Clinical significance of FBXO43 in hepatocellular carcinoma and its impact on tumor cell proliferation, migration and invasion
Background The effects of FBXO43 on hepatocellular carcinoma (HCC) and its clinical significance have not yet been determined. This study aims to determine the clinical significance of FBXO43 in HCC and its impact on the biological functions of HCC cells. Methods Data from TCGA database were downloaded to investigate the expression of FBXO43 in HCC and its correlation with prognosis and immune infiltration. Immunohistochemical staining images of FBXO43 in HCC were acquired from the HPA website. HCC cells (BEL-7404 and SMMC-7721) were transfected with the lentivirus targeting FBXO43 to decrease FBXO43 expression in HCC cells. Western blotting assay was conducted to evaluate the expression level of FBXO43 protein. MTT assay was used to detect the proliferation of HCC cells. The migration and invasion of HCC cells were investigated by performing scratch wound-healing and Transwell invasion assays, respectively. Results In comparison to normal tissues, FBXO43 is overexpressed in HCC tissue, and high FBXO43 expression is linked to late T stage, TNM stage and tumor grade. Elevated FBXO43 expression is a risk factor for HCC. In patients with high FBXO43 expression, the overall survival, disease-specific survival, progression-free survival and disease-free survival are poorer. The proliferation, migration and invasion of HCC cells are significantly attenuated in FBXO43 knockdown cells. Also, TCGA data analysis reveals that FBXO43 exhibits a positive correlation with immunosuppression of HCC. Conclusion FBXO43 is overexpressed in HCC, and is linked to late tumor stage, worse prognosis and tumor immunosuppression. FBXO43 knockdown restrains the proliferation, migration and invasion of HCC.
Ma et al. (2023) Clinical significance of FBXO43 in hepatocellular carcinoma and its impact on tumor cell proliferation, migration and invasion. PeerJ 11:e15373 https://doi.org/10.7717/peerj.15373
Optimising sampling of fish assemblages on intertidal reefs using remote underwater video
Background Assessing fish assemblages in subtidal and intertidal habitats is challenging due to the structural complexity of many of these systems. Trapping and collecting are regarded as optimal ways to sample these assemblages, but this method is costly and destructive, so researchers also use video techniques. Underwater visual census and baited remote underwater video stations are commonly used to characterise fish communities in these systems. More passive techniques such as remote underwater video (RUV) may be more appropriate for behavioural studies, or for comparing proximal habitats where the broad attraction caused by bait plumes could be an issue. However, data processing for RUVs can be time consuming and create processing bottlenecks. Methods Here, we identified the optimal subsampling method to assess fish assemblages on intertidal oyster reefs using RUV footage and bootstrapping techniques. We quantified how video subsampling effort and method (systematic vs random) affect the accuracy and precision of three different fish assemblage metrics; species richness and two proxies for the total abundance of fish, MaxNT and MeanCountT, which have not been evaluated previously for complex intertidal habitats. Results Results suggest that MaxNT and species richness should be recorded in real time, whereas optimal sampling for MeanCountT is every 60 s. Systematic sampling proved to be more accurate and precise than random sampling. This study provides valuable methodology recommendations which are relevant for the use of RUV to assess fish assemblages in a variety of shallow intertidal habitats.
Erickson et al. (2023) Optimising sampling of fish assemblages on intertidal reefs using remote underwater video. PeerJ 11:e15426 https://doi.org/10.7717/peerj.15426
Land abandonment as driver of woody vegetation dynamics in Tamaulipan thornscrub at Northeastern Mexico
Background Vegetation structure is defined as the temporal and spatial distribution of plant species in a particular site. Vegetation structure includes vertical and horizontal distribution and has been widely used as an indicator of successional changes. Ecological succession plays an essential role in the determination of the mechanisms that structure plant communities under anthropogenic disturbances. After an anthropogenic disturbance, such as grazing, forests follow changes in the original composition and vegetation structure, which eventually could restore some of their attributes to become mature forests again. To know how the time of abandonment affects woody plant communities, we ask the following questions: (1) How does the species richness, diversity, and vertical structure (A index) change concerning the time of abandonment? (2) Are species similarities among woody vegetation communities determined by land abandonment? (3) Which woody species have the highest ecological importance in each successional stage? Methods We explored how successional stages after land abandonment mediated the species richness, species diversity (alpha and beta), and ecological importance value index on four areas of Tamaulipan thornscrub. We selected four areas that differed in time of abandonment: 10, 20, 30, and >30 years. The first three areas were used for cattle grazing, whereas the >30-year area was selected as a control since it does not have a record of disturbance by cattle grazing or agriculture. During the summer of 2012, we randomly established four square plots (40 m × 40 m) in each area, separated at least 200 m from each other. In each plot, we recorded all woody individuals per species with a basal diameter ≥1 cm at 10 cm above ground level. We estimated species richness indices, species diversity (alpha and beta), and ecological importance value index. Results We recorded 27 woody species belonging to 23 genera and 15 families. Fabaceae accounted for 40% of the species. Acacia farnesiana was the most important and abundant species in the first three successional stages. We suggested that older successional stages of Tamaulipan thornscrub promote woody plant communities, characterized by a higher complex structure than younger communities. We observed the highest species similarity between the sites with a closer time of abandonment, while the lowest similarity was shown between the sites with extreme time of abandonment. We conclude that Tamaulipan thornscrub shows a similar trend of ecological succession to other dry forests and the time of abandonment has a high mediation on plant dynamics in the Tamaulipan thornscrub. Also, we stand out the importance of secondary forests for Tamaulipan thornscrub woody plant communities. Finally, we recommended future studies include aspects of regeneration speed, the proximity of mature vegetation, and the interactions of plants with their seed dispersers.
Alanís-Rodríguez et al. (2023) Land abandonment as driver of woody vegetation dynamics in Tamaulipan thornscrub at Northeastern Mexico. PeerJ 11:e15438 https://doi.org/10.7717/peerj.15438
Valence moderates the effect of stimulus-hand proximity on conflict processing and gaze-cueing
An effective interaction with the environment requires adaptation of one’s own behaviour to environmental demands. We do so by using cues from our environment and relating these cues to our body to predict the outcomes of events. The recent literature on embodied cognition suggests that task-relevant stimuli, presented near the hands, receive more attentional capacity and are processed differently than stimuli, presented spatially more distant to our body. It has also been proposed that near-hand processing is beneficial to conflict resolution. In the current study, we tested the assumption of an attentional bias towards the near hand space in the context of our previous work by combining a cueing paradigm (allocation of visual attention) with a conflict processing paradigm (Simon task) in the near vs far hand space. In addition, the relevance of processing was manipulated by using affective (angry vs neutral smileys) gaze cues (i.e., varying the valence of the cues). Our results indicate that (a) the interaction of valence × cue congruency × hand proximity was significant, indicating that the cueing effect was larger for negative valence in the proximal condition. (b) The interaction of valence × Simon compatibility × stimulus-hand proximity interaction was significant, indicating that for negative valence processing, the Simon effect was smaller in the proximal than in the distal stimulus-hand condition. This effect was at least numerically but not significantly reversed in the neutral valence condition. (c) Overall, cue congruency, indicating the correct vs incorrect attention allocation to the target stimulus onset, did not reveal any effect on Simon compatibility × stimulus-hand proximity. Our results suggest that valence, the allocation of attention, and conflict, seem to be decisive factors determining the direction and strength of hand proximity effects.
Hoffmann et al. (2023) Valence moderates the effect of stimulus-hand proximity on conflict processing and gaze-cueing. PeerJ 11:e15286 https://doi.org/10.7717/peerj.15286
A comparative analysis of small RNA sequencing data in tubers of purple potato and its red mutant reveals small RNA regulation in anthocyanin biosynthesis
Anthocyanins are a group of natural pigments acting as stress protectants induced by biotic/abiotic stress in plants. Although the metabolic pathway of anthocyanin has been studied in potato, the roles of miRNAs on the metabolic pathway remain unclear. In this study, a purple tetraploid potato of SD92 and its red mutant of SD140 were selected to explore the regulation mechanism of miRNA in anthocyanin biosynthesis. A comparative analysis of small RNAs between SD92 and SD140 revealed that there were 179 differentially expressed miRNAs, including 65 up- and 114 down-regulated miRNAs. Furthermore, 31 differentially expressed miRNAs were predicted to potentially regulate 305 target genes. KEGG pathway enrichment analysis for these target genes showed that plant hormone signal transduction pathway and plant-pathogen interaction pathway were significantly enriched. The correlation analysis of miRNA sequencing data and transcriptome data showed that there were 140 negative regulatory miRNA-mRNA pairs. The miRNAs included miR171 family, miR172 family, miR530b_4 and novel_mir170. The mRNAs encoded transcription factors, hormone response factors and protein kinases. All these results indicated that miRNAs might regulate anthocyanin biosynthesis through transcription factors, hormone response factors and protein kinase.
Liu et al. (2023) A comparative analysis of small RNA sequencing data in tubers of purple potato and its red mutant reveals small RNA regulation in anthocyanin biosynthesis. PeerJ 11:e15349 https://doi.org/10.7717/peerj.15349
Single fraction stereotactic radiosurgery and fractionated stereotactic radiotherapy provide equal prognosis with overall survival in patients with brain metastases at diagnosis without surgery at primary site
Background and purpose Stereotactic radiosurgery (SRS) and fractionated stereotactic radiation therapy (SRT) are both treatments shown to be effective in treating brain metastases (BMs). However, it is unknown how these treatments compare in effectiveness and safety in cancer patients with BMs regardless of the primary cancer. The main objective of this study is to investigate the SRS and SRT treatments’ associations with the overall survival (OS) of patients diagnosed with BMs using the National Cancer Database (NCDB). Materials and methods Patients in the NCDB with breast cancer, non-small cell lung cancer, small cell lung cancer, other lung cancers, melanoma, colorectal cancer, or kidney cancer who had BMs at the time of their primary cancer diagnosis and received either SRS or SRT as treatment for their BMs were included in the study. We analyzed OS with a Cox proportional hazard analysis that adjusted variables associated with improved OS during univariable analysis. Results Of the total 6,961 patients that fit the criteria for the study, 5,423 (77.9%) received SRS and 1,538 (22.1%) received SRT. Patients who received SRS treatment had a median survival time of 10.9 (95% CI [10.5–11.3]), and those who received SRT treatment had a median survival time of 11.3 (95% CI [10.4–12.3]) months. This difference was not found to be significant (Log-rank P = 0.31). Multivariable Cox proportional hazard analysis did not yield a significant difference between the treatments’ associations with OS (Hazard Ratio: 0.942, CI 95% [0.882–1.006]; P = .08) or SRS vs. SRT. Conclusions In this analysis, SRS and SRT did not show a significant difference in their associations with OS. Future studies investigating the neurotoxicity risks of SRS as compared to SRT are warranted.
Ostdiek-Wille et al. (2023) Single fraction stereotactic radiosurgery and fractionated stereotactic radiotherapy provide equal prognosis with overall survival in patients with brain metastases at diagnosis without surgery at primary site. PeerJ 11:e15357 https://doi.org/10.7717/peerj.15357
Prediction study of prognostic nutrition index on the quality of life of patients with cervical cancer undergoing radiotherapy and chemotherapy
Objective To assess the prognostic nutritional index (PNI) and quality of life (QOL) of patients with cervical cancer (CC) who underwent radiotherapy and chemotherapy and to reveal the effect of PNI on QOL and its prognostic value. Methods A total of 138 CC patients who underwent radiotherapy and chemotherapy in the Second Affiliated Hospital of Fujian Medical University from January 2020 to October 2022 were selected as the study subjects via convenient sampling. According to the PNI cut-off value of 48.8, they were divided into a high-PNI group and a low-PNI group, and the quality of life of the two groups was compared. The Kaplan-Meier method was used to draw the survival curve, and the Log-Rank test was employed to compare the survival rates of the two groups. Results The scores of physical functioning and overall QOL in the high-PNI group were significantly higher than those in the low-PNI group (P < 0.05). The scores of fatigue, nausea and vomiting, pain and diarrhea were higher than those in the low-PNI group, and the difference was statistically significant (P < 0.05). The objective response rates were 96.77% and 81.25% in the high-PNI group and the low-PNI group, respectively, and the difference was statistically significant (P = 0.045). The 1-year survival rates of patients with high PNI and low PNI were 92.55% and 72.56% in the high-PNI group and the low-PNI group, respectively; the difference in survival rates was statistically significant (P = 0.006). Conclusion The overall quality of life of CC patients with low PNI receiving radiotherapy and chemotherapy is lower than that of patients with high PNI. Low PNI reduces the tolerance to radiotherapy and chemotherapy and the objective response rate, which can be used as a prognostic indicator for cervical cancer patients.
Chen et al. (2023) Prediction study of prognostic nutrition index on the quality of life of patients with cervical cancer undergoing radiotherapy and chemotherapy. PeerJ 11:e15442 https://doi.org/10.7717/peerj.15442
Predictive value of immunoglobulin G, activated partial thromboplastin time, platelet, and indirect bilirubin for delayed viral clearance in patients infected with the Omicron variant
Background Omicron is the recently emerged highly transmissible severe acute respiratory syndrome coronavirus 2 variant that has caused a dramatic increase in coronavirus disease-2019 infection cases worldwide. This study was to investigate the association between demographic and laboratory findings, and the duration of Omicron viral clearance. Methods Approximately 278 Omicron cases at the Ruijin Hospital Luwan Branch, Shanghai Jiaotong University School of Medicine were retrospectively analyzed between August 11 and August 31, 2022. Demographic and laboratory data were also collected. The association between demographics, laboratory findings, and duration of Omicron viral clearance was analyzed using Pearson correlation analysis and univariate and multivariate logistic regression. Results Univariate logistic regression analyses showed that a prolonged viral clearance time was significantly associated with older age and lower immunoglobulin (Ig) G and platelet (PLT) levels. Using multinomial logistic regression analyses, direct bilirubin, IgG, activated partial thromboplastin time (APTT), and PLT were independent factors for longer viral shedding duration. The model combining direct bilirubin, IgG, APTT, and PLT identifies patients infected with Omicron whose viral clearance time was ≥7 days with 62.7% sensitivity and 83.4% specificity. Conclusion These findings suggest that direct bilirubin, IgG, PLT, and APTT are significant risk factors for a longer viral shedding duration in patients infected with Omicron. Measuring levels of direct bilirubin, IgG, PLT, and APTT is advantageous to identify patients infected with Omicron with longer viral shedding duration.
Zhang et al. (2023) Predictive value of immunoglobulin G, activated partial thromboplastin time, platelet, and indirect bilirubin for delayed viral clearance in patients infected with the Omicron variant. PeerJ 11:e15443 https://doi.org/10.7717/peerj.15443
Blood cells and hematological parameters of Chiala Mountain Salamander, Batrachuperus karlschmidti (Urodela, Hynobiidae)
Hematological parameters are essential indices for assessing the function of blood and reflecting not only the health status of animal but also their physiological adaptation to the environment. Herein, the composition of blood cells and the hematological parameters of wild Batrachuperus karlschmidti were examined for the first time, and the effects of sex, body size, body mass, and age on the hematological parameters were explored. The morphology and morphometric data of the blood cells, as well as the hematological parameters, of B. karlschmidti were slightly differ from those of its congener. However, hematological differences between sexes were only found in erythrocyte and leukocyte count, and mean cell volume (MCV), which possibly reflecting the need for better oxygen distribution and stronger immune protection for reproduction. Hematocrit (Hct) and mean cell hemoglobin (MCH) were strongly dependent on body mass. These also might have been attributed to higher oxygen requirements with larger body masses. This is a pilot project exploring the hematology of this species that may help establish hematological parameters in future for supporting species protection and monitoring studies, as well as help understanding the physiological adaptation of this species.
Liu et al. (2023) Blood cells and hematological parameters of Chiala Mountain Salamander, Batrachuperus karlschmidti (Urodela, Hynobiidae). PeerJ 11:e15446 https://doi.org/10.7717/peerj.15446
Kukri snakes Oligodon Fitzinger, 1826 of the Western Palearctic with the resurrection of Contia transcaspica Nikolsky, 1902 (Reptilia, Squamata, Colubridae)
The kukri snakes of the genus Oligodon Fitzinger, 1826 reach the westernmost limits of their distribution in Middle and Southwest Asia (Afghanistan, Iran, and Turkmenistan), and the Palearctic portions of Pakistan. In this article, we review the systematics and distribution of the two species native to this region, Oligodon arnensis (Shaw, 1802) and Oligodon taeniolatus (Jerdon, 1853) based on an integrative approach combining morphological, molecular, and species distribution modeling (SDM) data. Phylogenetic analyses recover O. taeniolatus populations from Iran and Turkmenistan in a clade with the O. arnensis species complex, rendering the former species paraphyletic relative to O. taeniolatus sensu stricto on the Indian subcontinent. To correct this, we resurrect the name Contia transcaspica Nikolsky, 1902 from the synonymy of O. taeniolatus and assign it to populations in Middle–Southwest Asia. So far, Oligodon transcaspicus comb. et stat. nov. is known only from the Köpet–Dag Mountain Range of northeast Iran and southern Turkmenistan, but SDM mapping suggests it may have a wider range. Genetic samples of O. “arnensis” from northern Pakistan are nested in a clade sister to the recently described Oligodon churahensis Mirza, Bhardwaj & Patel, 2021, and are phylogenetically separate from O. arnensis sensu stricto in south India and Sri Lanka. Based on morphological similarity, the Afghanistan and Pakistan populations are assigned to Oligodon russelius (Daudin, 1803) and we synonymize O. churahensis with this species. Our investigation leads us to remove O. taeniolatus from the snake fauna of Afghanistan, Iran, and Turkmenistan, with the consequence that only Oligodon transcaspicus comb. et stat. nov. and O. russelius are present in these countries. Additional studies are needed to resolve the taxonomy of the O. taeniolatus and O. arnensis species complexes on the Indian subcontinent, and an updated key for both groups is provided.
Lee et al. (2023) Kukri snakes Oligodon Fitzinger, 1826 of the Western Palearctic with the resurrection of Contia transcaspica Nikolsky, 1902 (Reptilia, Squamata, Colubridae). PeerJ 11:e15185 https://doi.org/10.7717/peerj.15185