Paleomass for R—bracketing body volume of marine vertebrates with 3D models
Body mass is arguably the most important characteristic of an organism, yet it is often not available in biological samples that have been skeletonized, liquid-preserved, or fossilized. The lack of information is especially problematic for fossil species, for which individuals with body mass information are not available anywhere. Multiple methods are available for estimating the body mass of fossil terrestrial vertebrates but those for their marine counterparts are limited. Paleomass is a software tool for estimating the body mass of marine vertebrates from their orthogonal silhouettes through bracketing. It generates a set of two 3D models from these silhouettes, assuming superelliptical body cross-sections with different exponent values. By setting the exponents appropriately, it is possible to bracket the true volume of the animal between those of the two models. The original version phased out together with the language platform it used. A new version is reported here as an open-source package based on the R scripting language. It inherits the underlying principles of the original version but has been completely rewritten with a new architecture. For example, it first produces 3D mesh models of the animal and then measures their volumes and areas with the VCG library, unlike the original version that did not produce a 3D model but instead computed the volume and area segment by segment using parametric equations. The new version also exports 3D models in polygon meshes, allowing later tests by other software. Other improvements include the use of NACA foil sections for hydrofoils such as flippers, and optional interpolation with local regression. The software has a high accuracy, with the mean absolute errors of 1.33% when the silhouettes of the animals are known.
Motani (2023) Paleomass for R—bracketing body volume of marine vertebrates with 3D models. PeerJ 11:e15957 https://doi.org/10.7717/peerj.15957
Effects of drought and salt stress on seed germination and seedling growth of Elymus nutans
Drought and soil salinization are global environmental issues, and Elymus nutans play an important role in vegetation restoration in arid and saline environments due to their excellent stress resistance. In the process of vegetation restoration, the stage from germination to seedling growth of forage is crucial. This experiment studied the effects of PEG-6000 simulated drought stress and NaCl simulated salinization stress on the germination of E. nutans seeds, and explored the growth of forage seedlings from sowing to 28 days under drought and salinization stress conditions. The results showed that under the same environmental water potential, there were significant differences in responses of seed germination, seedling growth, organic carbon, total nitrogen and total phosphorus of above-ground and underground parts of E. nutans to drought stress and salinization stress. Using the membership function method to comprehensively evaluate the seed germination and seedling indicators of E. nutans, it was found that under the same environmental water potential, E. nutans was more severely affected by drought stress during both the seed germination and seedling growth stages. E. nutans showed better salt tolerance than drought resistance.
Environmental Contamination and Remediation
Long et al. (2023) Effects of drought and salt stress on seed germination and seedling growth of Elymus nutans. PeerJ 11:e15968 https://doi.org/10.7717/peerj.15968
Understanding mental fatigue and its detection: a comparative analysis of assessments and tools
Mental fatigue has shown to be one of the root causes of decreased productivity and overall cognitive performance, by decreasing an individual’s ability to inhibit responses, process information and concentrate. The effects of mental fatigue have led to occupational errors and motorway accidents. Early detection of mental fatigue can prevent the escalation of symptoms that may lead to chronic fatigue syndrome and other disorders. To date, in clinical settings, the assessment of mental fatigue and stress is done through self-reported questionnaires. The validity of these questionnaires is questionable, as they are highly subjective measurement tools and are not immune to response biases. This review examines the wider presence of mental fatigue in the general population and critically compares its various detection techniques (i.e., self-reporting questionnaires, heart rate variability, salivary cortisol levels, electroencephalogram, and saccadic eye movements). The ability of these detection tools to assess inhibition responses (which are sensitive enough to be manifested in a fatigue state) is specifically evaluated for a reliable marker in identifying mentally fatigued individuals. In laboratory settings, antisaccade tasks have been long used to assess inhibitory control and this technique can potentially serve as the most promising assessment tool to objectively detect mental fatigue. However, more studies need to be conducted in the future to validate and correlate this assessment with other existing measures of mental fatigue detection. This review is intended for, but not limited to, mental health professionals, digital health scientists, vision researchers, and behavioral scientists.
Kunasegaran et al. (2023) Understanding mental fatigue and its detection: a comparative analysis of assessments and tools. PeerJ 11:e15744 https://doi.org/10.7717/peerj.15744
Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD)
Effective treatment and prevention of any disease necessitates knowledge of the causative agent, yet the causative agents of most coral diseases remain unknown, in part due to the difficulty of distinguishing the pathogenic microbe(s) among the complex microbial backdrop of coral hosts. Stony coral tissue loss disease (SCTLD) is a particularly destructive disease of unknown etiology, capable of transmitting through the water column and killing entire colonies within a matter of weeks. Here we used a previously described method to (i) isolate diseased and apparently healthy coral colonies within individual mesocosms containing filtered seawater with low microbial background levels; (ii) incubate for several days to enrich the water with coral-shed microbes; (iii) use tangential-flow filtration to concentrate the microbial community in the mesocosm water; and then (iv) filter the resulting concentrate through a sequential series of different pore-sized filters. To investigate the size class of microorganism(s) associated with SCTLD transmission, we used 0.8 µm pore size filters to capture microeukaryotes and expelled zooxanthellae, 0.22 µm pore size filters to capture bacteria and large viruses, and 0.025 µm pore size filters to capture smaller viruses. In an attempt to further refine which size fraction(s) contained the transmissible element of SCTLD, we then applied these filters to healthy “receiver” coral fragments and monitored them for the onset of SCTLD signs over three separate experimental runs. However, several factors outside of our control confounded the transmission results, rendering them inconclusive. As the bulk of prior studies of SCTLD in coral tissues have primarily investigated the associated bacterial community, we chose to characterize the prokaryotic community associated with all mesocosm 0.22 µm pore size filters using Illumina sequencing of the V4 region of the 16S rRNA gene. We identified overlaps with prior SCTLD studies, including the presence of numerous previously identified SCTLD bioindicators within our mesocosms. The identification in our mesocosms of specific bacterial amplicon sequence variants that also appear across prior studies spanning different collection years, geographic regions, source material, and coral species, suggests that bacteria may play some role in the disease.
Evans et al. (2023) Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD). PeerJ 11:e15836 https://doi.org/10.7717/peerj.15836
Calcification detection on upper extremity arteries: a comparison of ultrasonic and X-ray methods
Background Vascular calcification (VC) has been observed in patients with hemodialysis, whereas few studies have investigated calcification in the upper extremity vasculature. Both ultrasound and X-ray are used to investigate the calcification of arteries in patients. However, there is a lack of data on the consistency between these two methods. The aim of this study was to investigate the occurrence of VC in the radial and ulnar arteries of hemodialysis patients and investigate the detection consistency in VC between ultrasound and X-ray. Methods Ultrasound and X-ray examinations were performed in the radial and ulnar arteries of both the left and right upper extremities of 40 patients on hemodialysis. The calcification status of arteries was evaluated by the calcification index from ultrasound and X-ray respectively. Clinical variables of patients were collected from all the involved patients. Results Of the 40 patients, VC was detected in 31 patients by ultrasound, while X-ray detected VC in 22 patients. Compared to ultrasound assessment, X-ray assessment was 73.21% sensitive but only 66.35% specific with a positive predictive value of 53.95% for detecting calcifications in the radial or ulnar artery. The level of agreement between ultrasound and X-ray results was fair. In addition, our data showed that more ulnar arteries had VCs than the corresponding radial arteries. Conclusion Ultrasound is more sensitive in detecting the presence of calcified atherosclerotic lesions. Ultrasound and X-ray exhibited fair consistency. Ultrasound screening for upper extremity radial and ulnar arteries in hemodialysis patients may deserve attention to explore its clinical significance.
Yang et al. (2023) Calcification detection on upper extremity arteries: a comparison of ultrasonic and X-ray methods. PeerJ 11:e15855 https://doi.org/10.7717/peerj.15855
Evaluation of the validity of the HPV viral load compared to conventional techniques for the detection of high-grade anal intraepithelial lesions in men with HIV who have sex with men
Background The incidence of high-grade anal intraepithelial lesions (HSILs) has increased in recent years among men who have sex with men with human immunodeficiency virus (HIV). This work evaluated the validity of the human papilloma virus viral load (HPV-VL) versus cytological and qualitative HPV results to detect HSILs. Methods From May 2017 to January 2020, 93 men who have sex with men and HIV were included in an anal cancer screening program from the Infectious Diseases Unit at a tertiary-care hospital in Alicante (Spain). The gold-standard for the screening of anal HSILs is the anal biopsy using high-resolution anoscopy. The diagnostic methods compared against gold-standard were HPV-16-VL, HPV-18-VL, and HPV-16-18-VL co-testing, anal cytology, and qualitative HPV detection. The receiver operating characteristic (ROC) curve and cut-off points for HPV-VL were calculated. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Cohen’s Kappa coefficient (κ) were also calculated. Results The mean patient age was 44.6 ± 9.5 years. All of them received antiretroviral treatment, 96.8% had an HIV viral load of <50 copies/mL and 17.2% had a previous diagnosis of AIDS. The diagnosis of the anal biopsies were: 19.4% (n = 18) HSIL, 29.1% (n = 27) LSIL, and 51.6% (n = 48) negative. An HPV-16-VL >6.2 copies/cell was detected in the HSIL biopsy samples (p = 0.007), showing a sensitivity of 100% and a specificity of 46.2%. HPV-18-VL and HPV16-18-VL co-testing showed a sensitivity of 75% and 76.9% and a specificity of 72.7% and 61.3%, respectively. The highest PPV was 50% obtained with the cytology and HPV-18-VL. The HPV-16-VL showed a NPV of 100%, followed by 88.9% in the HPV-18-VL and 87% in the abnormal cytology. Cohen’s Kappa coefficient were: HPV-18-VL (κ = 0.412), abnormal cytology (κ = 0.353) and HPV-16-VL (κ = 0.338). Conclusions HPV-VL testing improved the detection sensitivity but not the specificity for HSIL biopsies compared to anal cytology and the qualitative detection of HPV. In men who have sex with men and HIV the HPV-VL could be an useful tool for diagnosis of HSILs in anal cancer screening programs. Further studies will be needed to evaluate the clinical implications of HPV-VL in these programs.
Díez-Martínez et al. (2023) Evaluation of the validity of the HPV viral load compared to conventional techniques for the detection of high-grade anal intraepithelial lesions in men with HIV who have sex with men. PeerJ 11:e15878 https://doi.org/10.7717/peerj.15878
CTRP3 attenuates inflammation, oxidative and cell death in cisplatin induced HK-2 cells
Cisplatin has been widely studied and found to be a highly effective anti-tumor drug. It has several side effects, including acute kidney injury (AKI). Cisplatin-induced AKI can be primarily attributed to oxidative stress, inflammation, and apoptosis. The CTRP3 adipokine is a new adipokine that exhibits antioxidant, anti-inflammatory, and antiapoptotic properties. Despite this, the role of CTRP3 in AKI remain unclear. In cisplatin-induced AKI models, our findings demonstrated that CTRP3 expression was decreased in human proximal tubule epithelial cells (HK-2). In the in vitro experiments, HK-2 cells were first transfected with an overexpression plasmid of CTRP3 (pcDNA-CTRP3) or a small interfering RNA for CTRP3 (si-CTRP3) and induced by cisplatin; and cell oxidative stress, inflammation, proliferation, and apoptosis were found to be present. Overexpressing CTRP3 inhibited oxidative stress through decreasing malondialdehyde (MDA) levels and increasing the activity of SOD and CAT. The mRNA levels of SOD1 and SOD2 were increased in response to CTRP3 overexpression. Additionally, CTRP3 decreased TNF-α and MCP-1 levels. Moreover, CTRP3 overexpression increased cisplatin-induced cell activity and decreased cell apoptosis, as indicated by the elevated numbers of EdU positive cells and decreased numbers of apoptotic cells. Consistent with these results, the overexpression of CTRP3 effectively elevated the mRNA levels of Bcl-2 and reduced the mRNA levels of Bax. In contrast, inhibition of CTRP3 expression by si-CTRP3 reversed the cisplatin-induced indices. Mechanistically, we found that the overexpression of CTRP3 can increase expression of Nrf2 and inhibit the activation of MAPK phosphorylation (ERK, JNK, and p38). Furthermore, inhibition of ERK, JNK and p38 activity eliminated aggravation of cisplatin-induced inflammation and apoptosis caused by CTRP3 knockdown. Additionally, the cisplatin-induced oxidative stress and activation of MAPK phosphorylation (ERK, JNK, and p38) in HK-2 cells were reversed by Nrf2 suppression by siRNA. Collectively, these results indicated that CTRP3 may identify as a novel target for AKI treatment and protect against cisplatin-induced AKI through the Nrf2/MAPK pathway.
Zou et al. (2023) CTRP3 attenuates inflammation, oxidative and cell death in cisplatin induced HK-2 cells. PeerJ 11:e15890 https://doi.org/10.7717/peerj.15890
No genetic causal association between dental caries and Alzheimer’s disease: a bidirectional two-sample Mendelian randomization analysis
Background An increasing number of observational studies have suggested an association between dental caries and Alzheimer’s disease (AD). The association between dental caries and Alzheimer’s disease may be mediated by confounders or reverse causality. In this study, we conducted bidirectional two-sample Mendelian randomization (MR) to estimate the bidirectional causality between dental caries and AD. Materials and Methods Genome-wide association study (GWAS) summary statistics of dental caries were extracted from a published meta-analysis which included a total of 487,823 participants. GWAS datasets of AD and AD onset age were obtained from the FinnGen bank. A bidirectional two-sample analysis was performed to explore the causality between dental caries and AD. Results For the dental caries-AD causality estimation, there was no significant association between dental caries and AD, neither with the AD GWASs from the FinnGen database (OR: 1.041, p = 0.874) nor with those from the International Genomics of Alzheimer’s Project (OR: 1.162, p = 0.409). In addition, the genetic susceptibility to dental caries was not related to the onset age of AD. No causality existed between dental caries and early-onset AD (OR: 0.515, p = 0.302) or late-onset AD (OR: 1.329, p = 0.347). For the AD-dental caries relationship, no causality was detected by the IVW method (OR: 1.000, p = 0.717). Findings from other MR methods were consistent. The pleiotropy test and sensitivity analysis confirmed the validity of these MR results. Conclusions In this bidirectional MR study, robust evidence to support a bidirectional causal effect between dental caries and AD from the GWAS results within large-scale European-descent populations was absent. Having dental caries would not alter the onset age of AD.
Liao et al. (2023) No genetic causal association between dental caries and Alzheimer’s disease: a bidirectional two-sample Mendelian randomization analysis. PeerJ 11:e15936 https://doi.org/10.7717/peerj.15936
Farmers’ perception of the ecosystem services provided by diurnal raptors in arid Rajasthan
Farmers are the most important stakeholders in wildlife conservation in the agricultural landscape. Understanding the farmer’s perceptions, attitude, behaviour, and knowledge toward conservation is critical in developing an effective conservation programme in human-dominated landscapes. We conducted semi-structured face-to-face interviews with 373 farmers to understand the farmer’s perception of ecosystem services provided by diurnal raptors in the arid region of Rajasthan from July 2020 to February 2021 and from August 2021 to January 2022. We grouped ecosystem services and disservices into larger categories and estimated the correlation between them, finding that disservices are negatively correlated with benefits. Raptors were perceived as beneficial for their role in controlling rodents and pests, but negatively for poultry predation. In addition, we built a binomial generalised linear model with a logit function to better understand the factors that influence farmers’ perceptions of raptors (positive or negative). We observed that males and females have different attitudes toward the ecosystem services provided by raptors. It is critical to understand social perceptions in order to conserve species that are rare on a global scale but may face negative perceptions on a local scale. Our study connects ecological information with socio-demographic factors, which can be useful in developing policy measures for raptor conservation.
Tiwari et al. (2023) Farmers’ perception of the ecosystem services provided by diurnal raptors in arid Rajasthan. PeerJ 11:e15996 https://doi.org/10.7717/peerj.15996
Comparative genomics of bacteria from amphibian skin associated with inhibition of an amphibian fungal pathogen, Batrachochytrium dendrobatidis
Chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), is a skin disease associated with worldwide amphibian declines. Symbiotic microbes living on amphibian skin interact with Bd and may alter infection outcomes. We completed whole genome sequencing of 40 bacterial isolates cultured from the skin of four amphibian species in the Eastern US. Each isolate was tested in vitro for the ability to inhibit Bd growth. The aim of this study was to identify genomic differences among the isolates and generate hypotheses about the genomic underpinnings of Bd growth inhibition. We identified sixty-five gene families that were present in all 40 isolates. Screening for common biosynthetic gene clusters revealed that this set of isolates contained a wide variety of clusters; the two most abundant clusters with potential antifungal activity were siderophores (N=17 isolates) and Type III polyketide synthases (N=22 isolates). We then examined various subsets of the 22 isolates in the phylum Proteobacteria for genes encoding specific compounds that may inhibit fungal growth, including chitinase and violacein. We identified differences in Agrobacterium and Sphingomonas isolates in the chitinase genes that showed some association with anti-Bd activity, as well as variation in the violacein genes in the Janthinobacterium isolates. Using a comparative genomics approach, we generated several testable hypotheses about differences among bacterial isolates from amphibian skin communities that could contribute to variation in the ability to inhibit Bd growth. Further work is necessary to explore and uncover the various mechanisms utilized by amphibian skin bacterial isolates to inhibit Bd.
Wax et al. (2023) Comparative genomics of bacteria from amphibian skin associated with inhibition of an amphibian fungal pathogen, Batrachochytrium dendrobatidis. PeerJ 11:e15714 https://doi.org/10.7717/peerj.15714