Hub gene associated with prognosis in bladder cancer is a novel therapeutic target
Objective Bladder cancer is a clinical and social conundrum due to its high incidence and recurrence rate. It is urgent to find new targets for the diagnosis and treatment of bladder cancer and improve the prognosis and survival rate of bladder cancer patients. We sought a prognosis-related gene, built related models of evaluated bladder cancer and identified the function of the hub gene in bladder cancer. Methods We downloaded the data of bladder cancer patients from the TCGA database, and used differentially expressed genes (DEGs), copy number variation (CNV) and survival analysis to scan the hub genes associated with prognosis in bladder cancer. Then, multi-factor cox regression was used to obtain the bladder cancer prognosis correlation model. Then, we analyzed the relationship between the expression of hub gene and immune microenvironment of bladder cancer. The relationship between the expression of hub gene and prognosis in bladder cancer patients was verified by immunohistochemistry. Cell proliferation assay and drug sensitivity test in vivo were used to verify the inhibition of bladder cancer by targeted inhibitors. Results In bladder cancer, we screened seven hub genes (ACLY, CNP, NKIRAS2, P3H4, PDIA6, VPS25 and XPO1) associated with survival. Moreover, the multifactor regression model constructed with hub gene can well distinguish the prognosis of bladder cancer. Hub gene is mostly associated with immune microenvironment. Immunohistochemical results basically confirmed the importance of XPO1 in bladder cancer. Selinexor (an inhibitor of XPO1) could effectively inhibit the proliferation of bladder cancer in the cell proliferation experiments by CCK-8 assays and it could suppress the growth of bladder cancer in mouse bladder cancer model. Conclusions In this study, a prognostic model with seven hub genes has provided great help for the prognosis prediction of bladder cancer patients. And XPO1 is an important target affecting the prognosis of bladder cancer, and inhibition of XPO1 can effectively inhibit bladder cancer proliferation and growth.
Fang et al. (2023) Hub gene associated with prognosis in bladder cancer is a novel therapeutic target. PeerJ 11:e15670 https://doi.org/10.7717/peerj.15670
Antifungal effects of eugenol on Candida albicans adherence to denture polymers
Background The study’s objective is to assess the adherence of C. albicans in different types of denture polymers and the effectiveness of eugenol and commercialized denture cleansers in the removal of C. albicans. Three types of denture base polymers (Lucitone® 199 (High-Impact PMMA), Impact® (conventional PMMA) and Eclipse® (UDMA)) and two hard denture reline materials (Kooliner® and Tokuyama® Rebase II Fast) were used in this study. Methods Three hundred samples were prepared (6 × 2 mm disc shape) and divided into five groups of denture polymers (n = 60) and further subjected into five treatment groups (Polident®, Steradent, distilled water, eugenol 5-minutes, and eugenol 10-min). Three samples were extracted from each treatment group for baseline data (n = 12). Baseline data were used to calculate the initial number of C. albicans adherence. A 0.5 ml immersion solution from each specimen was cultured on YPD agar and incubated for 48 h at 37 °C. Visible colonies were counted using a colony counter machine (ROCKER Galaxy 230). Results The result showed that the denture base polymer significantly affected the initial adherence (p = 0.007). The removal of C. albicans was also considerably affected by the denture base polymers and denture cleansers (p < 0.05). Lucitone®, Tokuyama®, and Kooliner® denture base polymers immersed for 3 min in eugenol showed the best results of removal. Discussion This study’s overall results showed that all denture polymers used as denture bases had an effect on C. albicans initial adherence and removal from the denture base, and eugenol is comparable to commercialised denture cleansers in reducing the number of attached C. albicans on denture base polymers.
Zanul Abidin et al. (2023) Antifungal effects of eugenol on Candida albicans adherence to denture polymers. PeerJ 11:e15750 https://doi.org/10.7717/peerj.15750
Life-expectancy changes during the COVID-19 pandemic from 2019–2021: estimates from Japan, a country with low pandemic impact
Background The COVID-19 pandemic had a low impact on Japan in 2020, but the size of the epidemic increased considerably there in 2021. This study made a statistical analysis of life expectancy changes up to the end of 2021 in Japan. Objective We aimed to estimate changes in life expectancy from 2019 to 2021 associated with the COVID-19 pandemic. To do so, we decomposed the life expectancy changes from 2020–2021 into age-specific and cause of death-specific contributions. Methods We used the absolute number of deaths by age and prefecture in Japan to calculate life expectancy from 2019–21 at both national and prefectural levels, and also examined the correlation between life expectancy gap and annual number of COVID-19 cases, total person-days spent in intensive care, and documented deaths due to COVID-19. We used the Arriaga decomposition method to decompose national life expectancy changes from 2020 to 2021 into age and cause of death components. Results From 2019–2020, Japan’s national level life expectancy across the entire population was extended by 0.24 years. From 2020–2021, it shortened by 0.15 years. The life expectancy shortened more among women (0.15 years) than men (0.12 years). There was significant heterogeneity in life expectancy changes from 2020–2021 by prefecture. It ranged from the maximum shortening of 0.57 years in Tottori prefecture to the maximum extension of 0.23 years in Fukui. The regression analysis revealed the negative correlation between the life expectancy change and burden of COVID-19 at prefectural level. The decomposition of life expectancy changes at birth from 2020–2021 showed that losses in life expectancy were largely attributable to the mortality of the population over 70 years old. Changes in life expectancy among infants and working-age adults mostly contributed to lengthening overall life expectancy. Among leading major causes of death, deaths due to neoplastic tumor and cardiovascular diseases contributed to shortening life expectancy, whereas respiratory diseases did not. Conclusion The decades-long increasing trend in life expectancy was suspended by the COVID-19 pandemic. However, life expectancy changes from 2019–2020 and 2020–2021 were small in Japan. This may be attributable to the small epidemiological impact of COVID-19 during this time period, but nonetheless, the negative impact of COVID-19 on life expectancy was indicated in the present study. The chance of death accelerated in older people in 2021, but a smaller number of deaths than usual among infants and working age adults contributed to extended life expectancy, and the change in the cause of death structure under the COVID-19 pandemic also significantly contributed to shortening life expectancy.
Munira et al. (2023) Life-expectancy changes during the COVID-19 pandemic from 2019–2021: estimates from Japan, a country with low pandemic impact. PeerJ 11:e15784 https://doi.org/10.7717/peerj.15784
Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies
Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.
Rollin et al. (2023) Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies. PeerJ 11:e15816 https://doi.org/10.7717/peerj.15816
LIDER: cell embedding based deep neural network classifier for supervised cell type identification
Background Automatic cell type identification has been an urgent task for the rapid development of single-cell RNA-seq techniques. Generally, the current approach for cell type identification is to generate cell clusters by unsupervised clustering and later assign labels to each cell cluster with manual annotation. Methods Here, we introduce LIDER (celL embeddIng based Deep nEural netwoRk classifier), a deep supervised learning method that combines cell embedding and deep neural network classifier for automatic cell type identification. Based on a stacked denoising autoencoder with a tailored and reconstructed loss function, LIDER identifies cell embedding and predicts cell types with a deep neural network classifier. LIDER was developed upon a stacked denoising autoencoder to learn encoder-decoder structures for identifying cell embedding. Results LIDER accurately identifies cell types by using stacked denoising autoencoder. Benchmarking against state-of-the-art methods across eight types of single-cell data, LIDER achieves comparable or even superior enhancement performance. Moreover, LIDER suggests comparable robust to batch effects. Our results show a potential in deep supervised learning for automatic cell type identification of single-cell RNA-seq data. The LIDER codes are available at https://github.com/ShiMGLab/LIDER.
Tang et al. (2023) LIDER: cell embedding based deep neural network classifier for supervised cell type identification. PeerJ 11:e15862 https://doi.org/10.7717/peerj.15862
Effects of post-activation protocols based on slow tempo bodyweight squat and isometric activity on vertical jump height enhancement in trained males: a randomized controlled trial
This study aimed to establish the effectiveness of slow tempo bodyweight squat combined with an isometric squat (ST-ISO), and an isometric squat alone (ISO), as a post-activation performance enhancement protocol (PAPE) for jump height improvement. The study sample consisted of 41 trained men aged 18–24. The ST-ISO group (n = 17) performed three five-second sets of the maximal voluntary back squat while pushing on an immovable bar and two sets of five repetitions of a slow-tempo (5-0-5-0) body squat immediately after isometry with a 2-m rest interval. The ISO (n = 14) group only performed isometric squats, and the control group (CG; n = 10) performed a 5-min treadmill run at 6 km/h. The countermovement jump (CMJ) height results were analyzed from the baseline and then at 3, 5, 7, and 9 min after the PAPE protocols. The statistical significance was set at p < 0.05. RM-ANOVA revealed differences in the group-minute interaction (F = 2.70; p = 0.0083; η2 = 0.1243), and post-hoc tests demonstrated a significant decrease in CMJ after 5 min in the ISO group (p < 0.0446). The performance of the ST-ISO group markedly decreased in the 3rd and 7th min after PAPE (p = 0.0137; p = 0.0424, respectively), though it improved significantly in the final minute (p < 0.0030). Chi-squared analysis revealed that the ST-ISO group peaked more frequently in the 9th min (X2 = 17.97; p = 0.0214). However, CMJ height improvement did not differ between the PAPE protocols, thus it was close to statistical significance (t = −1.82; p = 0.07; ES = 0.7). The ST-ISO protocol provided jump enhancement, though the deterioration observed in the first minutes after the protocols suggest the rest period after activity requires attention, and the methods need to be individualized.
Koźlenia et al. (2023) Effects of post-activation protocols based on slow tempo bodyweight squat and isometric activity on vertical jump height enhancement in trained males: a randomized controlled trial. PeerJ 11:e15753 https://doi.org/10.7717/peerj.15753
Non-destructive insect metabarcoding for surveillance and biosecurity in citrus orchards: recording the good, the bad and the psyllids
Background The Australian citrus industry remains one of the few in the world to be unaffected by the African and the Asian citrus psyllids, Trioza erytreae Del Guercio and Diaphorina citri Kuwayama, respectively, and the diseases their vectored bacteria can cause. Surveillance, early detection, and strict quarantine measures are therefore fundamental to safeguard Australian citrus. However, long-term targeted surveillance for exotic citrus pests can be a time-consuming and expensive activity, often relying on manually screening large numbers of trap samples and morphological identification of specimens, which requires a high level of taxonomic knowledge. Methods Here we evaluated the use of non-destructive insect metabarcoding for exotic pest surveillance in citrus orchards. We conducted an 11-week field trial, between the months of December and February, at a horticultural research farm (SuniTAFE Smart Farm) in the Northwest of Victoria, Australia, and processed more than 250 samples collected from three types of invertebrate traps across four sites. Results The whole-community metabarcoding data enabled comparisons between different trapping methods, demonstrated the spatial variation of insect diversity across the same orchard, and highlighted how comprehensive assessment of insect biodiversity requires use of multiple complimentary trapping methods. In addition to revealing the diversity of native psyllid species in citrus orchards, the non-targeted metabarcoding approach identified a diversity of other pest and beneficial insects and arachnids within the trap bycatch, and recorded the presence of the triozid Casuarinicola cf warrigalensis for the first time in Victoria. Ultimately, this work highlights how a non-targeted surveillance approach for insect monitoring coupled with non-destructive DNA metabarcoding can provide accurate and high-throughput species identification for biosecurity and biodiversity monitoring.
Martoni et al. (2023) Non-destructive insect metabarcoding for surveillance and biosecurity in citrus orchards: recording the good, the bad and the psyllids. PeerJ 11:e15831 https://doi.org/10.7717/peerj.15831
Evaluation of a biosecurity survey approach for contamination by Chlamydia pecorum in koala rehabilitation, field capture, and captive settings
Transmission of Chlamydia pecorum between koalas is a potential risk in field capture or rehabilitation settings, where koalas are held in proximity to each other, or equipment is shared between animals. Given the impact of C. pecorum on koala welfare and population viability it is surprising that quarantine and disinfection protocols in a koala rehabilitation facility or capture settings have not previously been evaluated. This study aimed to evaluate an approach, based on the detection of chlamydial DNA and cell viability, to determine the degree of environmental contamination within a koala care facility. Various fomite sites associated with koala care at a koala rehabilitation facility in New South Wales, Australia were identified as potential sources of chlamydial contamination, following exposure to koalas known to be infected with C. pecorum. Fomite sites were swabbed following exposure, and again after decontamination procedures were carried out. Samples were tested for the presence of chlamydial DNA using qPCR and viability using both RT-qPCR and cell culture. From a total of 239 sampling events, 30 tested qPCR positive for chlamydial DNA, with 19 and 11 samples corresponding to pre-decontamination and post-decontamination events respectively. Detection of chlamydial DNA appeared to be most common in the examination room, especially on fomite sites in direct contact with koalas. Physical removal of chlamydial DNA, or its degradation by the elements, appeared to be more common on outdoor enclosures, clothing, and hands. Based on the cell culture assay, of the pre-decontamination samples with chlamydial DNA, eight had viable chlamydial cells, two of these at low levels. Of the post-decontamination samples with chlamydial DNA, one had a moderate number, and one had a very low number of viable chlamydial cells. RT-qPCR was unsuccessful in determining cell viability due to low yields of RNA and high levels of contaminants from the environmental samples. The outcomes of this study provide a knowledge base for the design of future biosecurity evaluation guidelines in captive and koala rehabilitation facilities. The higher incidence of chlamydial DNA detection by qPCR than viable organism highlights the need to use viability assays in similar studies. However, further investment is still needed to optimise these methods and improve sensitivity for complex environmental samples.
Casteriano et al. (2023) Evaluation of a biosecurity survey approach for contamination by Chlamydia pecorum in koala rehabilitation, field capture, and captive settings. PeerJ 11:e15842 https://doi.org/10.7717/peerj.15842
Morphological changes in female reproductive organs in the African monarch butterfly, host to a male-killing Spiroplasma
Background Sexual selection and conflicts within and between sexes promote morphological diversity of reproductive traits within species. Variation in the morphology of diagnostic reproductive characters within species offer an excellent opportunity to study these evolutionary processes as drivers of species diversification. The African monarch, Danaus chrysippus (Linnaeus, 1758), is widespread across Africa. The species is polytypic, with the respective geographical ranges of the four colour morphs only overlapping in East Africa. Furthermore, some of the populations host an endosymbiotic bacterium, Spiroplasma, which induces son-killing and distorts the local host population sex-ratio, creating sexual conflicts between the females seeking to optimize their fecundity and the limited mating capacity of the rare males. Methods We dissected females from Kenya, Rwanda and South Africa, where Spiroplasma vary in presence and prevalence (high, variable and absent, respectively), and conducted microscopy imaging of their reproductive organs. We then characterized the effect of population, female body size, and female mating status, on the size and shape of different genitalia characters of the D. chrysippus female butterflies. Results We showed that although the general morphology of the organs is conserved in D. chrysippus, female genitalia vary in size and shape between and within populations. The virgin females have smaller organs, while the same organs were expanded in mated females. Females from highly female-biased populations, where the male-killing Spiroplasma is prevalent, also have a larger area of their corpus bursae covered with signa structures. However, this pattern occurs because a larger proportion of the females remains virgin in the female-biased populations rather than because of male depletion due to the symbiont, as males from sex-ratio distorted populations did not produce significantly smaller nutritious spermatophores.
Malmberg et al. (2023) Morphological changes in female reproductive organs in the African monarch butterfly, host to a male-killing Spiroplasma. PeerJ 11:e15853 https://doi.org/10.7717/peerj.15853
Repetition velocity as a measure of loading intensity in the free weight and Smith machine Bulgarian split squat
This study investigated the grouped and individualized load-velocity profile (GLVP vs. ILVP) in Bulgarian split squat using Smith machine and free weight. Seventy five recreational male lifters completed two incremental loading tests of Bulgarian split squat. Mean velocity was measured by a linear-position transducer (GymAware). Linear regression equation was applied to construct the GLVP and ILVP. The agreement of predicted %1RM and measured %1RM was assessed by a combination of intraclass correlation coefficient (ICC), coefficient of variation (CV), standard error of measurement (SEM) and Bland-Altman analysis. Acceptable validity was defined as ICC > 0.75, CV ≤ 10% and p ≥ 0.05 (a paired Wilcoxon signed-rank test). A very high level of inverse load-velocity relationships were demonstrated in Bulgarian split squat (r = − 0.92) with free weights and a Smith machine. ILVP (ICC ≥ 0.98, CV ≤ 8.73%, p ≥ 0.56) was valid enough to predict the %1RM, but GLVP of both limbs revealed large CVs in free weights (CV: 15.4%,15.63%) and a Smith machine (CV: 11.24%, 12.25%). Cross-validation between the actual %1RM and predicted %1RM using free weights and a Smith machine ILVP was not acceptable (p ≤ 0.03, CV ≥ 14.07%). A very high level of inverse relationship were observed between %1RM and MV in Bulgarian split squat using free weights and a Smith machine, indicating individualized load velocity properties, and the ILVP showed high between-devices variability in both scenarios. Using velocity as a measure of loading intensity in Bulgarian split squat needs to consider the individualized load velocity properties, and difference between free weights and a Smith machine.
Liao et al. (2023) Repetition velocity as a measure of loading intensity in the free weight and Smith machine Bulgarian split squat. PeerJ 11:e15863 https://doi.org/10.7717/peerj.15863