Body distribution of impetigo and association with host and pathogen factors
Background Impetigo or skin sores are estimated to affect >162 million people worldwide. Detailed descriptions of the anatomical location of skin sores are lacking. Methods We used prospectively collected data from a randomised control trial of treatments for impetigo in Aboriginal children in Australia. We generated heat-map distributions of skin sores on the human body from 56 predefined anatomical locations and stratified skin sore distribution by sex, age, causative pathogen and co-infection with scabies, tinea and head lice. We compared the distribution of sores between males and females, between sores with only Streptococcus pyogenes and sores with only Staphylococcus aureus; and across age groups with a Fisher’s exact test. Results There were 663 episodes of impetigo infections among 508 children enrolled in the trial. For all 663 episodes, the lower limbs were the most affected body sites followed by the distal upper limbs, face and scalp. On the anterior surface of the body, the pre-tibial region was the most affected while on the posterior surface, the dorsum of the hands and calves predominated. There was no observable difference between males and females in distribution of sores. Children up to 3 years of age were more likely to have sores on the upper posterior lower limbs and scalp than older age groups, with the distribution of sores differing across age groups (p = 3 × 10−5). Sores from which only Staphylococcus aureus was cultured differed in distribution to those with only Streptococcus pyogenes cultured (p = 3 × 10−4) and were more commonly found on the upper posterior lower limbs. Conclusions Skin sores were predominantly found on exposed regions of the lower leg and distal upper limbs. The distribution of sores varied by age group and pathogen. These results highlight key areas of the body for clinicians to pay attention to when examining children for skin sores.
Yerramilli et al. (2022) Body distribution of impetigo and association with host and pathogen factors. PeerJ 10:e14154 https://doi.org/10.7717/peerj.14154
Enhancing yogurt products’ ingredients: preservation strategies, processing conditions, analytical detection methods, and therapeutic delivery—an overview
As a dairy product, yogurt delivers nourishing milk components through the beneficial microbial fermentation process, improved by bioavailability and bioaccessibility–an exclusive combined food asset. In recent decades, there has been considerable attention to yogurt product development particularly in areas like influence by antioxidant-rich fruits, different factors affecting its probiotic viability, and the functionality of inulin and probiotics. Essentially, many published reviews frequently focus on the functionalities associated with yogurt products, however, those articulating yogurt ingredients specific to associated preservation strategies, processing conditions, and analytical detection techniques are very few, to the best of our knowledge. The knowledge and understanding of preservation strategies that enhance the ingredients in yogurt products, and their function as modern drug delivery systems are essential, given the opportunities it can provide for future research. Therefore, this overview discussed how yogurt product ingredients have been enhanced, from preservation strategies, processing conditions, analytical detection methods, and therapeutic delivery standpoints. The survey methodology involved major stages, from the brainstorming of research questions, search strategy, effective utilization of databases, inclusion and exclusion criteria, etc. The innovative successes of yogurts would be enhanced via the physicochemical, nutritional and therapeutic aspects of the ingredients/products. Besides processing conditions to influence the yogurt constituents, overall acceptability, quality, and shelf-life, the analytical assays would help detect the hidden product constituents, toxins, and other storage-related changes. The therapeutic role of yogurt-a modern drug delivery system, would be demonstrated via the supplementation (of yogurt) either alone or with bioactive ingredients. The future of yogurt requires the collective action of stakeholders to formulate unique variants with different natural blends, where synthetic ingredients become completely replaced by the plant’s derivatives, which enhance the acidification rate and extend shelf life.
Mehra et al. (2022) Enhancing yogurt products’ ingredients: preservation strategies, processing conditions, analytical detection methods, and therapeutic delivery—an overview. PeerJ 10:e14177 https://doi.org/10.7717/peerj.14177
Overexpression of LINC00551 promotes autophagy-dependent ferroptosis of lung adenocarcinoma via upregulating DDIT4 by sponging miR-4328
According to mounting evidence, long noncoding RNAs (lncRNAs) play a vital role in regulated cell death (RCD). A potential strategy for cancer therapy involves triggering ferroptosis, a novel form of RCD. Although it is thought to be an autophagy-dependent process, it is still unclear how the two processes interact. This study characterized a long intergenic noncoding RNA, LINC00551, expressed at a low level in lung adenocarcinoma (LUAD) and some other cancers. Overexpression of LINC00551 suppresses cell viability while promoting autophagy and RSL-3-induced ferroptosis in LUAD cells. LINC00551 acts as a competing endogenous RNA (ceRNA) and binds with miR-4328 which up-regulates the target DNA damage-inducible transcript 4 (DDIT4). DDIT4 inhibits the activity of mTOR, promotes LUAD autophagy, and then promotes the ferroptosis of LUAD cells in an autophagy-dependent manner. This study provided an insight into the molecular mechanism regulating ferroptosis and highlighted LINC00551 as a potential therapeutic target for LUAD.
Peng et al. (2022) Overexpression of LINC00551 promotes autophagy-dependent ferroptosis of lung adenocarcinoma via upregulating DDIT4 by sponging miR-4328. PeerJ 10:e14180 https://doi.org/10.7717/peerj.14180
When disturbances favour species adapted to stressful soils: grazing may benefit soil specialists in gypsum plant communities
Background Herbivory and extreme soils are drivers of plant evolution. Adaptation to extreme soils often implies substrate-specific traits, and resistance to herbivory involves tolerance or avoidance mechanisms. However, little research has been done on the effect of grazing on plant communities rich in edaphic endemics growing on extreme soils. A widespread study case is gypsum drylands, where livestock grazing often prevails. Despite their limiting conditions, gypsum soils host a unique and highly specialised flora, identified as a conservation priority. Methods We evaluated the effect of different grazing intensities on the assembly of perennial plant communities growing on gypsum soils. We considered the contribution of species gypsum affinity and key functional traits of species such as traits related to gypsum specialisation (leaf S accumulation) or traits related to plant tolerance to herbivory such as leaf C and N concentrations. The effect of grazing intensity on plant community indices (i.e., richness, diversity, community weighted-means (CWM) and functional diversity (FD) indices for each trait) were modelled using Generalised Linear Mixed Models (GLMM). We analysed the relative contribution of interspecific trait variation and intraspecific trait variation (ITV) in shifts of community index values. Results Livestock grazing may benefit gypsum plant specialists during community assembly, as species with high gypsum affinity, and high leaf S contents, were more likely to assemble in the most grazed plots. Grazing also promoted species with traits related to herbivory tolerance, as species with a rapid-growth strategy (high leaf N, low leaf C) were promoted under high grazing conditions. Species that ultimately formed gypsum plant communities had sufficient functional variability among individuals to cope with different grazing intensities, as intraspecific variability was the main component of species assembly for CWM values. Conclusions The positive effects of grazing on plant communities in gypsum soils indicate that livestock may be a key tool for the conservation of these edaphic endemics.
Cera et al. (2022) When disturbances favour species adapted to stressful soils: grazing may benefit soil specialists in gypsum plant communities. PeerJ 10:e14222 https://doi.org/10.7717/peerj.14222
Seasonal variation characteristics of water quality in the Sunxi River Watershed, Three Gorges Reservoir Area
The seasonal change characteristics of water quality in the Sunxi River watershed, which is a typical watershed in the tail area of the Three Gorges Reservoir Area, must be studied to provide remediation ideas and specific measures for agricultural nonpoint source pollution in the reservoir area. A two-way repeated measures ANOVA was used to analyze the variation characteristics of chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) concentrations in the upstream and downstream of the Sunxi River watershed in spring, summer, and autumn of 2018–2021. With data from autumn 2018 taken as an example, path analysis was applied to study the effect degree of influencing factors on TN concentrations. The two-way repeated measures ANOVA illustrated that the COD, TN, and TP concentrations in the downstream were significantly higher than those in the upstream (P < 0.05). In addition, the COD concentrations were the highest in summer 2019, followed by spring of 2019 and 2021, and TN and TP concentrations were higher in spring and summer. The TN and TP concentrations were comparatively lower in the autumn. The path analysis showed that electrical conductance and dissolved oxygen directly affected the TN concentrations, and water temperature mainly affected the TN concentrations via the indirect effects of electrical conductance and dissolved oxygen. The water quality of upstream Sunxi River watershed was better than that of downstream, and the water quality in autumn was better than spring and summer in 2018–2021. For water quality management and ecological restoration of the Sunxi River watershed, further attention should be paid to the water quality changes in the downstream and in spring and summer and to the impact of water temperature, electrical conductivity, and dissolved oxygen on the water quality.
Hou et al. (2022) Seasonal variation characteristics of water quality in the Sunxi River Watershed, Three Gorges Reservoir Area. PeerJ 10:e14233 https://doi.org/10.7717/peerj.14233
Intensive hunting changes human-wildlife relationships
Wildlife alter their behaviors in a trade-off between consuming food and fear of becoming food themselves. The risk allocation hypothesis posits that variation in the scale, intensity and longevity of predation threats can influence the magnitude of antipredator behavioral responses. Hunting by humans represents a threat thought to be perceived by wildlife similar to how they perceive a top predator, although hunting intensity and duration varys widely around the world. Here we evaluate the effects of hunting pressure on wildlife by comparing how two communities of mammals under different management schemes differ in their relative abundance and response to humans. Using camera traps to survey wildlife across disturbance levels (yards, farms, forests) in similar landscapes in southern Germany and southeastern USA, we tested the prediction of the risk allocation hypothesis: that the higher intensity and longevity of hunting in Germany (year round vs 3 months, 4x higher harvest/km2/year) would reduce relative abundance of hunted species and result in a larger fear-based response to humans (i.e., more spatial and temporal avoidance). We further evaluated how changes in animal abundance and behavior would result in potential changes to ecological impacts (i.e., herbivory and predation). We found that hunted species were relatively less abundant in Germany and less associated with humans on the landscape (i.e., yards and urban areas), but did not avoid humans temporally in hunted areas while hunted species in the USA showed the opposite pattern. These results are consistent with the risk allocation hypothesis where we would expect more spatial avoidance in response to threats of longer duration (i.e., year-round hunting in Germany vs. 3-month duration in USA) and less spatial avoidance but more temporal avoidance for threats of shorter duration. The expected ecological impacts of mammals in all three habitats were quite different between countries, most strikingly due to the decreases in the relative abundance of hunted species in Germany, particularly deer, with no proportional increase in unhunted species, resulting in American yards facing the potential for 25x more herbivory than German yards. Our results suggest that the duration and intensity of managed hunting can have strong and predictable effects on animal abundance and behavior, with the potential for corresponding changes in the ecological impacts of wildlife. Hunting can be an effective tool for reducing wildlife conflict due to overabundance but may require more intensive harvest than is seen in much of North America.
Parsons et al. (2022) Intensive hunting changes human-wildlife relationships. PeerJ 10:e14159 https://doi.org/10.7717/peerj.14159
Estimation methods for the ratio of medians of three-parameter lognormal distributions containing zero values and their application to wind speed data from northern Thailand
Wind speed has an important impact on the formation and dispersion of fine particulate matter (PM), which can cause several health problems. During the transition from the winter to the summer season in northern Thailand, the wind speed has been low for longer than usual, which has resulted in fine PM accumulating in the air. Motivated by this, we have identified a need to investigate wind speed due to its effect on PM formation and dispersion and to raise awareness among the general public. The hourly windspeed can be approximated by using confidence intervals for the ratio of the medians of three-parameter lognormal distributions containing zero values. Thus, we constructed them by using fiducial, normal approximation, and Bayesian methods. By way of comparison, the performance measures for all ofthe proposed methods (the coverage percentage, lower and upper error probabilities (LEP and UEP,respectively), and expected length) were assessed via Monte Carlo simulation. The results of Monte Carlo simulation studies show that the Bayesian method provided coverage percentages close to the nominal confidence level and shorter intervals than the other methods. Importantly, it maintained a good balance between LEP and UEP even for large variation and percentage of zero-valued observations. To illustrate the efficacy of our proposed methods, we applied them to hourly wind speed data from northern Thailand.
Environmental Contamination and Remediation
Maneerat et al. (2022) Estimation methods for the ratio of medians of three-parameter lognormal distributions containing zero values and their application to wind speed data from northern Thailand. PeerJ 10:e14194 https://doi.org/10.7717/peerj.14194
Association between hypomagnesemia and mortality among dialysis patients: a systematic review and meta-analysis
Background Malnutrition-inflammation-atherosclerosis (MIA) syndrome is caused by the inflammatory cytokines in end stage renal disease (ESRD) patients, and MIA complex-related factors may be associated with hypomagnesemia and mortality. However, the association between serum magnesium level and mortality for dialysis patients is still not clear. Additionally, no meta-analysis has investigated the impact of serum magnesium on peritoneal dialysis and hemodialysis, separately. Methods We searched published studies in PubMed, Embase, Cochrane, Collaboration Central Register of Controlled Clinical Trials, and Cochrane Systematic Reviews through April 2022. Studies associated with serum magnesium and all-cause mortality or cardiovascular (CV) mortality in ESRD on kidney replacement therapy (KRT) patients were included. A hazard ratio (HR) with 95% confidence intervals (CI) was used to report the outcomes. Results Twenty-one studies involving 55,232 patients were included. Overall, there was a significant association between hypomagnesemia and all-cause mortality for dialysis patients (HR: 1.67, 95% CI [1.412–2.00], p < 0.001; certainty of evidence: moderate) using a mixed unadjusted and adjusted HR for analysis. There was also a significantly increased risk of CV mortality for individuals with hypomagnesemia compared with the non-hypomagnesemia group (HR 1.56, 95% CI [1.08–2.25], p < 0.001; certainty of evidence: moderate). In addition, a subgroup analysis demonstrated that hypomagnesemia was associated with a high risk of both all-cause mortality and CV mortality (all-cause mortality, HR:1.80, 95% CI [1.48–2.19]; CV mortality, HR:1.84, 95% CI [1.10–3.07]) in hemodialysis (HD) patients, but not in participants receiving peritoneal dialysis (PD; all-cause mortality, HR:1.26, 95% CI [0.84–1.91]; CV mortality, HR:0.66, 95% CI [0.22–2.00]). The systematic review protocol was prespecified and registered in PROSPERO [CRD42021256187]. Conclusions Hypomagnesemia may be a significant risk factor for all-cause mortality and CV mortality in KRT patients, especially in those receiving hemodialysis. However, because of the limited certainty of evidence, more studies are required to investigate this association.
Huang et al. (2022) Association between hypomagnesemia and mortality among dialysis patients: a systematic review and meta-analysis. PeerJ 10:e14203 https://doi.org/10.7717/peerj.14203
Impact of silver nanoparticles on the nutritional properties of Arthrospira platensis
Background Arthrospira platensis is farmed worldwide due to its nutrient-rich properties and provides multiple benefits to human health. However, the wide usage of silver nanoparticles (Ag NPs) causes pollution which may affect the nutritional quality of A. platensis. Hence, this study aimed to investigate the interaction and accumulation of Ag NPs on A. platensis, and determine the changes in biomass and nutritional value of A. platensis due to the exposure to Ag NPs. Methods The interaction and accumulation of Ag NPs on A. platensis were examined through Fourier transformed infrared (FTIR) spectroscopy and scanning electron microscope (SEM). The loss in biomass together with the macromolecules, pigments, and phenolic compounds of A. platensis was investigated upon treating with various concentrations of Ag NPs (5, 10, 25, 50 and 100 µg/mL) for 24, 48, 72 and 96 h. Results The results showed that the treatment of A. platensis with Ag NPs caused a dose and time-dependent reduction in biomass, macronutrients, pigments and phenolic compounds. The highest detrimental effects were found at 96 h with the reported values of 65.71 ± 2.79%, 67.21 ± 3.98%, 48.99 ± 4.39% and 59.62 ± 3.96% reduction in biomass, proteins, carbohydrates and lipids, respectively, along with 82.99 ± 7.81%, 67.55 ± 2.63%, 75.03 ± 1.55%, and 63.43 ± 2.89% loss in chlorophyll-a, carotenoids, C-phycocyanin, and total phenolic compounds of A. platensis for 100 µg/mL of Ag NPs. The EDX analysis confirmed the surface accumulation of Ag NPs on Arthrospira cells, while SEM images evidenced the surface alterations and damage of the treated cells. The functional groups such as hydroxyl, amine, methyl, amide I, amide II, carboxyl, carbonyl and phosphate groups from the cell wall of the A. platensis were identified to be possibly involved in the interaction of Ag NPs with A. platensis. Conclusion The study confirmed that the exposure of Ag NPs is detrimental to A. platensis where the interaction and accumulation of Ag NPs on A. platensis caused reduction in biomass, macromolecules, pigments, and total phenolic compounds.
Liang et al. (2022) Impact of silver nanoparticles on the nutritional properties of Arthrospira platensis. PeerJ 10:e13972 https://doi.org/10.7717/peerj.13972
Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups
North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis, which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis, such as Cyprinella, Luxilus, Lythrurus, and Pteronotropis, the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius, Luxilus, and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae. Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis, elevation of the subgenus Hydrophlox, expansion of species included in Miniellus, movement of Hudsonius cummingsae to Pteronotropis, and resurrection of the genera Coccotis and Paranotropis. We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala, and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucleotides respectively).
Stout et al. (2022) Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups. PeerJ 10:e14072 https://doi.org/10.7717/peerj.14072