title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=519 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Optimal sample type and number vary in small shallow lakes when targeting non-native fish environmental DNA link: https://peerj.com/articles/15210 last-modified: 2023-05-02 description: Non-native fish have been shown to have deleterious impacts on freshwater ecosystems in New Zealand. Early detection is critical for their effective management. Traditional capture-based techniques may not detect newly introduced fish, especially if they are present in low abundance. Molecular techniques that target environmental DNA (eDNA) have been shown, in many instances, to be more sensitive, cost-effective and require lower sampling effort. However, appropriate sampling strategies are needed to ensure robust and interpretable data are obtained. In this study we used droplet digital PCR assays to investigate the presence of two non-native fish in New Zealand, the European perch (Perca fluviatilis) and rudd (Scardinius erythrophthalmus) in three small lakes. Samples were collected from water and surface sediment at near-shore and mid-lake sites. Probabilistic modelling was used to assess the occupancy of fish eDNA and develop guidance on sampling strategies. Based on the detection probability measures from the present study, at least six sites and five replicates per site are needed to reliably detect fish eDNA in sediment samples, and twelve sites with eight replicates per site for water samples. The results highlight the potential of developing monitoring and surveillance programs adapted to lakes, that include the use of assays targeting eDNA. This study focused on small shallow lakes, and it is likely that these recommendations may vary in larger, deeper, and more geomorphologically complex lakes, and this requires further research. creator: Maïlys H.V. Picard creator: Anastasija Zaiko creator: Annabel M. Tidy creator: David J. Kelly creator: Georgia Thomson-Laing creator: Shaun P. Wilkinson creator: Xavier Pochon creator: Marcus J. Vandergoes creator: Ian Hawes creator: Susanna A. Wood uri: https://doi.org/10.7717/peerj.15210 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Picard et al. title: Somatic mutation profiling, tumor-infiltrating leukocytes, tertiary lymphoid structures and PD-L1 protein expression in HER2-amplified colorectal cancer link: https://peerj.com/articles/15261 last-modified: 2023-05-02 description: The status of human epidermal growth factor receptor 2 (HER2) for the prognosis in colorectal cancer (CRC) is controversial, and the characteristics of the somatic mutation spectrum, tumor-infiltrating leukocytes, tertiary lymphoid structures and PD-L1 protein are unknown in HER2-amplified colorectal cancer (HACC). In order to explore these characteristics along with their correlation with clinicopathological factors and prognosis in HACC. Samples of 812 CRC patients was collected. After immunohistochemistry (IHC), 59 of 812 were found to be HER2-positive, then 26 of 59 samples were further determined to be HER2 amplification by fluorescence in situ hybridization (FISH). Somatic mutation profiling of HACC was analysed using whole exome sequencing (WES). Multiplex fluorescence immunohistochemistry (mIHC) was used for tumor-infiltrating leukocytes and tertiary lymphoid structures (TLSs), while PD-L1 protein was detected by IHC. Our results indicate that the detection rates of HER2 positivity by IHC and FISH were 7.3% and 3.2% respectively, and HER2 amplification is correlated with distant tumour metastasis. The somatic mutation profiling revealed no differences between HACC and HER2-negative CRC. However, TP 53 strongly correlated with poor prognosis in HACC. Furthermore, tumor-infiltrating T cells and TLSs in the tumor immune microenvironment, as well as PD-L1 expression, were higher in HACC than in HER2-negative controls. However, none of them were associated with the prognosis of HACC. In all, HER2 amplification is correlated with distant metastasis and TP53 gene mutation may be a potential protective mechanism of HACC. creator: Xiao-Ting Liu creator: Zhi-Yong Kou creator: Hushan Zhang creator: Jian Dong creator: Jian-Hua Zhang creator: You-Jun Peng creator: Shu Min Ma creator: Lei Liang creator: Xuan-Yu Meng creator: Yuan Zhou creator: Jun Yang uri: https://doi.org/10.7717/peerj.15261 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Can salivary lactate be used as an anaerobic biomarker? link: https://peerj.com/articles/15274 last-modified: 2023-05-02 description: BackgroundSalivary lactate has been suggested as a non-invasive anaerobic biomarker in sports medicine for decades, yet has not been widely applied until now. This study aimed to explore possible issues related to its application and suggest directions for future method improvement.MethodsA liquid chromatography–mass spectrometry (LC-MS) method for the determination of salivary lactate was developed, validated and applied on saliva samples collected from a group of professional sprinters (n = 20). The samples were collected via chewing a cotton ball for one minute and centrifuging it afterwards. The evaluation included variation with mouth rinse times, consistency at different sampling times, change after treadmill or cycle ergometer trainings, and association with blood lactate. Sample sizes were calculated prior to the study. One-way analysis of variance (ANOVA), intra-class correlation coefficients (ICC) and relative standard deviation (RSD) were used to evaluate data variances. Pearson correlation was applied to show correlation between salivary and blood lactate. Effect sizes and power were calculated following ANOVA and correlation analyses.ResultsThe RSD of the LC-MS method was 19.70%. Salivary lactate concentration was affected by mouth rinse times before sampling (ANOVA p = 0.025, η2 = 0.40, 1 − β = 0.99, ICC = 0.23, mean RSD of four sampling = 55.30%), and stabilized after mouth rinsing for three times. The concentrations at resting state across three weeks were consistent at group level (ANOVA p = 0.57, η2 = 0.03, 1 − β = 0.20), but varied greatly individually (ICC = 0.22, mean RSD = 56.16%). Salivary lactate level significantly increased after treadmill and cycle ergometer trainings (ANOVA p = 0.0002, η2 = 0.46, 1 − β = 0.9999 and ANOVA p = 0.0019, η2 = 0.40, 1 − β = 0.9993, respectively), and displayed positive correlation with blood lactate concentration (r = 0.61, p = 0.0004, 1 − β = 0.9596). Significant difference between male and female participants was observed in none of the tests conducted in this study.DiscussionSalivary lactate was found to be a potential anaerobic biomarker. However, reproducible methods for sample collection and analysis, as well as more knowledge on the secretion mechanism and pattern of salivary lactate are required to make it a practical anaerobic biomarker. creator: Pingping Yan creator: Chunli Qin creator: Zengyin Yan creator: Chang Chen creator: Fengjing Zhang uri: https://doi.org/10.7717/peerj.15274 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yan et al. title: Evidence for a novel cranial thermoregulatory pathway in thalattosuchian crocodylomorphs link: https://peerj.com/articles/15353 last-modified: 2023-05-02 description: Thalattosuchian crocodylomorphs were a diverse clade that lived from the Early Jurassic to the Early Cretaceous. The subclade Metriorhynchoidea underwent a remarkable transition, evolving from semi-aquatic ambush predators into fully aquatic forms living in the open oceans. Thalattosuchians share a peculiar palatal morphology with semi-aquatic and aquatic fossil cetaceans: paired anteroposteriorly aligned grooves along the palatal surface of the bony secondary palate. In extant cetaceans, these grooves are continuous with the greater palatine artery foramina, arteries that supply their oral thermoregulatory structures. Herein, we investigate the origins of thalattosuchian palatal grooves by examining CT scans of six thalattosuchian species (one teleosauroid, two early-diverging metriorhynchoids and three metriorhynchids), and CT scans of eleven extant crocodylian species. All thalattosuchians had paired osseous canals, enclosed by the palatines, that connect the nasal cavity to the oral cavity. These osseous canals open into the oral cavity via foramina at the posterior terminus of the palatal grooves. Extant crocodylians lack both the external grooves and the internal canals. We posit that in thalattosuchians these novel palatal canals transmitted hypertrophied medial nasal vessels (artery and vein), creating a novel heat exchange pathway connecting the palatal vascular plexus to the endocranial region. Given the general hypertrophy of thalattosuchian cephalic vasculature, and their increased blood flow and volume, thalattosuchians would have required a more extensive suite of thermoregulatory pathways to maintain stable temperatures for their neurosensory tissues. creator: Mark T. Young creator: Charlotte I. W. Bowman creator: Arthur Erb creator: Julia A. Schwab creator: Lawrence M. Witmer creator: Yanina Herrera creator: Stephen L. Brusatte uri: https://doi.org/10.7717/peerj.15353 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Young et al. title: Could an event of extreme drought (2019-2020) affect the feeding ecology of Bubo magellanicus (Gmelin 1788) (Strigiformes: Strigidae) in a Mediterranean region of Chile? link: https://peerj.com/articles/15020 last-modified: 2023-05-01 description: Global warming generates changes in environmental conditions, affecting the spatial-temporal dynamics of precipitation and temperature. Droughts, events of low rainfall, are becoming more frequent and severe. In central Chile, from 2010 to date, an unprecedented drought event has developed, affecting the ecosystem and creating pressure on the dynamics of food webs. The present study analysed the trophic ecology of Bubo magellanicus, a top predator in the Mediterranean region of Chile, between 2019 and 2020 a period with a rainfall deficit of 72.6%. Our results established a diet mainly described by invertebrates (97.75%), in particular by the Gramnostola rosea spider (87.86%), and a low contribution of small vertebrates (2.24%). The trophic niche breadth (B = 0.37) and the standardised Levin’s index (BSTA = 0.01) are the lowest recorded in the species B. magellanicus. A comparative analysis of trophic ecology with other studies developed in the same region established significant differences in the composition of the diet (frequency of occurrence of prey unit). This work provides evidence that droughts and other extreme environmental scenarios restructure the food webs of an ecosystem, with direct consequences on the trophic niche of the species, specifically top predators. creator: Sam Catchpole Ahumada creator: Luis Carrera Suárez creator: Reinaldo Rivera uri: https://doi.org/10.7717/peerj.15020 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Catchpole Ahumada et al. title: Regeneration dynamics of Portulacaria afra in restored succulent thicket of South Africa link: https://peerj.com/articles/15081 last-modified: 2023-05-01 description: IntroductionOver-grazing by livestock has resulted in the widespread degradation of South Africa’s succulent thicket ecosystems. This is characterised by a significant reduction in the cover of the dominant succulent shrub, Portulacaria afra. Because this species is unable to regenerate naturally in degraded habitat, active reintroduction is required to restore ecosystem function. However, reintroduction success is relatively low, and the recruitment barriers for this species are poorly understood.MethodsBy conducting pairwise plot surveys in actively restored and adjacent degraded succulent thicket habitats, the extent of P. afra seedling abundance in these contrasting ecosystem conditions is quantified.ResultsSeedling abundance was significantly greater in restored ecosystems (W = 23, p = 0.03225). Additionally, seedlings found in restored habitats were strongly associated with open habitat, whereas seedlings in degraded ecosystems were more restricted to nurse sites (X2 = 122.84, df = 2, p-value < 2.2e–16). A weak (R2 = 0,237), but significant (p = 0, 0295) correlation between P. afra cover and seedling abundance was recorded.ConclusionActive restoration of succulent thicket habitat through P. afra reintroduction appears to overcome recruitment barriers. This may suggest that, despite the poor survival of introduced individuals, natural recruitment could contribute to the regeneration of restored succulent thicket ecosystems. creator: Nicholas C. Galuszynski uri: https://doi.org/10.7717/peerj.15081 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Galuszynski title: A review on post-COVID-19 impacts and opportunities of agri-food supply chain in Malaysia link: https://peerj.com/articles/15228 last-modified: 2023-05-01 description: BackgroundMalaysia is strongly supported by the agriculture sector as the backbone to drive the economy. However, COVID-19 has significantly affected agriculture across the production, supply, and marketing chains. It also disturbs the balance of food supply and demand in Malaysia. COVID-19 was an unexpected pandemic that resulted in shock and panic and caused a huge global impact. However, the impacts of this pandemic on the agriculture sector in Malaysia, particularly in the production and supply chains, are still unclear and scarce. This review offers insights into the challenges, particularly in sustaining agri-food production and supply chains. It also highlights the opportunity and relevant measures towards sustainability in agriculture to avoid agri-food disasters in the future.MethodsThis study was carried out through a desk review of the secondary source of information covering the impact of COVID-19 in Malaysia particularly in the agri-food aspect, and a wide range of strategies and initiatives as the effective measures to overcome the crisis of this pandemic. Online desk research of the government published data and customer desk research were utilized to complete this study. Search engines such as Google Scholar and the statistical data from the official websites including the Department of Statistics Malaysia (DOSM) and the Food and Fertilizer Technology Center for the Asian and Pacific Region (FFTC-AP), were utilized. Keywords such as impact of COVID-19, pandemic, and agri-food supply chain were used to conduct the searches. The articles identified to be related to the study’s objective were then downloaded and included in the study. Descriptive methods were used as the primary analysis technique following the descriptive analysis and visual data analysis in performing the sources obtained.ResultsThis devastating impact damages the lives by causing 4.3 million confirmed infections and more than 290,000 deaths. This disease presents an unprecedented challenge to the public health. The lockdown restriction under the movement control order (MCO), for more than of the world’s population in the year 2020 to control the virus from spreading, has disrupted most of the economic sectors. The agriculture industry was seen as one of the essential industries and allowed to operate under strict standard operating procedures (SOP). Working under strict regulations came with a huge price paid for almost all industries.ConclusionThis pandemic has affected the national agri-food availability and accessibility in Malaysia. This outbreak created a reflection of opportunity for sharing a more flexible approaches in handling emergencies on agricultural food production and supply chains. Therefore, the government should be ready with the roadmap and enforce the measures to control the pandemic without disrupting the agri-food supply chain in the near future. creator: Say Peng Tan creator: Lee Chuen Ng creator: Novel Lyndon creator: Zaki Aman creator: Parthiban Kannan creator: Khairuman Hashim creator: Han Meng Teo creator: Muhamad Syazlie Che Ibrahim uri: https://doi.org/10.7717/peerj.15228 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Tan et al. title: Clinical characteristics and prognostic nomogram analysis of patients with dual primary cancers with first gastric cancer: a retrospective study in China link: https://peerj.com/articles/15278 last-modified: 2023-05-01 description: BackgroundWith the improvement in diagnosis and treatment of gastric cancer (GC), the survival time of patients has been gradually prolonged. However, these survivors are at increased risk for other diseases, including second primary cancers (SPCs). Currently, there remain few central studies concerning double primary cancers with first gastric cancer (DPCFGC). Thus, this study aimed to investigate these patients’ clinical characteristics and perform prognostic nomogram analysis.MethodsThe clinical data of 78 DPCFGC patients were retrospectively collected and analyzed through the hospital electronic medical record system. Univariate and multivariate Cox regression analyses were performed to screen independent risk factors, based on which the prognostic nomogram was further constructed and validated using the R software package. Finally, Kaplan–Meier curves were plotted to explore the association of overall survival (OS) with prognostic factors and the model.ResultsThe prevalence of DPCFGC was 0.86%, of which the proportions of synchronous and metachronous patients were 47.44% and 52.56% , respectively; 65.38% (51/78) and 34.62% (27/78) of patients were male and female, respectively. The median age at GC and SPC diagnosis was 63 and 65 years, respectively, and 52.57% of GC patients developed SPCs within 1 year. The top three SPCs were in the esophagus (19.24%), colon (16.67%), and rectum (15.39%). The most common features of GC and SPCs were adenocarcinoma, poorly and moderately differentiated histology, and pathological stages I and II. The radical resection rate of GC was significantly lower in synchronous patients than in metachronous patients (45.94% vs. 100.00%, P < 0.001), but no significant difference was noted in the radical resection rate of SPCs (35.13% vs. 46.34%, P = 0.315). The OS of DPCFGC patients was 31.03 ±  4.14 months. The pathological stage of GC and SPCs, whether to operate for GC, and diagnostic interval were independent risk factors. The predictive efficacy of the prognostic nomogram for 1-, 2- and 3-year OS in DPCFGC patients was 0.922, 0.935 and 0.796 , respectively, with good consistency and clinical applicability. The OS was significantly lower in the high-risk group than in the low-risk group.ConclusionsDuring follow-up, clinicians should attach great importance to the screening of GC survivors, especially at early stage in older men within 1 year after diagnosis, and be alert to the possibility of occurrent digestive system malignancies. The nomogram constructed in this study can provide a theoretical basis for the early clinical development of individualized treatment plans. creator: Bing Wang creator: Lu Liu uri: https://doi.org/10.7717/peerj.15278 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang and Liu title: Loot box consumption by adolescents pre- and post- pandemic lockdown link: https://peerj.com/articles/15287 last-modified: 2023-05-01 description: Loot boxes are virtual items that can be redeemed to receive randomly selected other virtual items, and have been criticized for being similar to gambling. The presence of loot boxes in video games has dramatically increased since 2010, with little evidence available for the current prevalence rate of loot box purchasing in the general population, particularly during and following the COVID-19 pandemic lockdowns. This study uses data from representative samples of American youth to estimate prevalence rates for video game play and loot box consumption before the pandemic (2019) and after the pandemic lockdowns (2022) to examine whether the pandemic has affected loot box usage in the general population and among gamers. The results suggest that youth loot box consumption has increased, rising from 24.9% in 2019 to 31.6% in 2022 among 8th grade (age 13–14) youth. The increase over this time period was larger for girls, though boys are still more likely to purchase loot boxes overall. creator: Whitney DeCamp creator: Kevin Daly uri: https://doi.org/10.7717/peerj.15287 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 DeCamp and Daly title: Indoor air quality in a training centre used for sports practice link: https://peerj.com/articles/15298 last-modified: 2023-05-01 description: BackgroundOne of the measures for controlling the coronavirus disease 2019 (COVID-19) pandemic was the mass closure of gyms. This measure leads us to determine the differences between indoor and outdoor air quality. That is why the objective of this study was to analyse the indoor air quality of a sports centre catering to small groups and rehabilitation.MethodsThe study was conducted in a single training centre, where 26 measurements were taken in two spaces (indoors and outdoors). The air quality index, temperature, relative humidity, total volatile compounds, carbon monoxide, ozone, formaldehyde, carbon dioxide, and particulate matter were measured indoors and outdoors using the same protocol and equipment. These measurements were taken twice, once in the morning and once in the afternoon, with all measurements made at the same time, 10 am and 6 pm, respectively. Additionally, four determinations of each variable were collected during each shift, and the number of people who had trained in the room and the number of trainers were counted.ResultsIn the different variables analysed, the results show that CO2 and RH levels are higher indoors than outdoors in both measurement shifts. Temperatures are higher outside than inside and, in the evening, than in the morning. TVOC, AQI and PM show less variation, although they are higher outdoors in the morning. CO is highest indoors. HCHO levels are almost negligible and do not vary significantly, except for a slight increase in the afternoon outside. Ozone levels are not significant. All the variables showed practically perfect reliability in all the measurements, except for ozone measured outside in the morning. On the other hand, the variables exhibit variations between indoors and outdoors during the morning and afternoon, except for the three types of PM. Also, the data show that all the main variables measured inside the sports training centre are similar between morning and afternoon. However, outside, temperature, relative humidity and HCHO levels show significant differences between morning and afternoon while no differences are observed for the other variables.ConclusionThe indoor air quality of the training centre assessed was good and met current regulations; some of its components even exhibited better levels than fresh air. This article is the first to measure indoor air quality in a sports training centre catering to rehabilitation and small groups. creator: Victoria Mazoteras-Pardo creator: Marta Elena Losa-Iglesias creator: Israel Casado-Hernández creator: César Calvo-Lobo creator: Ángel Morales-Ponce creator: Alfredo Medrano-Soriano creator: Sergio Coco-Villanueva creator: Ricardo Becerro-de-Bengoa-Vallejo uri: https://doi.org/10.7717/peerj.15298 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mazoteras-Pardo et al.