisingly, the two other assemblages were observed in the freshwater Mekong, with a spatial disjunction that did not match any biogeographic ecoregion or the Khone falls, the latter thought to be an important fish dispersion barrier. Between 60% and 95% of the freshwater species were potamodromous. This pioneer eDNA study in the Mekong River at this geographical and ecological scale clearly confirmed the potential of this approach for ecological and diversity monitoring. It also demonstrated the need to rapidly build an exhaustive Mekong fish barcode library to enable more accurate species’ assignment. More eDNA surveys can now be expected to better describe the ecological niche of different species, which is crucial for any models aimed at predicting the impact of future damming of the Mekong
... The normalization of the soil variables was carried out using the statistical package in R software version 4.0.2 (R Core Team, Austria) [44] based on the geometric mean, and a generalized logarithmic transformation using "glog" function in R was performed to make the variables comparable among themselves due to differences in the units to measure them [45,46]. Figure 8 shows the general scheme of the data analysis procedures followed in this work. ...
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Over the last few decades, a growing incidence of Banana Wilt (BW) has been detected in the banana-producing areas of the central zone of Venezuela. This disease is thought to be caused by a fungal–bacterial complex, coupled with the influence of specific soil properties. However, until now, there was no consensus on the soil characteristics associated with a high incidence of BW. The objective of this study was to identify the soil properties potentially associated with BW incidence, using supervised methods. The soil samples associated with banana plant lots in Venezuela, showing low (n = 29) and high (n = 49) incidence of BW, were collected during two consecutive years (2016 and 2017). On those soils, sixteen soil variables, including the percentage of sand, silt and clay, pH, electrical conductivity, organic matter, available contents of K, Na, Mg, Ca, Mn, Fe, Zn, Cu, S and P, were determined. The Wilcoxon test identified the occurrence of significant differences in the soil variables between the two groups of BW incidence. In addition, Orthogonal Least Squares Discriminant Analysis (OPLS-DA) and the Random Forest (RF) algorithm was applied to find soil variables capable of distinguishing banana lots showing high or low BW incidence. The OPLS-DA model showed a proper fitting of the data (R2Y: 0.61, p value < 0.01), and exhibited good predictive power (Q2: 0.50, p value < 0.01). The analysis of the Receiver Operating Characteristics (ROC) curves by RF revealed that the combination of Zn, Fe, Ca, K, Mn and Clay was able to accurately differentiate 84.1% of the banana lots with a sensitivity of 89.80% and a specificity of 72.40%. So far, this is the first study that identifies these six soil variables as possible new indicators associated with BW incidence in soils of lacustrine origin in Venezuela.
... Statistical analyses of the tests BMP I and BMP II were performed in the Software R [39]. Residual normality and homogeneity of variances assumptions were evaluated by the Shapiro-Wilk [40] and Breusch-Pagan [41] tests, respectively. ...
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This study aimed to improve the efficiency in methane production of anaerobic digestion of fruit and vegetable waste. For this purpose, two strategies were evaluated: the first was the anaerobic co-digestion with coffee grounds and landfill leachate using different carbon–nitrogen ratios (C/N ratio 25:1 and 12.5:1); the second strategy was the use of two different inoculum sources (digested swine manure and a mixture composed of different inoculums—Mix). The samples were characterized before and after the biochemical methane potential (BMP) tests and methane production was monitored. The modified Gompertz kinetic model was used to predict the process of AD. The Mix inoculum and the co-digestion of FVW and SCG, with a C/N ratio of 25:1, resulted in the highest methane yield (198.1 Nml gVS⁻¹). The results highlight that the choice of co-substrates with different properties than the FVW and the composition of an inoculum adapted to different types of substrates can contribute to the improvement in methane conversion from FVW. The kinetic analysis proved that the modified Gompertz model was adequate to describe the AD process, indicating that the studied conditions were favorable for methane production. Graphical Abstract
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It is increasingly recognised that intraspecific variation in traits, such as morphology, behaviour, or diet is both ubiquitous and ecologically important. While many species of predators and herbivores are known to display high levels of between-individual diet variation, there is a lack of studies on pollinators. It is important to fill in this gap because individual-level specialisation of flower-visiting insects is expected to affect their efficiency as pollinators with consequences for plant reproduction. Accordingly, the aim of our study was to quantify the level of individual-level specialisation and foraging preferences, as well as interspecific resource partitioning, in three co-occurring species of bees of the genus Ceratina (Hymenoptera: Apidae: Xylocopinae), C. chalybea , C. nigrolabiata , and C. cucurbitina . We conducted a field experiment where we provided artificial nesting opportunities for the bees and combined a short-term mark-recapture study with the dissection of the bees’ nests to obtain repeated samples from individual foraging females and complete pollen provisions from their nests. We used DNA metabarcoding based on the ITS2 locus to identify the composition of the pollen samples. We found that the composition of pollen carried on the bodies of female bees and stored in the brood provisions in their nests significantly differed among the three co-occurring species. At the intraspecific level, individual females consistently differed in their level of specialisation and in the composition of pollen carried on their bodies and stored in their nests. We also demonstrate that higher generalisation at the species level stemmed from larger among-individual variation in diets, as observed in other types of consumers, such as predators. Our study thus reveals how specialisation and foraging preferences of bees change from the scale of individual foraging bouts to complete pollen provisions accumulated in their nests over many days. Such a multi-scale view of foraging behaviour is necessary to improve our understanding of the functioning of plant-flower visitor communities.
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Surveys are essential tools in assessing the performance of local government units in their basic societal service deliveries. Using the Citizen Satisfaction Index System (CSIS) which measures the respondent's satisfaction with public services, interviewed 150 respondents covering 29 barangays in Lambunao, Iloilo. Survey was based on this tool's core concepts of awareness, availment, satisfaction and need for action on the service delivery system of the government. Our objectives were to assess the service delivery performance; identify the patterns and trends and correlations among services areas and socio-demographic profiles of the respondents; and rank the service areas accordingly based on the respondent's satisfaction ratings. Results revealed a high awareness rating (81%) but only 51% of those who were aware have availed the basic services. The satisfactory rating was 95%. The unemployed (86%), young adults (36%), and female groups (50%) were well-satisfied with the economic and investment promotion services and support for education programs. Whereas, the male (50%), middle-aged (42%), and employed clusters (14%) were highly concerned about the governance and response of the government. The satisfaction of the elderly group (22%) was very closely related to health services. Ranking the overall satisfaction on services areas using a generalized additive modeling was in the order of health services > support to education > social welfare > environmental management > governance and response > economic and investment promotion > public works and infrastructure. Our findings aid the government officials towards more improved service delivery to its constituents.
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Background Insulin receptor substrate‐1 ( IRS‐1 ) rs956115 is associated with vascular risk in patients with coronary artery disease and concomitant diabetes. CYP2C19*2 (rs4244285) modulates clopidogrel response and predicts the outcome of coronary artery disease. This study was designed to explore the association between IRS‐1 , CYP2C19*2 genotypes, platelet reactivity, and 1‐year outcome in patients with coronary artery disease undergoing percutaneous coronary intervention. Methods and Results Genotyping was performed using an improved multiplex ligation detection reaction technique. Platelet aggregation was assessed by light transmission aggregometry. Major adverse cardiovascular events were defined as a composite of cardiovascular death, myocardial infarction, and ischemic stroke. A total of 2213 consecutive patients were screened and 1614 were recruited. At 1 month, patients with IRS‐1 CG genotype had significantly lower levels of ADP‐induced platelet aggregation compared with patients with CC homozygotes. Patients with IRS‐1 CG or GG genotype had a 2.09‐fold higher risk of major adverse cardiovascular events compared with those with CC homozygotes (95% CI, 1.04–4.19; P =0.0376). By comparison, patients with CYP2C19*2 GA or AA genotype had higher ADP‐induced platelet aggregation compared with patients with GG homozygotes. Although there was no significant difference in risk of major adverse cardiovascular events between patients with GA/AA and GG genotypes, patients with GA genotype had a 2.19‐fold higher risk than those with GG homozygotes (95% CI, 1.13–4.24; P =0.0200). No interaction between IRS‐1 and CYP2C19*2 genotypes was observed. Conclusions In patients following percutaneous coronary intervention, IRS‐1 GG/CG and CYP2C19*2 GA genotypes were associated with 2.09‐ and 2.19‐fold increased cardiovascular risk, respectively, at 1‐year follow‐up. The association between IRS‐1 genotypes and major adverse cardiovascular events appeared to be independent of known clinical predictors. Registration URL: https://www.clinicaltrials.gov ; Unique identifier: NCT01968499.
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The cranial casques of modern cassowaries (Casuarius) have long intrigued researchers; however, in‐depth studies regarding their morphological variation are scarce. Through visual inspection, it has been recognized that casque variability exists between conspecifics. Understanding casque variation has both evolutionary and ecological importance. Although hypothesized to be targeted by selection, intraspecific casque variation has not been quantified previously. Through a large sample of C. casuarius (n = 103), we compared casque shape (lateral and rostral views) between sexes and between individuals from non‐overlapping geographical regions using two‐dimensional (2D) geometric morphometrics. We found no statistically significant differences between the casque shape of females and males and few substantial shape differences between individuals from different geographic areas. Much of the intraspecific variation within C. casuarius is due to casque asymmetries (77.5% rightward deviating, 20.7% leftward deviating, and 1.8% non‐deviating from the midline; n = 111), which explain the high variability of southern cassowary casque shape, particularly from the rostral aspect. Finally, we discuss how our non‐significant findings implicate social selection theory, and we identify the benefits of quantifying such variation for further elucidating casque function(s) and the social biology of cassowaries. Cassowary casques are among the most iconic cranial ornaments among modern Aves. Geometric morphometric shape analysis of southern cassowary ornaments indicates no sexual dimorphism and few differences between regional populations. Instead, intraspecific casque shape variation is primarily due to directional, cranial asymmetries (illustrated as five typical casque orientations referenced to a single adult skull). These data from living cassowaries are crucial to our understanding of ornament evolution and functional morphology
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Trophic interaction in tropical regions is influenced by factors such as the size of organisms and the presence of intermediate predators. Macrophytes can act directly on predator–prey dynamics through the habitat structure provided by plants. We conducted an in situ mesocosm experiment (100 L) in a Brazilian reservoir to evaluate the top-down and bottom-up control promoted by the fish Astyanax lacustris, and to evaluate the effects of floating and submerged macrophytes’ morphology on trophic interaction. The experiment lasted ten days and consisted of four treatments in triplicate (n = 12): a control (C) without fish, with only the natural plankton community, and treatments with addition of fish (+ F), fish + floating macrophyte (+ FFM) and fish + submerged macrophyte (+ FSM). In treatments with macrophytes, artificial plants were added to serve as shelter for zooplankton and Chaoborus. Our results showed that fish reduced small cladoceran and Chaoborus biomass by top-down control and increased edible phytoplankton biomass by increasing nutrient concentrations by bottom-up control. Chaoborus increased the food chain length to four levels, with negative effects on the biomass of small cladocerans. Submerged macrophytes were more efficient in providing refuge for copepods and Chaoborus. In general, planktivorous fish had a direct effect on zooplankton and an indirect effect on phytoplankton, and the invertebrate Chaoborus interfered with the functioning of trophic networks. Our results show that, in experimental conditions, macrophytes can play a fundamental role in tropical reservoirs by reducing the strength of top-down control in the trophic cascade.
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American Viticultural Areas are wine appellation areas in the United States formally and legally defined by the US Alcohol and Tobacco Tax and Trade Bureau (TTB) through a petition process and are used in marketing wine. The TTB’s petition process is intended to define areas containing unique environmental conditions. In this paper, I investigate how similar AVA boundaries are in their environmental characteristics though a hierarchical cluster analysis, using the environmental variables required to be described in the petition process. The AVAs fell into six groups, driven largely by their physical features such as topography, elevation, or location on a coastline, rather than into geographic clusters.
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Anthropogenic disturbances are increasing worldwide, causing wildlife habitat loss, alteration, and fragmentation. In Canada, the decommissioning of linear anthropogenic structures is identified as a promising tool to restore the habitat of threatened populations of boreal caribou (Rangifer tarandus caribou) by reducing food availability for alternate prey and decreasing encounter probabilities with predators. In this study, we monitored the use of 40 km of decommissioned forest roads by caribou, gray wolves (Canis lupus), black bears (Ursus americanus), and moose (Alces americanus) 1–3 years after reclamation, using 232 motion-activated camera traps. We compared four additive treatments (meaning that each successive treatment included the treatment prior): closing the road to human access, decompacting its soil, planting black spruce (Picea mariana) trees, and adding enriched soil. We assessed the influence of treatments, use by other large mammals, and characteristics of the surrounding environment on road use by the four species. Caribou used the planted treatment (which also included closing and decompacting) more than the closed-only (reference) treatment, but treatments did not influence the use of decommissioned roads by bears and moose. We could not assess the use of treated roads by wolves because of low sample size. Road use by caribou declined with local moose density, but increased with local bear density. Caribou were observed more frequently on roads surrounded by regenerating and mature coniferous stands; caribou also preferentially used roads surrounded by wetlands. Our results suggest that the treatment combining road closure, soil decompaction, and tree planting could be beneficial to caribou, highlighting the relevance of including active restoration efforts in caribou conservation programs. We recommend that such a treatment be added to road decommissioning protocols for the conservation of caribou, alongside broad-scale habitat protection.
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Quality of life is severely impacted by Hidradenitis Suppurativa. This cross‐sectional survey based study highlights that the impact of Hidradenitis Suppurativa on quality of life measured by the World Health Organisation Quality of Life (WHOQOL‐BREF) survey is worse than published data for atopic dermatitis and other acute and chronic medical conditions including myocardial infarction and inflammatory bowel disease.
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Antibiotic resistance (AR) was increasingly recognized as a global and national problem. Prevention efforts are hampered by a lack of complete understanding of how transmission pathways contribute to human AR exposure. Many reports have indicated the presence of antibiotic-resistant bacteria in foods at retail, suggesting that food consumption, animal-derived foods in particular, can represent a significant source of AR exposure among consumers. The presence of Salmonella, including antibiotic-resistant Salmonella, has been frequently reported in terrestrial animal-derived foods such as meat, poultry, and dairy products, as well as in aquaculture products. Identification of the significant food sources that harbor relatively substantial antibiotic-resistant Salmonella is the key for the design and implementation of effective and target AR mitigation strategies. Thus, a systematic evaluation of the relative contribution of different food sources to human antibiotic-resistant Salmonella was imperative. This thesis aimed to gather qualitative and quantitative information about the contamination of antibiotic-resistant non-typhoidal Salmonella in various retail foods in the U.S. and identify knowledge gaps using systematic review (SR) and meta-analysis (MA) approaches. The data on resistant Salmonella concentration in foods has not been found. Resistant Salmonella prevalence in regulated commodities (beef, chicken, turkey, pork) and other food categories were conducted for major antibiotic classes. Generally, poultry, pork, and turkey had a higher prevalence of resistant Salmonella than beef, while vegetables and imported foods (mainly spices in documented studies) had a lower prevalence. For antibiotics classes, tetracycline resistance was the most prevalent across major commodities. There is a moderate level of resistance to beta-lactam antibiotics, but the significance in clinical practice indicates a potential threats to public health. Another objective was to develop a stochastic comparative exposure assessment model to estimate the relative contribution of various animal-derived food groups to overall foodborne exposure to cephem-resistant Salmonella. The model consists of four modules: retail, transport, storage, and preparation. Generally, the results showed that ground beef and chicken parts accounted for the largest proportion of total exposure to cephem-resistant Salmonella compared to pork cuts and ground turkey. The contamination level in products at retail and cooking temperature were the top influencing factors of the foodborne exposure for all food products evaluated in the present study. Foodborne illness source attribution is the foundation of a risk-based food safety system. The present project provides a risk-based estimation of the degree to which different food categories are responsible for resistant Salmonella infections. With these estimates, target prevention measures can be designed and implemented to effectively mitigate the AR threat to public health attributable to the food consumption. Advisor: Bing Wang
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Avian pox is a highly contagious poultry disease that causes significant economic losses. Mosquitoes belonging to the genus Culex (Diptera: Culicidae) have a fundamental role in disseminating Avipoxvirus (Poxviridae). This study proposes investigating the presence of Avipoxvirus (APV) DNA in Culex spp. from Rio de Janeiro to determine its frequency and perform a phylogenetic analysis based on the core like the 4b protein (p4b) gene. The detection of APVs was conducted individually on four hundred Culex spp. mosquitoes. A total of 12.23% (47/384) of the Culex spp. were positive in the PCR. Sequencing the p4b gene revealed that this study’s sequences displayed 98.8–99% identity with Fowlpoxvirus (FWPW) sequences available in GenBank. In the phylogenetic analysis, these APVs were clustered in the A1 subclade together with FWPW sequences from several countries. The evolutionary distance of the p4b gene was 0.61 ± 0.21% in rural areas and 0.38 ± 0.16% in peri-urban areas. The current investigation is the first study to report the detection of APVs in field-caught mosquitoes. Moreover, a high frequency of APV DNA was observed in Culex spp. captured in domestic areas, where backyard poultry is present. This data demonstrates the importance of implementing control measures for Culex spp. to mitigate the transmission of APVs in backyard poultry in Rio de Janeiro.
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One of the main limiting factors of plant yield is drought, and while the physiological responses to this environmental stress have been broadly described, research addressing its impact on mineral nutrition is scarce. Brassica napus and Triticum aestivum were subjected to moderate or severe water deficit, and their responses to drought were assessed by functional ionomic analysis, and derived calculation of the net uptake of 20 nutrients. While the uptake of most mineral nutrients decreased, Fe, Zn, Mn, and Mo uptake were impacted earlier and at a larger scale than most physiological parameters assessed (growth, ABA concentration, gas exchanges and photosynthetic activity). Additionally, in B. napus, the patterns of 183 differentially expressed genes in leaves related to the ionome (known ionomic genes, KIGs) or assumed to be involved in transport of a given nutrient were analyzed. This revealed three patterns of gene expression under drought consisting of up (transport of Cl and Co), down (transport of N, P, B, Mo, and Ni), or mixed levels (transport of S, Mg, K, Zn, Fe, Cu, or Mn) of regulation. The three patterns of gene regulations are discussed in relation to specific gene functions, changes of leaf ionomic composition and with consideration of the crosstalks that have been established between elements. It is suggested that the observed reduction in Fe uptake occurred via a specific response to drought, leading indirectly to reduced uptake of Zn and Mn, and these may be taken up by common transporters encoded by genes that were downregulated. In wheat and rapeseed, drought downregulates the uptake of Fe, Mo, Zn, and Mn before reduction of growth, and this was associated with differential expressions of transport‐related genes.
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Partial migration is one of the most widespread migratory strategies among taxa. Investigating the trade-off between environmental/social factors — fitness and energetic consequences — is essential to understand the coexistence of migratory and resident behaviours. Here, we compiled field monitoring data of wintering population size and telemetry data of 25 migrant and 14 resident Egyptian Vultures Neophron percnopterus to analyse how environmental and social factors modulate overwintering immature population size, compare energetic consequences between migratory and resident individuals across wintering and non-wintering seasons and evaluate fitness components (i.e. survival and reproduction) between the two migratory forms. We observed that social attraction may influence the number of overwintering immature individuals, which increased linearly with adult birds surveyed. Residents spent more energy but exhibited higher survival probabilities and lower breeding activity. On the contrary, migratory birds showed lower energy expenditure during winter but also lower survival and more breeding attempts. These results suggest that social attraction may modulate population dynamics and promote residency in immature birds. Resident individuals benefit from enhancing their survival at the expense of higher energy expenditure during winter. Migrant birds, on the contrary, may compensate for the higher costs in terms of survival by a reduction in the energy cost, which may benefit more frequent breeding. Our results offer new insights to understand how species benefit from one strategy or another and that the coexistence of both migratory forms is context-dependent. Significance statement Animal populations exhibiting partial migration are composed of migrant and resident individuals who share the same breeding areas but different overwintering quarters. Deciphering the causes and consequences that affect each migratory behaviour is essential to understand the balance and persistence of the two strategies. Here, we investigate the environmental and social factors affecting number of immatures during winter and evaluate both migratory strategies in terms of energy expenditure, reproduction and survival. We found that social attraction modulates wintering population size of immature individuals and that the residency is energetically more costly but beneficial in terms of survival but not for breeding. By contrast, migration lessens the energy costs, increases the breeding activity, but also reduces survival probability.
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In agroecosystems, omnivorous predators are recognized as potential biological control agents because of the numerous pest species they prey on. Nonetheless, it could be possible to enhance their efficiency through artificial selection on traits of economical or ecological relevance. Aggressiveness, which defines the readiness of an individual to display agonistic actions toward other individuals, is expected to be related to zoophagy, diet preferences and to a higher attack rate. The study aimed to assess the aggressiveness degree of the damsel bug, Nabis americoferus, and to estimate its heritability. We hypothesized that a high aggressiveness degree can be selected, and that males are more aggressive than females. Using artificial selection, we reared two separate populations, each composed of nine genetically isolated lines characterized by their different aggressiveness degree (aggressive, docile and non-selected). After three generations, we had efficiently selected aggressive behavior. The realized heritability was 0.16 and 0.27 for aggressiveness and docility in the first population. It was 0.25 and 0.23 for the second population. Males were more aggressive than females only for the second population. The potential of these individuals as biological control agents and the ecological consequences of aggressiveness are discussed.
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Background Niemann-Pick type C (NPC) is an autosomal recessive progressive neurodegenerative disorder caused by mutations in the NPC1 or NPC2 genes. Patients with this disorder have variable phenotypic presentations that often include neuropsychiatric manifestations, cognitive decline, and movement disorders. There is considerable interpatient variation in movement disorders, with limited quantitative measurements describing the movements observed. Objective measurements using wearable sensors provide clinically applicable monitoring of patients with Parkinson’s disease, and hence may be utilized in patients with NPC. Objective To explore the relationship between objective measurements of movement obtained via the use of the Personal KinetiGraph (PKG) with the clinical information obtained via questionnaires and clinical rating tools of patients with Niemann-Pick type C. Methods Twelve patients with Niemann-Pick type C were recruited who wore the PKG for 6 days during regular activities. A 6-day output was provided by the manufacturer, which provided bradykinesia (BK) and dyskinesia (DK) scores. BK and DK scores were further divided into their interquartile ranges. A fluctuation score (FDS), percentage time immobile (PTI), and percent time with tremors (PTT) were also provided. Clinical assessments included Abnormal Involuntary Movement Scale (AIMS), Epworth Sleepiness Score (ESS), Falls, Neuropsychiatric Unit Assessment Tool (NUCOG), Parkinson’s disease questionnaire (PDQ), and modified Unified Parkinson’s Disease Rating Scale (UPDRS) which were performed over telehealth within 2 weeks of PKG use. Pearson’s correlation analyses were utilized to explore the relationship between DK and BK quartiles and clinical measures. Results We found bradykinesia to be a feature among this cohort of patients, with a median BKS of 22.0 (7.4). Additionally, PTI scores were elevated at 4.9 (8.2) indicating elevated daytime sleepiness. Significant correlations were demonstrated between BK25 and Falls ( r = − 0.74, 95% CI = [− 0.95, − 0.08]), BK50 and Falls ( r = − 0.79, 95% CI = [− 0.96, − 0.19]), and BK75 and Falls ( r = − 0.76, 95% CI = [− 0.95, − 0.11]). FDS correlated with PDQ ( r = − 0.7, 95% CI = [− 0.92, − 0.18]), UPDRS IV ( r = − 0.65, 95% CI = [− 0.90, − 0.09]), UPDRS ( r = − 0.64, 95% CI = [− 0.9, − 0.06]), and AIMS ( r = − 0.96, 95% CI = [− 0.99, − 0.49]). DK25 in comparison with NUCOG-A ( r = 0.72, 95% CI = [0.17, 0.93]) and DK75 in comparison with NUCOG ( r = 0.64, 95% CI = [0.02, 0.91]) and NUCOG-A ( r = 0.63, 95% CI = [0.01, 0.90]) demonstrated significant correlations. Additionally, duration of illness in comparison with PTI ( r = 0.72, 95% CI = [0.22, 0.92]) demonstrated significance. Conclusions Utilization of PKG measures demonstrated that bradykinesia is under recognized among NPC patients, and the bradykinetic patients were less likely to report concerns regarding falls. Additionally, the FDS rather than the DKS is sensitive to the abnormal involuntary movements of NPC—reflecting a differing neurobiology of this chorea compared to levodopa-induced dyskinesias. Furthermore, dyskinetic individuals performed better in cognitive assessments of attention which may indicate an earlier timepoint within disease progression.
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Although generally given little attention in vegetation studies, ground-dwelling (terricolous) lichens are major contributors to overall carbon and nitrogen cycling, albedo, biodiversity and biomass in many high-latitude ecosystems. Changes in biomass of mat-forming pale lichens have the potential to affect vegetation, fauna, climate and human activities including reindeer husbandry. Lichens have a complex spectral signature and terricolous lichens have limited growth height, often growing in mixtures with taller vegetation. This has, so far, prevented the development of remote sensing techniques to accurately assess lichen biomass, which would be a powerful tool in ecosystem and ecological research and rangeland management. We present a Landsat based remote sensing model developed using deep neural networks, trained with 8914 field records of lichen volume collected for >20 years. In contrast to earlier proposed machine learning and regression methods for lichens, our model exploited the ability of neural networks to handle mixed spatial resolution input. We trained candidate models using input of 1 × 1 (30 × 30 m) and 3 × 3 Landsat pixels based on 7 reflective bands and 3 indices, combined with a 10 m spatial resolution digital elevation model. We normalised elevation data locally for each plot to remove the region-specific variation, while maintaining informative local variation in topography. The final model predicted lichen volume in an evaluation set (n = 159) reaching an R 2 of 0.57. NDVI and elevation were the most important predictors, followed by the green band. Even with moderate tree cover density, the model was efficient, offering a considerable improvement compared to earlier methods based on specific reflectance. The model was in principle trained on data from Scandinavia, but when applied to sites in North America and Russia, the predictions of the model corresponded well with our visual interpretations of lichen abundance. We also accurately quantified a recent historic (35 years) change in lichen abundance in northern Norway. This new method enables further spatial and temporal studies of variation and changes in lichen biomass related to multiple research questions as well as rangeland management and economic and cultural ecosystem services. Combined with information on changes in drivers such as climate, land use and management, and air pollution, our model can be used to provide accurate estimates of ecosystem changes and to improve vegetation-climate models by including pale lichens.
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Background There is inconsistent data about condom use at the last sexual intercourse (LSI) among university students in sub-Saharan Africa (SSA) and its association with sex, age, and condom negotiation efficacy. The primary objective of this study was to summarize the proportion of condom use at the LSI among university students in SSA. The secondary objective was to determine the association between condom use at the LSI with sex, age, and condom negotiation efficacy among university students in SSA. Methods In this systematic review and meta-analysis, two reviewers independently searched electronic databases and grey literature for eligible studies published until July 30, 2020, extracted data, and assessed the risk of bias in the included studies. We used the Dersimonian-Liard random-effects model to pool the proportion of condom use at the LSI and the association between condom use at the LSI with sex, age, and condom negotiation efficacy, reported using risk ratio (RR). We assessed publication bias using funnel plot and Egger’s test, and explored sources of heterogeneity using sub-group and meta-regression analyses. Results We meta-analyzed 44 studies with a combined sample size of 27,948 participants.Of 14,778 sexually active participants, 8,744 (pooled proportion, 52.9%; 95% CI, 45.0–60.7; 95% prediction interval, 2.8–98.9; I-squared = 99.0%, p< 0.0001) reported condom use at the LSI and the proportion of condom use at the LSI remained stagnant between 2000 and 2019 ( p = 0.512). Condom use at the LSI was not associated with being a female compared to a male (pooled RR, 1.08; 95% CI, 0.68–1.71), being of a younger age (≤24 years old) compared to older age (25 years and more) (pooled RR, 1.16; 95% CI, 0-85-1.57), and having a higher condom negotiation efficacy compared to a lower condom negotiation efficacy (pooled RR, 1.54; 95% CI, 0-81-2.94). Conclusions We found a low and heterogenous use of a condom at the LSI among university students in SSA which was not associated with sex, age, or condom negotiation efficacy. Accordingly, context-relevant interventions are needed to improve condom use at the LSI among university students in SSA.
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Celiac disease is a systemic, chronic and autoimmune disorder that affects genetically susceptible individuals. Due to the increasing incidence of this pathology and the precision of new detection methods, celiac disease diagnosis has improved dramatically in recent years. Hereby, a study was performed to evaluate celiac disease's prevalence, attending to associated diseases as well as clinical determinants. A convenience sample of 254 patients diagnosed between 2007 and 2017 in the South of Spain was selected: 212 were confirmed for celiac disease, 18 remained with suspected celiac disease and 24 were considered silent patients. Multivariate logistic regression models were applied to patients' data. 95.3% of the subjects obtained a positive result in the genetic-molecular diagnosis, with prevalence of female patients' group (58.7%). Moreover, females were associated with diarrhea and abdominal pain to a greater extent (54.3% and 66.2%, respectively). Youngsters had accused villi atrophy and larger concentrations of anti-tTG antibodies compared to adults, but had more adhesion to treatment and recovered better than the older group. Deficit in Fe and multimorbidity were also factors associated with villi atrophy. The multivariate analysis adjusted for sex and age showed a direct association between intestinal lesion and Fe deficit, the presence of vomiting and the number of diseases associated with celiac disease. Novel results of the present study refer to the association between the level of intestinal injury and the multimorbidity associated with celiac disease.
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