Identification of key genes and biological pathways in Chinese lung cancer population using bioinformatics analysis
Background Identification of accurate prognostic biomarkers is still particularly urgent for improving the poor survival of lung cancer patients. In this study, we aimed to identity the potential biomarkers in Chinese lung cancer population via bioinformatics analysis. Methods In this study, the differentially expressed genes (DEGs) in lung cancer were identified using six datasets from Gene Expression Omnibus (GEO) database. Subsequently, enrichment analysis was conducted to evaluate the underlying molecular mechanisms involved in progression of lung cancer. Protein-protein interaction (PPI) and CytoHubba analysis were performed to determine the hub genes. The GEPIA, Human Protein Atlas (HPA), Kaplan-Meier plotter, and TIMER databases were used to explore the hub genes. The receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic value of hub genes. Reverse transcription quantitative PCR (qRT-PCR) was used to validate the expression levels of hub genes in 10 pairs of lung cancer paired tissues. Results A total of 499 overlapping DEGs (160 upregulated and 339 downregulated genes) were identified in the microarray datasets. DEGs were mainly associated with pathways in cancer, focal adhesion, and protein digestion and absorption. There were nine hub genes (CDKN3, MKI67, CEP55, SPAG5, AURKA, TOP2A, UBE2C, CHEK1 and BIRC5) identified by PPI and module analysis. In GEPIA database, the expression levels of these genes in lung cancer tissues were significantly upregulated compared with normal lung tissues. The results of prognostic analysis showed that relatively higher expression of hub genes was associated with poor prognosis of lung cancer. In HPA database, most hub genes were highly expressed in lung cancer tissues. The hub genes have good diagnostic efficiency in lung cancer and normal tissues. The expression of any hub gene was associated with the infiltration of at least two immune cells. qRT-PCR confirmed that the expression level of CDKN3, MKI67, CEP55, SPAG5, AURKA, TOP2A were highly expressed in lung cancer tissues. Conclusions The hub genes and functional pathways identified in this study may contribute to understand the molecular mechanisms of lung cancer. Our findings may provide new therapeutic targets for lung cancer patients.
Liu et al. (2022) Identification of key genes and biological pathways in Chinese lung cancer population using bioinformatics analysis. PeerJ 10:e12731 https://doi.org/10.7717/peerj.12731
The effect of 2,4-dichlorophenoxyacetic acid on the production of oat (Avena sativa L.) doubled haploid lines through wide hybridization
Background Development of new cultivars is one of the vital options for adapting agriculture to climate change, and the production of doubled haploid (DH) plants can make a significant contribution to accelerating the breeding process. Oat is one of the cereals with particular health benefits, but it unfortunately still remains recalcitrant to haploidization. Our previous studies have clearly demonstrated that post-pollination with hormone treatment is a key step in haploid production through wide hybridization and indicated it as the most effective method for this species. Therefore, we subsequently addressed the problem of the influence of 2,4-dichlorophenoxyacetic acid (2,4-D) concentration on consecutive stages of DH production. Methods Twenty-nine genotypes were tested, 9,465 florets were pollinated with maize pollen 2 days after emasculation and then treated with 2,4-D at 50 mg/L and 100 mg/L. Results The applied treatments did not reveal any differences in the number of obtained haploid embryos. However, almost twice as many haploid plants formed on MS medium after applying a higher auxin concentration and 20% more successfully acclimatized. Moreover, 100 mg/L 2,4-D treatment resulted in twice as many DH lines that produced almost three times more seeds compared to 50 mg/L treatment. Nevertheless, the results have confirmed the existence of strong genotypic variation, which may significantly limit the development of an effective and economically feasible method that could be incorporated into breeding programs.
Juzoń et al. (2022) The effect of 2,4-dichlorophenoxyacetic acid on the production of oat (Avena sativa L.) doubled haploid lines through wide hybridization. PeerJ 10:e12854 https://doi.org/10.7717/peerj.12854
Effect of biological treatment used before harvesting and storage methods on the quality, health and microbial characteristics of unripe hazelnut in the husk (Corylus avellana L.)
Background The hazelnut (Corylus avellana) is still one of the most profitable nut crop species. In recent years, however, there has been growing interest in this species in the form of “fresh nuts” that are picked before falling out of the fruit cover. The aim of this study was to evaluate the effect of storage conditions for hazelnuts protected with biological preparations on selected morphological features of the fruits, their health status and the count of bacteria and fungi colonizing the fruits. Results The hazelnuts harvested from the trees protected with a preparation containing Pythium oligandrum and stored for 2 months under the controlled atmosphere conditions and in Xtend® bags (MAP) had the greatest weight and the highest percentage of the kernel. After 3 months of storage, the hazelnuts had reduced commercial value. Only a few hazelnuts displayed symptoms of infectious diseases caused by species of Botrytis and Monilia. The protection applied before the hazelnut harvesting contributed to a multiple increase in the bacterial and yeasts count on the husks and shells of the hazelnuts stored for 3 months. The bacterial count on the nuts stored under the controlled atmosphere (CA, 3%O2:3%CO2, a temperature of 0–1 °C, humidity of 85–95%) and under the controlled atmosphere conditions and in Xtend® bags (MAP) increased significantly. An analysis of the ITS region sequence revealed the presence of bacteria Arthrobacter luteolus and Pantoea agglomerans. A Koch test proved that both non-pathogenic bacteria and pathogenic fungi can cause the browning of the C. avellana leaf under conditions of high humidity. The application of a controlled atmosphere is recommended for a short-term storage of hazelnuts in the husk. Conclusion This research showed that 2 months’ storage of hazelnuts under controlled atmosphere conditions and Xtend® bags (MAP) prevented a reduction in the weight of hazelnuts in the husk, without the husk, and of the kernel and prevented the nut separation from the husk. In general, the application of biopreparations for the protection of the hazelnut had a positive effect on the kernel weight and size.
Markuszewski et al. (2022) Effect of biological treatment used before harvesting and storage methods on the quality, health and microbial characteristics of unripe hazelnut in the husk (Corylus avellana L.). PeerJ 10:e12760 https://doi.org/10.7717/peerj.12760
Dimensional changes of commercial and novel polyvinyl siloxane impression materials following sodium hypochlorite disinfection
Background Dental impressions are used to record anatomy of teeth and surrounding oral structures. Impression materials become contaminated with saliva and blood requiring disinfection, which may have negative impact on dimensional stability of materials. Objective Comparatively evaluate linear dimensional changes of synthesized Tetra-functional (dimethylsilyl) orthosilicate (TFDMOS) containing Polyvinylsiloxane (PVS) impressions following sodium hypochlorite disinfection. Methods Percentage dimensional changes of three commercial PVS (Elite HD Monophase, Extrude and Aquasil Ultra Monophase) and five experimental PVS impression materials were measured. Experimental material contained novel cross-linking agent (TFDMOS) and a non-ionic surfactant (Rhodasurf CET-2) that is Exp-A (without TFDMOS), Exp-B (with TFDMOS), Exp-C (TFDMOS+ 2% Rhodasurf CET-2), Exp-D (TFDMOS+ 2.5% Rhodasurf CET-2) Exp-E (TFDMOS+ 3% Rhodasurf CET-2). Samples were made using rectangular stainless-steel molds (40 × 10 × 3 mm3) and linear dimensional changes were measured using a calibrated travelling microscope at 10× magnification after immersion in distilled water (D.W) and 1% Sodium Hypochlorite solution at two different time intervals i.e., 30 min and 24 h. Results Samples immersed in 1% NaOCl showed significant (p < 0.05) dimensional changes after 30 min of immersion. Exp-E showed significantly greater dimensional changes than their control (Exp-A and Exp-B). In distilled water, there were no significant difference among the tested materials. Aquasil exhibited highest expansion (0.06%) in both solutions. At 24 h, among the commercial materials, Extrude had the greatest expansion followed by Aquasil and Elite in DW while Aquasil showed the greatest expansion followed by Extrude and Elite in NaOCl. Conclusion Experimental PVS had linear dimensional changes within the ISO 4823; 2015 recommended range. However, extended immersion can negatively affect the linear dimensions.
Ud Din et al. (2022) Dimensional changes of commercial and novel polyvinyl siloxane impression materials following sodium hypochlorite disinfection. PeerJ 10:e12812 https://doi.org/10.7717/peerj.12812
Factors of influence in prisoner’s dilemma task: a review of medical literature
The Prisoner’s Dilemma (PD) is one of the most popular concepts amongst the scientific literature. The task is used in order to study different types of social interactions by giving participants the choice to defect or cooperate in a specific social setting/dilemma. This review focuses on the technical characteristics of the PD task as it is used in medical literature and describes how the different PD settings could influence the players’ behaviour. We identify all the studies that have used the PD task in medical research with human participants and distinguish, following a heuristic approach, seven parameters that can differentiate a PD task, namely (a) the opponent parties’ composition; (b) the type of the opponent as perceived by the players; (c) the interaction flow of the game; (d) the number of rounds; (e) the instructions narrative and options that are given to players; (f) the strategy and (g) the reward matrix and payoffs of the game. We describe how each parameter could influence the final outcome of the PD task and highlight the great variability concerning the settings of these parameters in medical research. Our aim is to point out the heterogeneity of such methods in the past literature and to assist future researchers with their methodology design.
Mantas et al. (2022) Factors of influence in prisoner’s dilemma task: a review of medical literature. PeerJ 10:e12829 https://doi.org/10.7717/peerj.12829
Response of Pinus tabuliformis saplings to continuous autumn fertilization treatments in the mountains of Eastern Liaoning Province, China
Autumn fertilization is an important cultivation and management measure used to provide nutrients at the hardening stage during the end of the growing season—bolstering nutrient reserves and promoting additional growth in the following spring. Previous studies mainly focused on short-term or one-time fertilization treatment of container seedlings, and few studies have observed the effects of autumn fertilization of large-area forests over multiple continuous years. The growth dynamics and nutrient changes during autumn in 324 Pinus tabuliformis saplings in the temperate zone of China (in the eastern Liaoning mountains) were studied under field conditions with different fertilizer treatments for three consecutive years. The second year of autumn fertilization promoted the growth of tree height and annual leaf length more significantly than that in the first year, the change in diameter at breast height (DBH) was significant. Tree height (TH) in spring increased at a faster rate than in autumn, while DBH stably increased throughout the year. The increase in TH, DBH, and annual leaf length (ALL) under all fertilization treatments was higher than that of the control group, and the decrease in annual branch length (ABL) was higher than that of the control group. High N significantly increased the concentration of new coniferous N (NLN), soil total N (STN), and soil alkali-hydrolyzable N (SAHN) in P. tabuliformis saplings. High P significantly increased the concentration of P in annual needles and soil total P (STP), and decreased the concentration of N in new needles. In addition, there is a certain correlation between the N and P concentration in the needles and soil, representing the competition and interactions between plant nutrient demand and soil nutrient supply. The most favorable fertilizer treatment consisted of high N and low P (urea 204 g, calcium superphosphate 104 g), which provide support for the formulation of a reasonable fertilization technology for P. tabuliformis in the mountains of Eastern Liaoning Province, China.
Zhang et al. (2022) Response of Pinus tabuliformis saplings to continuous autumn fertilization treatments in the mountains of Eastern Liaoning Province, China. PeerJ 10:e12853 https://doi.org/10.7717/peerj.12853
Leopard and spotted hyena densities in the Lake Mburo National Park, southwestern Uganda
Robust measures of animal densities are necessary for effective wildlife management. Leopards (Panthera pardus) and spotted hyenas (Crocuta Crocuta) are higher order predators that are data deficient across much of their East African range and in Uganda, excepting for one peer-reviewed study on hyenas, there are presently no credible population estimates for these species. A lack of information on the population status and even baseline densities of these species has ramifications as leopards are drawcards for the photo-tourism industry, and along with hyenas are often responsible for livestock depredations from pastoralist communities. Leopards are also sometimes hunted for sport. Establishing baseline density estimates for these species is urgently needed not only for population monitoring purposes, but in the design of sustainable management offtakes, and in assessing certain conservation interventions like financial compensation for livestock depredation. Accordingly, we ran a single-season survey of these carnivores in the Lake Mburo National Park of south-western Uganda using 60 remote camera traps distributed in a paired format at 30 locations. We analysed hyena and leopard detections under a Bayesian spatially explicit capture-recapture (SECR) modelling framework to estimate their densities. This small national park (370 km2) is surrounded by Bahima pastoralist communities with high densities of cattle on the park edge (with regular park incursions). Leopard densities were estimated at 6.31 individuals/100 km2 (posterior SD = 1.47, 95% CI [3.75–9.20]), and spotted hyena densities were 10.99 individuals/100 km2, but with wide confidence intervals (posterior SD = 3.35, 95% CI [5.63–17.37]). Leopard and spotted hyena abundance within the boundaries of the national park were 24.87 (posterior SD 7.78) and 39.07 individuals (posterior = SD 13.51) respectively. Leopard densities were on the middle end of SECR studies published in the peer-reviewed literature over the last 5 years while spotted hyena densities were some of the first reported in the literature using SECR, and similar to a study in Botswana which reported 11.80 spotted hyenas/100 km2. Densities were not noticeably lower at the park edge, and in the southwest of our study site, despite repeated cattle incursions into these areas. We postulate that the relatively high densities of both species in the region could be owed to impala Aepyceros melampus densities ranging from 16.6–25.6 impala/km2. Another, potential explanatory variable (albeit a speculative one) is the absence of interspecific competition from African lions (Panthera leo), which became functionally extinct (there is only one male lion present) in the park nearly two decades ago. This study provides the first robust population estimate of these species anywhere in Uganda and suggests leopards and spotted hyenas continue to persist in the highly modified landscape of Lake Mburo National Park.
Braczkowski et al. (2022) Leopard and spotted hyena densities in the Lake Mburo National Park, southwestern Uganda. PeerJ 10:e12307 https://doi.org/10.7717/peerj.12307
Effects of media multitasking frequency on a novel volitional multitasking paradigm
The effect of media multitasking (e.g., listening to podcasts while studying) on cognitive processes has seen mixed results thus far. To date, the tasks used in the literature to study this phenomenon have been classical paradigms primarily used to examine processes such as working memory. While perfectly valid on their own, these paradigms do not approximate a real-world volitional multitasking environment. To remedy this, as well as attempt to further validate previously found effects in the literature, we designed a novel experimental framework that mimics a desktop computer environment where a “popup” associated with a secondary task would occasionally appear. Participants could choose to attend to the popup, or to ignore it. Attending to the popup would prompt a word stem completion task, while ignoring it would continue the primary math problem verification task. We predicted that individuals who are more impulsive, more frequent media multitaskers, and individuals who prefer to multitask (quantified with the Barratt Impulsiveness Scale, a modified version of the Media Use Questionnaire, and the Multitasking Preference Inventory) would be more distracted by popups, choose to switch tasks more often and more quickly, and be slower to return to the primary task compared to those who media multitask to a lesser degree. We found that as individuals media multitask to a greater extent, they are slower to return to the previous (primary) task set and are slower to complete the primary task overall whether a popup was present or not, among other task performance measures. We found a similar pattern of effects within individuals who prefer to multitask. Our findings suggest that overall, more frequent media multitaskers show a marginal decrease in task performance, as do preferential multitaskers. Attentional impulsivity was not found to influence any task performance measures, but was positively related to a preference for multitasking. While our findings may lack generalizability due to the modifications to the Media Use Questionnaire, and this initial study is statically underpowered, this paradigm is a crucial first step in establishing a more ecologically valid method to study real-world multitasking.
Lopez et al. (2022) Effects of media multitasking frequency on a novel volitional multitasking paradigm. PeerJ 10:e12603 https://doi.org/10.7717/peerj.12603
Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities
Fungal communities are known to contribute to the functioning of living plant microbiomes as well as to the decay of dead plant material and affect vital ecosystem services, such as pathogen resistance and nutrient cycling. Yet, factors that drive structure and function of phyllosphere mycobiomes and their fate in leaf litter are often ignored. We sought to determine the factors contributing to the composition of communities in temperate forest substrates, with culture-independent amplicon sequencing of fungal communities of pre-senescent leaf surfaces, internal tissues, leaf litter, underlying humus soil of co-occurring red maple (Acer rubrum) and shagbark hickory (Carya ovata). Paired samples were taken at five sites within a temperate forest in southern Michigan, USA. Fungal communities were differentiable based on substrate, host species, and site, as well as all two-way and three-way interactions of these variables. PERMANOVA analyses and co-occurrence of taxa indicate that soil communities are unique from both phyllosphere and leaf litter communities. Correspondence of endophyte, epiphyte, and litter communities suggests dispersal plays an important role in structuring fungal communities. Future work will be needed to assess how this dispersal changes microbial community functioning in these niches.
Liber et al. (2022) Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities. PeerJ 10:e12701 https://doi.org/10.7717/peerj.12701
Conservation paleobiology on Minami-Daito Island, Okinawa, Japan: anthropogenic extinction of cave-dwelling bats on a tropical oceanic island
Background With strong environmental and geographic filtration, vertebrates incapable of flying and swimming are often extirpated from island ecosystems. Minami-Daito Island is an oceanic island in Okinawa, Japan that harbors the Daito flying fox (Pteropus dasymallus daitoensis), a subspecies of the fruit bat and the only extant mammal endemic to the island. However, the skeleton of a cave-dwelling bat Rhinolophus sp. and fossil guano were briefly reported in a previous study. Methods Here, we present evidence for the anthropogenic extirpation of two species of cave-dwelling bats (Miniopterus sp. & Rhinolophus sp.) from Minami-Daito Island. Our goal is to reliably constrain the ages of the extirpated bat species by a multiproxy approach. Because skeletal materials did not preserve sufficient bone collagen for direct radiocarbon dating, we alternatively examined guano-like deposits based on SEM observation and Fourier-transform infrared spectroscopy (FTIR) along with stable carbon and nitrogen isotope analyses for possible indirect dating. We also examined stable carbon isotopes in bone apatite, assuming that an isotopic signal of C4 plants on the bat bones links to sugarcane plantation on the island based on the historical knowledge that early human settlers quickly replaced the island’s native C3 forests with sugarcane (C4 perennial grass) plantation from 1900 onward. Results Our cave survey documents the remains of Miniopterus sp. from the island for the first time. Based on the unique taphonomic conditions (unpermineralized bones, disarticulated skeletons closely scattered without sediment cover, various degrees of calcite crystal growth around bones) and a radiocarbon age of a humic sample, we suggest that the maximum age constraint of Miniopterus sp. and Rhinolophus sp. is 4,640 calBP. Based on a series of analyses, we conclude that the guano-like deposits are composed not of bat guano but mainly of humic substances; however, a hydroxyapatite crust associated with bat-lying stalagmites may be derived from bat feces. Stable carbon isotope analysis of bone apatite revealed C4 signals in various degrees, confirming that small populations of cave-dwelling bats persisted on Minami-Daito Island after 1900. Conclusions The results of this study indicate that these populations remained rather small and did not leave many generations and that the estimated ages can be bracketed from 4,640 calBP to the post-1900 (perhaps, until the 1950s). They likely faced a continuously high mortality risk due to severe anthropogenic stresses on the island, where most of the forests were turned into sugarcane plantations within a few decades in the early 20th century. A result of hearing surveys to local residents suggests the latest remnants most likely disappeared on the island concurrently with the introduction of chemical pesticides after World War II.
Kimura et al. (2022) Conservation paleobiology on Minami-Daito Island, Okinawa, Japan: anthropogenic extinction of cave-dwelling bats on a tropical oceanic island. PeerJ 10:e12702 https://doi.org/10.7717/peerj.12702