Disturbance has lasting effects on functional traits and diversity of grassland plant communities
Background Localized disturbances within grasslands alter biological properties and may shift species composition. For example, rare species in established communities may become dominant in successional communities if they exhibit traits well-suited to disturbance conditions. Although the idea that plant species exhibit different trait ‘strategies’ is well established, it is unclear how ecological selection for specific traits may change as a function of disturbance. Further, there is little data available testing whether disturbances select for single trait-characters within communities (homogenization), or allow multiple trait-types to persist (diversification). We investigated how (a) traits and (b) functional diversity of post-disturbance gap communities compared to those in adjacent undisturbed grasslands, and (c) if altered functional diversity resulted in the homogenization or diversification of functional traits. Methods Here we emulate the impacts of an extreme disturbance in a native grassland site. We measured plant community composition of twelve paired 50 × 50 cm plots (24 total) in Alberta, Canada. Each pair consisted of one undisturbed plot and one which had all plants terminated 2 years prior. We used species abundances and a local trait database to calculate community weighted means for maximum height, specific leaf area, specific root length, leaf nitrogen percent, and root nitrogen percent. To test the impacts of disturbance on community functional traits, we calculated functional diversity measures and compared them between disturbed and undisturbed communities. Results Within 2 years, species richness and evenness in disturbed communities had recovered and was equivalent to undisturbed communities. However, disturbed and undisturbed communities had distinct community compositions, resulting in lower functional divergence in disturbed plots. Further, disturbance was linked to increases in community-weighted mean trait values for resource-acquisitive traits, such as specific leaf area, and leaf and root nitrogen. Discussion Disturbance had lasting effects on the functional traits and diversity of communities, despite traditional biodiversity measures such as richness and evenness recovering within 2 years. The trait space of gap communities shifted compared to undisturbed communities such that gap communities were dominated by traits enhancing resource uptake and growth rates. Overall, these results show that short-term disturbance fundamentally changes the functional character of early-successional communities, even if they superficially appear recovered.
Smith et al. (2022) Disturbance has lasting effects on functional traits and diversity of grassland plant communities. PeerJ 10:e13179 https://doi.org/10.7717/peerj.13179
A longitudinal study of risk factors associated with white spot disease occurrence in marine shrimp farming in Rayong, Thailand
Background A longitudinal study was conducted to analyze farm characteristics, farm practices, and biosecurity measures that influenced the occurrence of white spot disease (WSD) in shrimp farming in Rayong, Thailand. Methods Data were collected using a structured interview schedule administered between October 2017 and September 2019. A generalized estimating equations (GEE) model was used to identify risk factors. From the 270 responses, 86 possible risk factors were analyzed using univariate and multivariate analysis. Results We found that 17 possible risk factors were statistically significant with an alpha level of 1% and associated with WSD status. In the final model, multivariate analysis found that two independent variables were statistically significant. First, the absence of inclement weather during ponding was a statistically significant factor associated with WSD occurrence and it prevented WSD occurrence as the odds ratio (OR) was <1 (OR = 0.196, P = 1.3 × 10−5). Second, the separation of ponds into three specific types (cultured, water treatment, and pond for water reservoir) was significantly associated with WSD occurrence. Likewise, the presence of this ponding system was a protective factor against WSD (OR = 0.0828, P = 0.001). Conclusions The results of this study offer a reference for farmers and relevant authorities when addressing WSD occurrence in shrimp farming. In addition, our results can help relevant authorities in controlling WSD in other endemic areas.
Yaemkasem et al. (2022) A longitudinal study of risk factors associated with white spot disease occurrence in marine shrimp farming in Rayong, Thailand. PeerJ 10:e13182 https://doi.org/10.7717/peerj.13182
Acute kidney injury-attributable mortality in critically ill patients with sepsis
Background To assess whether acute kidney injury (AKI) is independently associated with hospital mortality in ICU patients with sepsis, and estimate the excess AKI-related mortality attributable to AKI. Methods We analyzed adult patients from two distinct retrospective critically ill cohorts: (1) Medical Information Mart for Intensive Care IV (MIMIC IV; n = 15,610) cohort and (2) Wenzhou (n = 1,341) cohort. AKI was defined by Kidney Disease: Improving Global Outcomes (KDIGO) criteria. We applied multivariate logistic and linear regression models to assess the hospital and ICU mortality, hospital length-of-stay (LOS), and ICU LOS. The excess attributable mortality for AKI in ICU patients with sepsis was further evaluated. Results AKI occurred in 5,225 subjects in the MIMIC IV cohort (33.5%) and 494 in the Wenzhou cohort (36.8%). Each stage of AKI was an independent risk factor for hospital mortality in multivariate logistic regression after adjusting for baseline illness severity. The excess attributable mortality for AKI was 58.6% (95% CI [46.8%–70.3%]) in MIMIC IV and 44.6% (95% CI [12.7%–76.4%]) in Wenzhou. Additionally, AKI was independently associated with increased ICU mortality, hospital LOS, and ICU LOS. Conclusion Acute kidney injury is an independent risk factor for hospital and ICU mortality, as well as hospital and ICU LOS in critically ill patients with sepsis. Thus, AKI is associated with excess attributable mortality.
Wang et al. (2022) Acute kidney injury-attributable mortality in critically ill patients with sepsis. PeerJ 10:e13184 https://doi.org/10.7717/peerj.13184
Crop damage by vertebrates in Latin America: current knowledge and potential future management directions
Background Crop farming contributes to one of the most extensive land use activities in the world, and cropland areas continue to rise. Many vertebrate species feed on crops, which has caused an increase in human-wildlife conflicts in croplands. Crop-feeding damages the economy of local communities and causes retaliation against the responsible vertebrates in several forms, including lethal practices such as hunting and poisoning. Lethal control may cause the local extirpation of some species, affecting ecological processes and patterns. Therefore, it is necessary to find non-lethal alternatives that can protect both local economies and wildlife. Research has been conducted in Africa and Asia, focusing on elephants and primates, and the effectiveness of some non-lethal alternatives, such as chili-based repellents and beehives, is being investigated. However, there has been very little research on this topic in Central and South America. The goal of this review is to assess the current knowledge on crop damage by vertebrates in Central and South America and indicate future research directions. Survey methodology We reviewed the available scientific literature reporting crop damage by vertebrates in Central and South America, and the Caribbean, published between 1980 and 2020, through systematic searches on Web of Science, Scopus, and Google Scholar. We analyzed the temporal and geographical distributions of the studies, the crops and vertebrate species these studies considered, the crop protection techniques used, and their effectiveness. Results We retrieved only 113 studies on crop damage by vertebrates in Latin America, but there was an increasing trend in the number of studies published over time. Most of the studies were conducted in Brazil, Argentina, Mexico, and Costa Rica. Four orders of mammals (Rodentia, Carnivora, Artiodactyla, and Primates) and four orders of birds (Passeriformes, Columbiformes, Psittaciformes, and Anseriformes) were the most common groups of crop-feeding vertebrates. The most prominent crop was corn, which was featured in 49% of the studies. Other notable crops include rice, sorghum, and sugarcane. The most reported method for protecting crops was lethal control through hunting or poisoning. Non-lethal techniques were found to be less prevalent. Less than half of the studies that mentioned the use of protection techniques indicated their effectiveness, and only 10 studies evaluated it by performing scientific experiments and reporting their results. Conclusions Central and South America is still underrepresented in research on vertebrate crop-feeding. There is a need for experimentation-based robust research to find crop protection techniques that minimize harm to vertebrates while effectively reducing damage to crops. While this is being studied, habitat loss and fragmentation need to be halted to prevent the native vertebrates from turning to crops for food.
© 2022 Alejandro Cuesta Hermira and Michalski
Cuesta Hermira et al. (2022) Crop damage by vertebrates in Latin America: current knowledge and potential future management directions. PeerJ 10:e13185 https://doi.org/10.7717/peerj.13185
A worldwide comparison of long-distance running training in 2019 and 2020: associated effects of the COVID-19 pandemic
Objective The goal of the present study was to investigate possible effects of the COVID-19 pandemic on long-distance running training. Methods This is a retrospective study with a within-subject design. We analyzed 10,703,690 records of running training during 2019 and 2020, from 36,412 athletes from around the world. The records were obtained through web scraping of a large social network for athletes on the internet. A potential long-distance runner was defined as a user of the social network who had a record of running at least one of the six World Marathon Majors by 2019. Results In 2020, compared with 2019, in total there was a 3.6% decrease in the number of athletes running, a 7.5% decrease in the distance and 6.7% in the duration of running training. There were large variations in these variables throughout 2020, reaching 16% fewer athletes running weekly and 35% lower running distance (Cohen’s d = 0.34, p < 0.001) and 33% lower running duration (Cohen’s d = 0.30, p < 0.001) in September 2020. The beginning of the decrease in running training in the first quarter of 2020 coincides with the beginning of the adoption of measures to restrict the COVID-19 pandemic; but as of the second quarter of 2020, running training appears to have undergone variations unrelated to the preventive measures. Among the ten most represented countries in the dataset, running training in Brazil appears to have been the most affected by the COVID-19 pandemic and restriction measures. Conclusion The wide variations in long-distance running training throughout 2020 are likely related to the COVID-19 pandemic. As for the total volume, the observed decreases of up to 7.5% in the outcome variables related to running training in 2020 could also be attributed to the COVID-19 pandemic, but other factors such as injury, illness or lack of interest, may also have contributed to these decreases.
Afonseca et al. (2022) A worldwide comparison of long-distance running training in 2019 and 2020: associated effects of the COVID-19 pandemic. PeerJ 10:e13192 https://doi.org/10.7717/peerj.13192
Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study
Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieve the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend that users verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest.
Arizmendi Cárdenas et al. (2022) Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study. PeerJ 10:e12784 https://doi.org/10.7717/peerj.12784
First fossil-leaf floras from Brunei Darussalam show dipterocarp dominance in Borneo by the Pliocene
The Malay Archipelago is one of the most biodiverse regions on Earth, but it suffers high extinction risks due to severe anthropogenic pressures. Paleobotanical knowledge provides baselines for the conservation of living analogs and improved understanding of vegetation, biogeography, and paleoenvironments through time. The Malesian bioregion is well studied palynologically, but there have been very few investigations of Cenozoic paleobotany (plant macrofossils) in a century or more. We report the first paleobotanical survey of Brunei Darussalam, a sultanate on the north coast of Borneo that still preserves the majority of its extraordinarily diverse, old-growth tropical rainforests. We discovered abundant compression floras dominated by angiosperm leaves at two sites of probable Pliocene age: Berakas Beach, in the Liang Formation, and Kampong Lugu, in an undescribed stratigraphic unit. Both sites also yielded rich palynofloral assemblages from the macrofossil-bearing beds, indicating lowland fern-dominated swamp (Berakas Beach) and mangrove swamp (Kampong Lugu) depositional environments. Fern spores from at least nine families dominate both palynological assemblages, along with abundant fungal and freshwater algal remains, rare marine microplankton, at least four mangrove genera, and a diverse rainforest tree and liana contribution (at least 19 families) with scarce pollen of Dipterocarpaceae, today’s dominant regional life form. Compressed leaves and rare reproductive material represent influx to the depocenters from the adjacent coastal rainforests. Although only about 40% of specimens preserve informative details, we can distinguish 23 leaf and two reproductive morphotypes among the two sites. Dipterocarps are by far the most abundant group in both compression assemblages, providing rare, localized evidence for dipterocarp-dominated lowland rainforests in the Malay Archipelago before the Pleistocene. The dipterocarp fossils include winged Shorea fruits, at least two species of plicate Dipterocarpus leaves, and very common Dryobalanops leaves. We attribute additional leaf taxa to Rhamnaceae (Ziziphus), Melastomataceae, and Araceae (Rhaphidophora), all rare or new fossil records for the region. The dipterocarp leaf dominance contrasts sharply with the family’s <1% representation in the palynofloras from the same strata. This result directly demonstrates that dipterocarp pollen is prone to strong taphonomic filtering and underscores the importance of macrofossils for quantifying the timing of the dipterocarps’ rise to dominance in the region. Our work shows that complex coastal rainforests dominated by dipterocarps, adjacent to swamps and mangroves and otherwise similar to modern ecosystems, have existed in Borneo for at least 4–5 million years. Our findings add historical impetus for the conservation of these gravely imperiled and extremely biodiverse ecosystems.
Wilf et al. (2022) First fossil-leaf floras from Brunei Darussalam show dipterocarp dominance in Borneo by the Pliocene. PeerJ 10:e12949 https://doi.org/10.7717/peerj.12949
Genome-wide characterization and expression of the TLP gene family associated with Colletotrichum gloeosporioides inoculation in Fragaria × ananassa
Background Colletotrichum gloeosporioides, a soil-borne fungal pathogen, causes significant yield losses in many plants, including cultivated strawberry (Fragaria × ananassa, 2n = 8x = 56). Thaumatin-like proteins (TLPs) are a large and complex family of proteins that play a vital role in plant host defense and other physiological processes. Methods To enhance our understanding of the antifungal activity of F. × ananassa TLPs (FaTLP), we investigated the genome-wide identification of FaTLP gene families and their expression patterns in F. × ananassa plants upon pathogen infection. Moreover, we used RNA sequencing (RNA-seq) to detect the differences in the expression patterns of TLP genes between different resistant strawberry cultivars in response to C. gloeosporioides infection. Results In total, 76 TLP genes were identified from the octoploid cultivated strawberry genome with a mean length of 1,439 bp. They were distributed on 24 F. × ananassa chromosomes. The FaTLP family was then divided into ten groups (Group I–X) according to the comparative phylogenetic results. Group VIII contained the highest number of TLP family genes. qRT-PCR analysis results indicated that FaTLP40, FaTLP41, FaTLP43, FaTLP68, and FaTLP75 were upregulated following C. gloeosporioides infection in the resistant octoploid strawberry. Conclusions The data showed some differences in TLP gene expression patterns across different resistant strawberry cultivars, as well as faster TLP defense responses to pathogenic fungi in resistant cultivars. This study will aid in the characterization of TLP gene family members found in octoploid strawberries and their potential biological functions in plants’ defenses against pathogenic fungi.
Zhang et al. (2022) Genome-wide characterization and expression of the TLP gene family associated with Colletotrichum gloeosporioides inoculation in Fragaria × ananassa. PeerJ 10:e12979 https://doi.org/10.7717/peerj.12979
A prognostic risk model based on DNA methylation levels of genes and lncRNAs in lung squamous cell carcinoma
Background Recurrence is a risk factor for the prognosis of lung squamous carcinoma (LUSC). DNA methylation levels of RNAs are also associated with LUSC prognosis. This study aimed to construct a prognostic model with high performance in predicting LUSC prognosis using the methylation levels of lncRNAs and genes. Methods The differentially expressed RNAs (DERs) and differentially methylated RNAs (DMRs) between the recurrent and non-recurrent LUSC tissues in The Cancer Genome Atlas (TCGA; training dataset) were identified. Weighted correlation network analysis was performed to identify co-methylation networks. Differentially methylated genes and lncRNAs with opposite expression-methylation levels were used for the screening of prognosis-associated RNAs. The prognostic model was constructed and its performance was validated in the GSE39279 dataset. Results A total of 664 DERs and 981 DMRs (including 972 genes) in recurrent LUSC tissues were identified. Three co-methylation modules, including 226 differentially methylated genes, were significantly associated with LUSC. Among prognosis-associated RNAs, 18 DERs/DMRs with opposite methylation-expression levels were included in the methylation prognostic risk model. LUSC patients with high risk scores had a poor prognosis compared with patients who had low risk scores (TCGA: HR = 3.856, 95% CI [2.297–6.471]; GSE39279: HR = 3.040, 95% CI [1.435–6.437]). This model had a high accuracy in predicting the prognosis (AUC = 0.903 and 0.800, respectively), equivalent to the nomogram model inclusive of clinical variables. Conclusions Referring to the methylation levels of the 16-RNAs might help to predict the survival outcomes in LUSC.
Wang et al. (2022) A prognostic risk model based on DNA methylation levels of genes and lncRNAs in lung squamous cell carcinoma. PeerJ 10:e13057 https://doi.org/10.7717/peerj.13057
Development of a Japanese version of the Psychological Ownership Scale
The present study addresses the need for a valid instrument for measuring dimensions of psychological ownership, including that of owned and non-owned objects, for use in the language and culture of Japan. Although the theory of psychological ownership has expanded self-extension theory, the most widely used scale of psychological ownership does not measure the extent to which one feels that it (the owned object) is a part of them. Thus, the present study aimed to develop a Japanese version of the Psychological Ownership Scale (POS-J) and examine its reliability and validity. Study 1 measured the POS-J of an owned object, finding the POS-J to have a two-factor structure (possession-self link and feeling of ownership) and its internal consistency and reliability to be adequate. Moreover, POS-J scores were positively correlated with perceived control and self-extension tendency, but not monetary value, indicating that conceptual validity was generally supported. To confirm whether the POS-J could be used for a non-owned object, Study 2 rephrased the expressions of item descriptions and examined the effect of imagining touching a non-owned object on the POS-J scores, showing that doing so increased the POS-J scores for the object. Our findings suggest that the POS-J is a reliable and valid measure of the psychological ownership of owned and non-owned objects for use in Japan.
Iseki et al. (2022) Development of a Japanese version of the Psychological Ownership Scale. PeerJ 10:e13063 https://doi.org/10.7717/peerj.13063