Type of organic fertilizer rather than organic amendment per se increases abundance of soil biota
Addition of organic amendments is a commonly used practice to offset potential loss of soil organic matter from agricultural soils. The aim of the present study was to examine how long-term addition of organic matter affects the abundance of different soil biota across trophic levels and the role that the quality of the organic amendments plays. Here we used a 17-year-old fertilization experiment to investigate soil biota responses to four different organic fertilizers, compared with two mineral nitrogen fertilizers and no fertilization, where the organic fertilizers had similar carbon content but varied in their carbon to nitrogen ratios. We collected soil samples and measured a wide range of organisms belonging to different functional groups and trophic levels of the soil food web. Long-term addition of organic and mineral fertilizers had beneficial effects on the abundances of most soil organisms compared with unfertilized soil, but the responses differed between soil biota. The organic fertilizers generally enhanced bacteria and earthworms. Fungi and nematodes responded positively to certain mineral and organic fertilizers, indicating that multiple factors influenced by the fertilization may affect these heterogeneous groups. Springtails and mites were less affected by fertilization than the other groups, as they were present at relatively high abundances even in the unfertilized treatment. However, soil pH had a great influence on springtail abundance. In summary, the specific fertilizer was more important in determining the numerical and compositional responses of soil biota than whether it was mineral or organic. Overall, biennial organic amendments emerge as insufficient, by themselves, to promote soil organisms in the long run, and would need to be added annually or combined with other practices affecting soil quality, such as no or reduced tillage and other crop rotations, to have a beneficial effect.
Viketoft et al. (2021) Type of organic fertilizer rather than organic amendment per se increases abundance of soil biota. PeerJ 9:e11204 https://doi.org/10.7717/peerj.11204
The regulation of immune checkpoints by the hypoxic tumor microenvironment
The tumor microenvironment (TME) influences the occurrence and progression of tumors, and hypoxia is an important characteristic of the TME. The expression of programmed death 1 (PD1)/programmed death-ligand 1 (PDL1), cytotoxic T-lymphocyte-associated antigen 4 (CTLA4), and other immune checkpoints in hypoxic malignant tumors is often significantly increased, and is associated with poor prognosis. The application of immune checkpoint inhibitors (ICIs) for treating lung cancer, urothelial carcinoma, and gynecological tumors has achieved encouraging efficacy; however, the rate of efficacy of ICI single-drug treatment is only about 20%. In the present review, we discuss the possible mechanisms by which the hypoxic TME regulates immune checkpoints. By activating hypoxia-inducible factor-1α (HIF-1α), regulating the adenosine (Ado)-A2aR pathway, regulating the glycolytic pathway, and driving epithelial-mesenchymal transition (EMT) and other biological pathways, hypoxia regulates the expression levels of CTLA4, PD1, PDL1, CD47, lymphocyte activation gene 3 (LAG3), T-cell immunoglobulin and mucin domain 3 (TIM3), and other immune checkpoints, which interfere with the immune effector cell anti-tumor response and provide convenient conditions for tumors to escape immune surveillance. The combination of HIF-1α inhibitors, Ado-inhibiting tumor immune microenvironment regulatory drugs, and other drugs with ICIs has good efficacy in both preclinical studies and phase I-II clinical studies. Exploring the effects of TME hypoxia on the expression of immune checkpoints and the function of infiltrating immune cells has greatly clarified the relationship between the hypoxic TME and immune escape, which is of great significance for the development of new drugs and the search for predictive markers of the efficacy of immunotherapy for treating malignant tumors. In the future, combination therapy with hypoxia pathway inhibitors and ICIs may be an effective anti-tumor treatment strategy.
Hu et al. (2021) The regulation of immune checkpoints by the hypoxic tumor microenvironment. PeerJ 9:e11306 https://doi.org/10.7717/peerj.11306
DNA methylome and transcriptome analysis established a model of four differentially methylated positions (DMPs) as a diagnostic marker in esophageal adenocarcinoma early detection
Background Esophageal carcinogenesis involves in alterations of DNA methylation and gene transcription. This study profiled genomic DNA methylome vs. gene expression using transcriptome data on esophageal adenocarcinoma (EAC) tissues from the online databases in order to identify methylation biomarkers in EAC early diagnosis. Materials and Methods The DNA methylome and transcriptome data were downloaded from the UCSC Xena, Gene Expression Omnibus (GEO), and The Cancer Genome Atlas (TCGA) databases and then bioinformatically analyzed for the differentially methylated positions (DMPs) vs. gene expression between EAC and normal tissues. The highly methylated DMPs vs. reduced gene expression in EAC were selected and then stratified with those of the corresponding normal blood samples and other common human cancers to construct an EAC-specific diagnostic model. The usefulness of this model was further verified in other three GEO datasets of EAC tissues. Result A total of 841 DMPs were associated with expression of 320 genes, some of which were aberrantly methylated in EAC tissues. Further analysis showed that four (cg07589773, cg10474350, cg13011388 and cg15208375 mapped to gene IKZF1, HOXA7, EFS and TSHZ3, respectively) of these 841 DMPs could form and establish a diagnostic model after stratified them with the corresponding normal blood samples and other common human cancers. The data were further validated in other three GEO datasets on EAC tissues in early EAC diagnosis. Conclusion This study revealed a diagnostic model of four genes methylation to diagnose EAC early. Further study will confirm the usefulness of this model in a prospective EAC cases.
Peng et al. (2021) DNA methylome and transcriptome analysis established a model of four differentially methylated positions (DMPs) as a diagnostic marker in esophageal adenocarcinoma early detection. PeerJ 9:e11355 https://doi.org/10.7717/peerj.11355
Transgenerational effects on development following microplastic exposure in Drosophila melanogaster
Background Plastic pollution affects all ecosystems, and detrimental effects to animals have been reported in a growing number of studies. However, there is a paucity of evidence for effects on terrestrial animals in comparison to those in the marine realm. Methods We used the fly Drosophila melanogaster to study the effects that exposure to plastics may have on life history traits and immune response. We reared flies in four conditions: In media containing 1% virgin polyethylene, with no chemical additives; in media supplemented with 1% or 4% polyvinyl chloride, known to have a high content of added chemicals; and control flies in non-supplemented media. Plastic particle size ranged from 23–500 µm. We studied fly survival to viral infection, the length of the larval and pupal stage, sex ratios, fertility and the size of the resultant adult flies. We then performed crossings of F1 flies in non-supplemented media and looked at the life history traits of the F2. Results Flies treated with plastics in the food media showed changes in fertility and sex ratio, but showed no differences in developmental times, adult size or the capacity to fight infections in comparison with controls. However, the offspring of treated flies reared in non-supplemented food had shorter life cycles, and those coming from both polyvinyl chloride treatments were smaller than those offspring of controls.
Jimenez-Guri et al. (2021) Transgenerational effects on development following microplastic exposure in Drosophila melanogaster. PeerJ 9:e11369 https://doi.org/10.7717/peerj.11369
The impact of COVID-19 pandemic on nitrogen dioxide levels in Nigeria
The Coronavirus disease (COVID-19) has been transmitted worldwide over a very short time after it originated in China in December 2019. In an attempt to control its spread and reduce its health impacts, several countries including those in the African continent imposed restrictive measures that was termed “lockdown”. The outcomes of this lockdown have been reported to be beneficial to air quality worldwide. The main objective of this study is to assess the impact of lockdown due to COVID-19 on nitrogen dioxide (NO2) levels over six major cities in Nigeria. Maps extracted from satellite (Sentinel-5P) were used to indicate the significant reduction in the level of NO2 in the selected cities in Nigeria during two time-intervals, pre-lockdown (December, 2019) and during lockdown (April, 2020). The results show a significant reduction in NO2 levels during the lockdown period compared with its levels during the pre-lockdown period in 2019. The reduction in NO2 concentration levels during lockdown is likely due to less traffic, social distancing and restrictions on business and human activities. There could be an element of uncertainty in the results due to seasonality, as the comparison is done with a different season. However, the magnitude of change due to lockdown is probably much higher than the seasonal variability. Although COVID-19 has negatively impacted the health and economic status of all regions worldwide, it has benefited some aspects of air quality in most countries including Nigeria. This indicates that anthropogenic activities may be managed to reduce air pollution and positively impact the health of human beings.
Olusola et al. (2021) The impact of COVID-19 pandemic on nitrogen dioxide levels in Nigeria. PeerJ 9:e11387 https://doi.org/10.7717/peerj.11387
Effects of education methods on self-efficacy of smoking cessation counseling among medical students
Background Medical students need to receive training in providing smoking cessation counseling to provide effective smoking cessation interventions to smokers when they become doctors. This study examined the smoking cessation education curricula and factors affecting counseling self-efficacy (CSE) in smoking cessation treatment among medical students. Methods In a multicenter cross-sectional study, we obtained demographic information, personal history of tobacco use and intention to quit smoking, exposure to secondhand smoke in the school premises during the past week, the experience of learning about tobacco in each medical school, tobacco-related medical knowledge, and self-efficacy in smoking cessation counseling on medical students of four Korean medical schools. Results Among 1,416 medical students eligible, 313 (22.1%) students completed a self-administered questionnaire. Only 20.3% of the students reported positive CSE on smoking cessation. The factors affecting positive CSE were scores of ≥ 60 on tobacco-related medical knowledge, smoking experience, and blended learning (p = 0.014, 0.005, and 0.015, respectively). Conclusion This study shows that high scores in tobacco-related medical knowledge and blended learning are correlated with positive CSE for smoking cessation counseling.
Cho et al. (2021) Effects of education methods on self-efficacy of smoking cessation counseling among medical students. PeerJ 9:e11408 https://doi.org/10.7717/peerj.11408
Competing endogenous RNA network identifies mRNA biomarkers for overall survival of lung adenocarcinoma: two novel on-line precision medicine predictive tools
Background Individual mortality risk predicted curve at the individual level can provide valuable information for directing individual treatment decision. The present study attempted to explore potential post-transcriptional biological regulatory mechanism related with overall survival of lung adenocarcinoma (LUAD) patients through competitive endogenous RNA (ceRNA) network and develop two precision medicine predictive tools for predicting the individual mortality risk curves for overall survival of LUAD patients. Methods Multivariable Cox regression analyses were performed to explore the potential prognostic indicators, which were used to construct a prognostic model for overall survival of LUAD patients. Time-dependent receiver operating characteristic (ROC) curves were used to assess the predictive performance of prognostic model. Results There were 494 LUAD patients in model cohort and 233 LUAD patients in validation cohort. Differentially expressed mRNAs, miRNAs, and lncRNAs were identified between LUAD tissues and normal tissues. A ceRNA regulatory network was constructed on previous differentially expressed mRNAs, miRNAs, and lncRNAs. Fourteen mRNA biomarkers were identified as independent risk factors by multivariate Cox regression and used to develop a prognostic model for overall survival of LUAD patients. The C-indexes of prognostic model in model group were 0.786 (95% CI [0.744–0.828]), 0.736 (95% CI [0.694–0.778]) and 0.766 (95% CI [0.724–0.808]) for one year, two year and three year overall survival respectively. Two precision medicine predicted tools were developed for predicting individual mortality risk curves for LUAD patients. Conclusion The current study explored potential post-transcriptional biological regulatory mechanism and prognostic biomarkers for overall survival of LUAD patients. Two on-line precision medicine predictive tools were helpful to predict the individual mortality risk predicted curves for overall survival of LUAD patients. Smart Cancer Survival Predictive System could be used at https://zhangzhiqiao2.shinyapps.io/Smart_cancer_predictive_system_9_LUAD_E1002/.
Lin et al. (2021) Competing endogenous RNA network identifies mRNA biomarkers for overall survival of lung adenocarcinoma: two novel on-line precision medicine predictive tools. PeerJ 9:e11412 https://doi.org/10.7717/peerj.11412
Cranial anatomy of Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 (Reptilia: Ichthyosauria) from the Middle Triassic Besano Formation of Monte San Giorgio, Italy/Switzerland: taxonomic and palaeobiological implications
Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 was described on the basis of a single fossil excavated near Besano (Italy) nearly three decades ago. Here, we re-examine its cranial osteology and assign five additional specimens to B. leptorhynchus, four of which were so far undescribed. All of the referred specimens were collected from the Middle Triassic outcrops of the Monte San Giorgio area (Italy/Switzerland) and are housed in various museum collections in Europe. The revised diagnosis of the taxon includes the following combination of cranial characters: extreme longirostry; an elongate frontal not participating in the supratemporal fenestra; a prominent ‘triangular process’ of the quadrate; a caudoventral exposure of the postorbital on the skull roof; a prominent coronoid (preglenoid) process of the surangular; tiny conical teeth with coarsely-striated crown surfaces and deeply-grooved roots; mesial maxillary teeth set in sockets; distal maxillary teeth set in a short groove. All these characters are shared with the holotype of Mikadocephalus gracilirostris Maisch & Matzke, 1997, which we consider as a junior synonym of B. leptorhynchus. An updated phylogenetic analysis, which includes revised scores for B. leptorhynchus and several other shastasaurids, recovers B. leptorhynchus as a basal merriamosaurian, but it is unclear if Shastasauridae form a clade, or represent a paraphyletic group. The inferred body length of the examined specimens ranges from 1 m to about 8 m. The extreme longirostry suggests that B. leptorhynchus primarily fed on small and elusive prey, feeding lower in the food web than an apex predator: a novel ecological specialisation never reported before the Anisian in a large diapsid. This specialization might have triggered an increase of body size and helped to maintain low competition among the diverse ichthyosaur fauna of the Besano Formation.
Bindellini et al. (2021) Cranial anatomy of Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 (Reptilia: Ichthyosauria) from the Middle Triassic Besano Formation of Monte San Giorgio, Italy/Switzerland: taxonomic and palaeobiological implications. PeerJ 9:e11179 https://doi.org/10.7717/peerj.11179
Function, structure and quality of striated muscles in the lower extremities in patients with late onset Pompe Disease—an MRI study
Background Pompe Disease (PD) is a rare inherited metabolic myopathy, caused by lysosomal-α-glucosidase (GAA) deficiency, which leads to glycogen accumulation within the lysosomes, resulting in cellular and tissue damage. Due to the emergence of a disease modifying treatment with recombinant GAA there has been a large increase in studies of late onset Pompe Disease (LOPD) during the last decade. Methods The present study evaluates muscle quality in 10 patients with LOPD receiving treatment with enzyme replacement therapy and in 10 age and gender matched healthy controls applying T1-weighted Dixon MR imaging and isokinetic dynamometry. Muscle quality was determined by muscle strength in relation to muscle size (contractile cross-sectional area, CSA) and to muscle quality (fat fraction). A follow-up evaluation of the patients was performed after 8–12 months. Patient evaluations also included: six-minute walking test (6MWT), forced vital capacity, manual muscle testing and SF-36 questionnaire. Results Fat fraction of knee flexors (0.15 vs 0.07, p < 0.05) and hip muscles (0.11 vs 0.07, p < 0.05) were higher in patients than controls. In patients, contractile CSA correlated with muscle strength (knee flexors: r = 0.86, knee extensors: r = 0.88, hip extensors: r = 0.83, p < 0.05). No correlation was found between fat fraction and muscle strength. The fat fraction of thigh muscles did not correlate with scores from the clinical tests nor did it correlate with the 6MWT. During follow-up, the contractile CSA of the knee extensors increased by 2%. No other statistically significant change was observed. Quantitative MRI reflects muscle function in patients with LOPD, but larger long-term studies are needed to evaluate its utility in detecting changes over time.
Vaeggemose et al. (2021) Function, structure and quality of striated muscles in the lower extremities in patients with late onset Pompe Disease—an MRI study. PeerJ 9:e10928 https://doi.org/10.7717/peerj.10928
Concurrent anemia and stunting among schoolchildren in Wonago district in southern Ethiopia: a cross-sectional multilevel analysis
Background Even if many schoolchildren in Ethiopia are anemic and stunted, few have studied the co-existence of anemia and stunting among schoolchildren in Ethiopia. In addition, multilevel analysis to explore the variation in prevalence of concurrent anemia and stunting (CAS) across schools and classes is rarely applied. Thus, we aimed to assess the prevalence and risk factors of CAS at the individual, household, and school level among schoolchildren in southern Ethiopia. Methods We recruited 864 students aged 7–14 years from the Wonago district in southern Ethiopia using a three-stage random sampling, assigning four schools to level one, 24 classes to level two. We then randomly selected 36 children from each class, and recorded their weight, height, haemoglobin, intestinal helminthic infections, hygienic practices, dietary practices, household food insecurity, and socio-demographic information. A multivariate, multilevel logistic regression model was applied to detect potential risk factors for CAS. Results The prevalence of CAS was 10.5% (85/810) among schoolchildren, which increased with age in years (adjusted odds ratio [aOR] 1.39 [95% confidence interval 1.13, 1.71, P = 0.002]) and among children who always did not wash their hands with soap after use of latrine (aOR 4.30 [1.21, 15.3, P = 0.02]). Children who walked barefoot (aOR 10.4 [2.77, 39.1, P = 0.001]), were infected with Trichuris trichiura (aOR 1.74 [1.05, 2.88, P = 0.03]), or had head lice infestation (aOR 1.71 [1.01, 2.92, P = 0.04]) had higher CAS prevalence. Prevalence rates of CAS were low in those using treated drinking water (aOR 0.32 [95% CI 0.11, 0.97, P = 0.04]). Most of the risk factors for CAS were identified at the individual level. The clustering effect measured by the intra-cluster correlation coefficient was 6.8% at school level and 19% at class. Conclusion CAS prevalence is a moderate public health problem among schoolchildren in southern Ethiopia and varies across classes and schools. After controlling for clustering effects at the school and class levels, we found an association between CAS and increasing age, not always washing hands with soap after using latrine, walking barefoot, and T. trichiura infection. Using treated water for drinking was found to have a protective effect against CAS. Thus, educating children on personal hygiene and provision of safe drinking water could reduce the CAS burden in schoolchildren in rural areas of southern Ethiopia.
Amare et al. (2021) Concurrent anemia and stunting among schoolchildren in Wonago district in southern Ethiopia: a cross-sectional multilevel analysis. PeerJ 9:e11158 https://doi.org/10.7717/peerj.11158