Hierarchical multistate models from population data: an application to parity statuses
Hierarchical models are characterized by having N living states connected by N − 1 rates of transfer. Demographic measures for such models can be calculated directly from counts of the number of persons in each state at two nearby points in time. Exploiting the ability of population stocks to determine the flows in hierarchical models expands the range of demographic analysis. The value of such analyses is illustrated by an application to childbearing, where the states of interest reflect the number of children a woman has born. Using Census data on the distribution of women by age and parity, a parity status life table for US Women, 2005–2010, is constructed. That analysis shows that nearly a quarter of American women are likely to remain childless, with a 0–3 child pattern replacing the 2–4 child pattern of the past.
Schoen (2016) Hierarchical multistate models from population data: an application to parity statuses. PeerJ 4:e2535 https://doi.org/10.7717/peerj.2535
Hypernasality associated with basal ganglia dysfunction: evidence from Parkinson’s disease and Huntington’s disease
Background Although increased nasality can originate from basal ganglia dysfunction, data regarding hypernasality in Parkinson’s disease (PD) and Huntington’s disease (HD) are very sparse. The aim of the current study was to analyze acoustic and perceptual correlates of velopharyngeal seal closure in 37 PD and 37 HD participants in comparison to 37 healthy control speakers. Methods Acoustical analysis was based on sustained phonation of the vowel /i/ and perceptual analysis was based on monologue. Perceptual analysis was performed by 10 raters using The Great Ormond Street Speech Assessment ’98. Acoustic parameters related to changes in a 1/3-octave band centered on 1 kHz were proposed to reflect nasality level and behavior through utterance. Results Perceptual analysis showed the occurrence of mild to moderate hypernasality in 65% of PD, 89% of HD and 22% of control speakers. Based on acoustic analyses, 27% of PD, 54% of HD and 19% of control speakers showed an increased occurrence of hypernasality. In addition, 78% of HD patients demonstrated a high occurrence of intermittent hypernasality. Further results indicated relationships between the acoustic parameter representing fluctuation of nasality and perceptual assessment (r = 0.51, p < 0.001) as well as the Unified Huntington Disease Rating Scale chorea composite subscore (r = 0.42, p = 0.01). Conclusions In conclusion the acoustic assessment showed that abnormal nasality was not a common feature of PD, whereas patients with HD manifested intermittent hypernasality associated with chorea.
Novotný et al. (2016) Hypernasality associated with basal ganglia dysfunction: evidence from Parkinson’s disease and Huntington’s disease. PeerJ 4:e2530 https://doi.org/10.7717/peerj.2530
Bacterial community diversity of the deep-sea octocoral Paramuricea placomus
Compared to tropical corals, much less is known about deep-sea coral biology and ecology. Although the microbial communities of some deep-sea corals have been described, this is the first study to characterize the bacterial community associated with the deep-sea octocoral, Paramuricea placomus. Samples from five colonies of P. placomus were collected from Baltimore Canyon (379–382 m depth) in the Atlantic Ocean off the east coast of the United States of America. DNA was extracted from the coral samples and 16S rRNA gene amplicons were pyrosequenced using V4-V5 primers. Three samples sequenced deeply (>4,000 sequences each) and were further analyzed. The dominant microbial phylum was Proteobacteria, but other major phyla included Firmicutes and Planctomycetes. A conserved community of bacterial taxa held in common across the three P. placomus colonies was identified, comprising 68–90% of the total bacterial community depending on the coral individual. The bacterial community of P. placomus does not appear to include the genus Endozoicomonas, which has been found previously to be the dominant bacterial associate in several temperate and tropical gorgonians. Inferred functionality suggests the possibility of nitrogen cycling by the core bacterial community.
Kellogg et al. (2016) Bacterial community diversity of the deep-sea octocoral Paramuricea placomus. PeerJ 4:e2529 https://doi.org/10.7717/peerj.2529
Discovery pattern and species number of scale insects (Hemiptera: Coccoidea)
Few investigations have been made of the species description trend of scale insects. The present study reports the discovery pattern and taxonomic efforts for this group based on global species and a literature dataset. In addition, three asymptotic models (Logistic, Gompertz, and Extreme Value) based on a discovery curve were used to predict the species number of scale insects. Our results showed that the species description rate has been changing over time, with certain peaks and valleys in the past 250 years. The mean number of species described per year was 30, with the highest number of 195 described species in 1985. The increasing number of authors and the almost constant proportion of species described by 10% most prolific authors since the 1900s suggested that taxonomic effort has been increasing over time. The Gompertz model with lowest AIC value suggested that there are about 10,450 species of scale insects on Earth, nearly 30% of which remain to be described. Our study offers insights into the discovery pattern of scale insect diversity.
Deng et al. (2016) Discovery pattern and species number of scale insects (Hemiptera: Coccoidea). PeerJ 4:e2526 https://doi.org/10.7717/peerj.2526
Noise pollution has limited effects on nocturnal vigilance in peahens
Natural environments are increasingly exposed to high levels of noise pollution. Noise pollution can alter the behavior of animals but we know little about its effects on antipredator behavior. We therefore investigated the impact of noise pollution on vigilance behavior and roost selection in an avian species, peafowl (Pavo cristatus), that inhabits urban environments. Captive peahens were exposed to noise pollution at night and their vigilance levels and roost selections were monitored. The vigilance levels of peahens were unaffected by exposure to noise pollution within trials. Furthermore, the peahens exhibited no preference for roosting farther or closer to noise pollution. Interestingly, predators often avoided the experimental area during nights with noise pollution, which could explain why vigilance rates were higher overall during control compared to noise trials. The results suggest that peahens’ perception of risk is not drastically impacted by noise pollution but longer-term studies will be necessary to assess any chronic effects.
Yorzinski et al. (2016) Noise pollution has limited effects on nocturnal vigilance in peahens. PeerJ 4:e2525 https://doi.org/10.7717/peerj.2525
Reef-scale trends in Florida Acropora spp. abundance and the effects of population enhancement
Since the listing of Acropora palmata and A. cervicornis under the US Endangered Species Act in 2006, increasing investments have been made in propagation of listed corals (primarily A. cervicornis, A. palmata to a much lesser extent) in offshore coral nurseries and outplanting cultured fragments to reef habitats. This investment is superimposed over a spatiotemporal patchwork of ongoing disturbances (especially storms, thermal bleaching, and disease) as well as the potential for natural population recovery. In 2014 and 2015, we repeated broad scale (>50 ha), low precision Acropora spp. censuses (i.e., direct observation by snorkelers documented via handheld GPS) originally conducted in appropriate reef habitats during 2005–2007 to evaluate the trajectory of local populations and the effect of population enhancement. Over the decade-long study, A. palmata showed a cumulative proportional decline of 0.4 –0.7x in colony density across all sites, despite very low levels of outplanting at some sites. A. cervicornis showed similar proportional declines at sites without outplanting. In contrast, sites that received A. cervicornis outplants showed a dramatic increase in density (over 13x). Indeed, change in A. cervicornis colony density was significantly positively correlated with cumulative numbers of outplants across sites. This study documents a substantive reef-scale benefit of Acropora spp. population enhancement in the Florida Keys, when performed at adequate levels, against a backdrop of ongoing population decline.
Miller et al. (2016) Reef-scale trends in Florida Acropora spp. abundance and the effects of population enhancement. PeerJ 4:e2523 https://doi.org/10.7717/peerj.2523
Feeding bovine milks with low or high IgA levels is associated with altered re-establishment of murine intestinal microbiota after antibiotic treatment
Antibiotics are a vital and commonly used therapeutic tool, but their use also results in profound changes in the intestinal microbiota that can, in turn, have significant health consequences. Understanding how the microbiota recovers after antibiotic treatment will help to devise strategies for mitigating the adverse effects of antibiotics. Using a mouse model, we have characterized the changes occurring in the intestinal microbiota immediately after five days exposure to ampicillin, and then at three and fourteen days thereafter. During the fourteen day period of antibiotic recovery, groups of mice were fed either water, cows’ milk containing high levels of IgA, or cows’ milk containing low levels of IgA as their sole source of liquid. Effects on microbiota of feeding milks for 14 days were also assessed in groups of mice that had no ampicillin exposure. Changes in microbiota were measured by high throughput sequencing of the V4 to V6 variable regions of the 16S ribosomal RNA gene. As expected, exposure to ampicillin led to profound changes to the types and abundance of bacteria present, along with a loss of diversity. At 14 days following antibiotic exposure, mice fed water had recovered microbiota compositions similar to that prior to antibiotics. However, feeding High-IgA milk to mice that has been exposed to antibiotics was associated with altered microbiota compositions, including increased relative abundance of Lactobacillus and Barnesiella compared to the start of the study. Mice exposed to antibiotics then fed Low-IgA milk also showed increased Barnesiella at day 14. Mice without antibiotic perturbation, showed no change in their microbiota after 14 days of milk feeding. Overall, these findings add to a knowledge platform for optimizing intestinal function after treatment with antibiotics in the human population.
Hodgkinson et al. (2016) Feeding bovine milks with low or high IgA levels is associated with altered re-establishment of murine intestinal microbiota after antibiotic treatment. PeerJ 4:e2518 https://doi.org/10.7717/peerj.2518
Atlantic salmon (Salmo salar) require increased dietary levels of B-vitamins when fed diets with high inclusion of plant based ingredients
Aiming to re-evaluate current recommendations for nutrient supplementations when Atlantic salmon are fed diets based on plant ingredients, two regression experiments, with parr and post-smolt, were conducted. A control diet was included to evaluate if ingredients supplied sufficient nutrients without any added nutrient package (NP). The nutrient package consisted of vitamins B, C, E, minerals, cholesterol, methionine, taurine and histidine. This paper focus on B-vitamins. In parr, growth, health and welfare parameters responded on NP additions, but this was not observed in the seawater stage. During three months of feeding, parr tripled their weight. Parr given diets added the NP above NRC (2011) showed improved protein retention, and reduced liver and viscera indices. Post-smolt fed the same diets during five months showed a doubling of weight, but did not respond to the variation in NP to the same extent as parr. Significant regressions were obtained in body compartments for several of the B-vitamins in the premix. Whole body biotin concentration was unaffected by micronutrient premix level, and mRNA expression of the enzymes dependent of biotin showed only weak increases with increased biotin. Muscle thiamine plateaued at a diet level similar to NRC (2011) recommendation in freshwater, and showed stable values independent on premix addition in seawater. The mRNA expression of the enzyme G6PDH (glucose-6-phosphate dehydrogenase) is sensitive to thiamine availability; results did not indicate any need to add thiamine above levels recommended for fish in general. Niacin showed a steady increase in whole body concentrations as feed niacin increased. Muscle riboflavin peaked at a diet level of 12.4 mg kg−1. Sufficient riboflavin is important to avoid e.g., development of cataract. Cataract was not registered to be any problem, neither in fresh- nor in seawater. Cobalamin (B 12) in muscle and liver was saturated at 0.17 mg kg−1 diet. Muscle pyridoxine showed a dose-dependent level in muscle, and peaked around 10 mg kg −1 diet. White muscle ASAT (asparagine amino transferase) activity steadily increased, with indications of stable values when dietary pyridoxine was around 10–16 mg kg −1 diet. Pantothenic acid increased in gill tissue up to a level of 5.5 mg kg −1 soft gill tissue; at a dietary level of 22 mg kg−1. Improved performance, and coverage of metabolic need for niacin was at a dietary level of 66 mg kg −1, riboflavin 10–12 mg kg−1, pyridoxine 10 mg kg−1 and panthotenic acid 22 mg kg−1. Based on these results, recommended B-vitamin supplementation in plant based diets for Atlantic salmon should be adjusted.
Hemre et al. (2016) Atlantic salmon (Salmo salar) require increased dietary levels of B-vitamins when fed diets with high inclusion of plant based ingredients. PeerJ 4:e2493 https://doi.org/10.7717/peerj.2493
RBioplot: an easy-to-use R pipeline for automated statistical analysis and data visualization in molecular biology and biochemistry
Background Statistical analysis and data visualization are two crucial aspects in molecular biology and biology. For analyses that compare one dependent variable between standard (e.g., control) and one or multiple independent variables, a comprehensive yet highly streamlined solution is valuable. The computer programming language R is a popular platform for researchers to develop tools that are tailored specifically for their research needs. Here we present an R package RBioplot that takes raw input data for automated statistical analysis and plotting, highly compatible with various molecular biology and biochemistry lab techniques, such as, but not limited to, western blotting, PCR, and enzyme activity assays. Method The package is built based on workflows operating on a simple raw data layout, with minimum user input or data manipulation required. The package is distributed through GitHub, which can be easily installed through one single-line R command. A detailed installation guide is available at http://kenstoreylab.com/?page_id=2448. Users can also download demo datasets from the same website. Results and Discussion By integrating selected functions from existing statistical and data visualization packages with extensive customization, RBioplot features both statistical analysis and data visualization functionalities. Key properties of RBioplot include: -Fully automated and comprehensive statistical analysis, including normality test, equal variance test, Student’s t-test and ANOVA (with post-hoc tests); -Fully automated histogram, heatmap and joint-point curve plotting modules; -Detailed output files for statistical analysis, data manipulation and high quality graphs; -Axis range finding and user customizable tick settings; -High user-customizability.
Zhang et al. (2016) RBioplot: an easy-to-use R pipeline for automated statistical analysis and data visualization in molecular biology and biochemistry. PeerJ 4:e2436 https://doi.org/10.7717/peerj.2436
Influence of age and sex on winter site fidelity of sanderlings Calidris alba
Many migratory bird species show high levels of site fidelity to their wintering sites, which confers advantages due to prior knowledge, but may also limit the ability of the individual to move away from degrading sites or to detect alternative foraging opportunities. Winter site fidelity often varies among age groups, but sexual differences have seldom been recorded in birds. We studied a population of individually colour-marked sanderlings wintering in and around the Tejo estuary, a large estuarine wetland on the western coast of Portugal. For 160 individuals, sighted a total of 1,249 times between November 2009 and March 2013, we calculated the probability that they moved among five distinct wintering sites and how this probability is affected by distance between them. To compare site fidelity among age classes and sexes, as well as within the same winter and over multiple winters, we used a Site Fidelity Index (SFI). Birds were sexed using a discriminant function based on biometrics of a large set of molecularly sexed sanderlings (n = 990). The vast majority of birds were observed at one site only, and the probability of the few detected movements between sites was negatively correlated with the distance among each pair of sites. Hardly any movements were recorded over more than 15 km, suggesting small home ranges. SFI values indicated that juveniles were less site-faithful than adults which may reflect the accumulated knowledge and/or dominance of older animals. Among adults, females were significantly less site faithful than males. A sexual difference in winter site fidelity is unusual in shorebirds. SFI values show site-faithfulness is lower when multiple winters were considered, and most birds seem to chose a wintering site early in the season and use that site throughout the winter. Sanderlings show a very limited tendency to explore alternative wintering options, which might have implications for their survival when facing habitat change or loss (e.g., like severe beach erosion as can be the case at one of the study sites).
Lourenço et al. (2016) Influence of age and sex on winter site fidelity of sanderlings Calidris alba. PeerJ 4:e2517 https://doi.org/10.7717/peerj.2517