lncRNA TMEM51-AS1 and RUSC1-AS1 function as ceRNAs for induction of laryngeal squamous cell carcinoma and prediction of prognosis
Background Long non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs) to interact with miRNAs to regulate target genes and promote cancer initiation and progression. The expression of lncRNAs and miRNAs can be epigenetically regulated. The goal of this study was to construct an lncRNA-miRNA-mRNA ceRNA network in laryngeal squamous cell carcinoma (LSCC) and reveal their methylation patterns, which was not investigated previously. Methods Microarray datasets available from the Gene Expression Omnibus database were used to identify differentially expressed lncRNAs (DELs), miRNAs (DEMs), and genes (DEGs) between LSCC and controls, which were then overlapped with differentially methylated regions (DMRs). The ceRNA network was established by screening the interaction relationships between miRNAs and lncRNAs/mRNAs by corresponding databases. TCGA database was used to identify prognostic biomarkers. Results Five DELs (downregulated: TMEM51-AS1, SND1-IT1; upregulated: HCP5, RUSC1-AS1, LINC00324) and no DEMs were overlapped with the DMRs, but only a negative relationship occurred in the expression and methylation level of TMEM51-AS1. Five DELs could interact with 11 DEMs to regulate 242 DEGs, which was used to construct the ceRNA network, including TMEM51-AS1-miR-106b-SNX21/ TRAPPC10, LINC00324/RUSC1-AS1-miR-16-SPRY4/MICAL2/ SLC39A14, RUSC1-AS1-miR-10-SCG5 and RUSC1-AS1-miR-7-ZFP1 ceRNAs axes. Univariate Cox regression analysis showed RUSC1-AS1 and SNX21 were associated with overall survival (OS); LINC00324, miR-7 and ZFP1 correlated with recurrence-free survival (RFS); miR-16, miR-10, SCG5, SPRY4, MICAL2 and SLC39A14 were both OS and RFS-related. Furthermore, TRAPPC10 and SLC39A14 were identified as independent OS prognostic factors by multivariate Cox regression analysis. Conclusion DNA methylation-mediated TMEM51-AS1 and non-methylation-mediated RUSC1-AS1 may function as ceRNAs for induction of LSCC. They and their ceRNA axis genes (particularly TMEM51-AS1-miR-106b-TRAPPC10; RUSC1-AS1-miR-16-SLC39A14) may be potentially important prognostic biomarkers for LSCC.
Hui et al. (2019) lncRNA TMEM51-AS1 and RUSC1-AS1 function as ceRNAs for induction of laryngeal squamous cell carcinoma and prediction of prognosis. PeerJ 7:e7456 https://doi.org/10.7717/peerj.7456
Wedge resection is equal to segmental resection for pulmonary typical carcinoid patients at localized stage: a population-based analysis
Background Medical institutions worldwide have not reached a consensus on what surgery is the most advisable for pulmonary typical carcinoid (TC) patients at the localized stage. This research focuses on exploring whether wedge resection or segmental resection is the superior option. Methods The demographic and clinical information of 1,887 TC patients diagnosed at the localized stage from 2004 to 2015 was collected from the Surveillance, Epidemiology, and End Results (SEER) Program. Patient prognosis was evaluated by KM curves. The chi-square test was used to examine the variation between different groups that would be eliminated by propensity score matching (PSM). Univariate and multivariate Cox proportional hazard model analyses were used to evaluate prognostic values of relative factors. Results The prognosis of TC was the most favorable for patients suffering from pulmonary squamous cell carcinoma (SCC), adenocarcinoma (ADC), and pulmonary carcinoids (PCs). The choice to have surgery, not the type of surgery chosen, was the most significant independent prognostic factor correlated with overall survival (OS) and lung cancer-special survival (LCSS). The prognostic result of the comparison between wedge resection and segmental resection was not statistically significant before or after PSM. In subgroup analysis, the inference still held.
Yan et al. (2019) Wedge resection is equal to segmental resection for pulmonary typical carcinoid patients at localized stage: a population-based analysis. PeerJ 7:e7519 https://doi.org/10.7717/peerj.7519
Oceanographic habitat and the coral microbiomes of urban-impacted reefs
Coral reefs are in decline worldwide. In response to this habitat loss, there are efforts to grow, outplant, and restore corals in many regions. The physical oceanographic habitat of corals—such as sea temperature, waves, ocean currents, and available light—is spatially heterogeneous. We therefore hypothesize that outplant location may affect microbiomes, and ultimately, coral health and restoration success. We evaluated the influence of the physical oceanographic habitat on microbes in wild Porites astreoides and Siderastrea siderea. Tissue samples were collected at four Florida reefs in March, June, and September of 2015. We estimated oceanographic conditions from moored instruments, diver observations, remote sensing data, and numerical models. We analyzed microbiomes using amplicon 16S rRNA high-throughput sequencing data. We found microbial alpha-diversity negatively correlated with in situ sea temperature (which represented both the annual cycle and upwelling), as well as modeled alongshore currents, in situ sea-level, and modeled tide. Microbial beta-diversity correlated positively with significant wave height and alongshore currents from models, remotely-sensed relative turbidity, and in situ temperature. We found that archaea from the order Marine Group II decrease with increases in significant wave height, suggesting that this taxon may be influenced by waves. Also, during times of high wave activity, the relative abundance of bacteria from the order Flavobacteriales increases, which may be due to resuspension and cross-shelf transport of sediments. We also found that bacteria from the order SAR86 increase in relative abundance with increased temperature, which suggests that this taxon may play a role in the coral microbiome during periods of higher temperature. Overall, we find that physical oceanographic variability correlates with the structure of these coral microbiomes in ways that could be significant to coral health.
Rosales et al. (2019) Oceanographic habitat and the coral microbiomes of urban-impacted reefs. PeerJ 7:e7552 https://doi.org/10.7717/peerj.7552
Plant density and life history traits of Aconitum spicatum in North-central Nepal: effects of elevation and anthropogenic disturbances
Increasing cross-border trade of medicinal and aromatic plants (MAPs) has put heavy pressure on a considerable number of species in the Himalayas. One of the threatened species in Nepal is Aconitum spicatum. Unfortunately for this species and for many others, our knowledge on population ecology and performance across the distribution range is insufficient, hindering the formulation of species-specific management plans. We therefore studied density and population structure of A. spicatum and assessed variation in its life history traits among three populations (subalpine, lower alpine and alpine) along an elevation gradient (3,000–4,200 m a.s.l.) in Annapurna Conservation Area, north-central Nepal. The results show that human disturbances and topographic factors contributed to the variation in density and life history traits. The overall density ranged between 0.56 ± 0.09 (Mean ± SE) and 2.48 ± 0.24 plants/m2 with highest mean density in the lower alpine and lowest in the subalpine population. The subalpine population was also characterized by lower investment in reproductive structures with lowest seed mass and low seed viability and fecundity. Among the environmental variables tested, harvesting, animal droppings and fire appeared to be the most important factors affecting density of different life stages of A. spicatum. The prevailing harvesting pattern is destructive as it involves uprooting of the whole plant and this appears to be a main reason for low recruitment and reduced density of the subalpine population. The level of disturbance decreased with increasing elevation. In terms of reproductive effort, the alpine population performed best. Our results indicate that the viability of A. spicatum populations depends on controlling over-harvesting and pre-mature harvesting of tubers and protecting younger life stages from grazing, trampling and fire. We therefore recommend that when formulating management guidelines, measures aiming to mitigate such anthropogenic disturbances should be considered.
Chapagain et al. (2019) Plant density and life history traits of Aconitum spicatum in North-central Nepal: effects of elevation and anthropogenic disturbances. PeerJ 7:e7574 https://doi.org/10.7717/peerj.7574
Technical emptiability of dairy product packaging and its environmental implications in Austria
Background Food waste is a major ecological concern around the globe. While the main function of packaging is to contain and protect food, it may also lead to food waste if residues remain in a package after emptying. Such residues could be attributed to wasteful behavior of consumers, but also to properties of packaging (e.g., geometry, surface tension) and food (e.g., surface tension, viscosity). Methods In this study, the technical emptiability (ability of packaging to be emptied entirely) of 36 dairy products is analyzed. Firstly, the amount of food residues in packaging after emptying at room and refrigerator temperature was weighed and set in relation to the original filling quantity. Secondly, streamlined life cycle assessments (LCAs) based on the Product Environmental Footprint guidance with a functional unit of “one kg of consumed dairy product at room or refrigerator temperature in the home of the consumer” are conducted. Finally, technical emptiability was included in the streamlined LCA and attributed to the primary packaging in order to evaluate its environmental impact. Results Technical emptiability for both temperatures combined was found to be between 0.25% (±0.11) and 5.79% (±0.43) for the analyzed dairy products. While there were differences in emptiability results of the same product and different temperatures, no significant trend (p = 0.94) between emptiability and temperature could be observed. Liquid yogurt, cream, and buttermilk in beverage cartons and plastic bottles yielded the highest amounts, while milk in beverage cartons and glass bottles yielded the lowest amounts regarding food residues. Looking at global warming potential, poor technical emptiability of cream in a beverage carton leads to even higher environmental impacts than the production and waste management of its packaging. Discussion The streamlined LCA results show that food residues can contribute substantially to the footprint of packaging and can have similar or even higher environmental impacts than packaging production and waste management. Yet, emptiability is remarkably under-researched to this day. Future studies should further develop the methods presented in this paper, while LCA analysts should include technical emptiability when assessing the sustainability of packaging, particularly for those containing resource-intensive goods.
Wohner et al. (2019) Technical emptiability of dairy product packaging and its environmental implications in Austria. PeerJ 7:e7578 https://doi.org/10.7717/peerj.7578
Allergic rhinitis, rather than asthma, might be associated with dental caries, periodontitis, and other oral diseases in adults
Background The association between asthma (AS), allergic rhinitis (AR) and oral diseases remains inconclusive in adults. AS and AR often coexist. However, studies that investigate AS, AR together and their association with oral diseases are scarce. Methods Data from 22,898 men and 28,541 women, aged 21 to 25 years, were collected from a national database in Taiwan. Five common oral diseases: dental caries, periodontitis, pulpitis, gingivitis, and stomatitis/aphthae were studied. Differences in the incidence of the five oral diseases in AR vs. non-AR, and AS vs. non-AS groups were compared. The incidence of the five oral diseases in men/ women, urban/country citizen, and high/low income groups was studied. The frequencies of clinical visits and impact of topical steroid use between the groups were also studied. The confounding factors included sex, socioeconomic status, urbanization, dentofacial anomalies, disease of salivary flow, diabetes mellitus, and esophageal reflux. Results The incidence and the frequencies of clinical visits for all five oral diseases were higher in those with AR than in the non-AR group after adjusting for confounding factors and AS. Similar observation was made for the AS group, without adjusting for AR. However, if AR was included for adjustment, no relationship was found between AS and oral diseases. In the AR group, those with higher incomes, and country residents had a high risk of developing oral disease. Intranasal steroids, rather than inhaled steroids, were also associated with oral diseases. Conclusion AR, rather than AS, may be associated with oral diseases in young adults.
Ho et al. (2019) Allergic rhinitis, rather than asthma, might be associated with dental caries, periodontitis, and other oral diseases in adults. PeerJ 7:e7643 https://doi.org/10.7717/peerj.7643
Histological changes of female reproductive organs subjected to different jumping exercise intensities and honey supplementation in rats
Background We assessed histopathological changes of ovaries and uterus in female rats subjected to different jumping exercise intensities combined with honey supplementation at one g/kg body weight/day. Methods A total of 72 rats were divided into six groups, 12 rats in each: control (C), 20 and 80 jumps (20E, 80E), honey (H), and 20 and 80 jump with honey (20EH, 80EH). Results The endometrium was significantly thicker in the rats in H, 20EH and 80EH groups compared to C, 20E, and 80E. The myometrium thickness was significantly lower in 80E and significantly higher in 80EH compared to C, respectively. There was significantly higher myometrium thickness in 20EH and 80EH compared to 20E and 80E and H. The number of glands of the uterus in 20E and 80E was significantly lower than C. However, there was a significantly higher number of glands in H, 20EH, and 80EH compared to 20E and 80E. The numbers of uterus vessels were significantly lower in 80E compared to 20E. However, the numbers of vessels were significantly higher in H, 20EH, and 80EH compared to 80E. The number of ovarian haemorregia was significantly lower in 20E, 80E, H, 20EH, and 80EH compared to C. The number of corpora lutea was significantly lower in 80EH, H, 80E, and 20E compared to C. However, the number of corpora lutea was significantly higher in 20EH compared to J20 and H. Conclusion This study suggested that jumping exercises in particularly high-intensity exercise may induce histopathological changes in uterus and ovary in rats, and honey supplementation may ameliorate these effects.
Mosavat et al. (2019) Histological changes of female reproductive organs subjected to different jumping exercise intensities and honey supplementation in rats. PeerJ 7:e7646 https://doi.org/10.7717/peerj.7646
Rate and success of study replication in ecology and evolution
The recent replication crisis has caused several scientific disciplines to self-reflect on the frequency with which they replicate previously published studies and to assess their success in such endeavours. The rate of replication, however, has yet to be assessed for ecology and evolution. Here, I survey the open-access ecology and evolution literature to determine how often ecologists and evolutionary biologists replicate, or at least claim to replicate, previously published studies. I found that approximately 0.023% of ecology and evolution studies are described by their authors as replications. Two of the 11 original-replication study pairs provided sufficient statistical detail for three effects so as to permit a formal analysis of replication success. Replicating authors correctly concluded that they replicated an original effect in two cases; in the third case, my analysis suggests that the finding by the replicating authors was consistent with the original finding, contrary the conclusion of “replication failure” by the authors.
Kelly (2019) Rate and success of study replication in ecology and evolution. PeerJ 7:e7654 https://doi.org/10.7717/peerj.7654
Diets with and without edible cricket support a similar level of diversity in the gut microbiome of dogs
The gut microbiome plays an important role in the health of dogs. Both beneficial microbes and overall diversity can be modulated by diet. Fermentable sources of fiber in particular often increase the abundance of beneficial microbes. Banded crickets (Gryllodes sigillatus) contain the fermentable polysaccharides chitin and chitosan. In addition, crickets are an environmentally sustainable protein source. Considering crickets as a potential source of both novel protein and novel fiber for dogs, four diets ranging from 0% to 24% cricket content were fed to determine their effects on healthy dogs’ (n = 32) gut microbiomes. Fecal samples were collected serially at 0, 14, and 29 days, and processed using high-throughput sequencing of 16S rRNA gene PCR amplicons. Microbiomes were generally very similar across all diets at both the phylum and genus level, and alpha and beta diversities did not differ between the various diets at 29 days. A total of 12 ASVs (amplicon sequence variants) from nine genera significantly changed in abundance following the addition of cricket, often in a dose-response fashion with increasing amounts of cricket. A net increase was observed in Catenibacterium, Lachnospiraceae [Ruminococcus], and Faecalitalea, whereas Bacteroides, Faecalibacterium, Lachnospiracaeae NK4A136 group and others decreased in abundance. Similar changes in Catenibacterium and Bacteroides have been associated with gut health benefits in other studies. However, the total magnitude of all changes was small and only a few specific taxa changed in abundance. Overall, we found that diets containing cricket supported the same level of gut microbiome diversity as a standard healthy balanced diet. These results support crickets as a potential healthy, novel food ingredient for dogs.
Jarett et al. (2019) Diets with and without edible cricket support a similar level of diversity in the gut microbiome of dogs. PeerJ 7:e7661 https://doi.org/10.7717/peerj.7661
Rituximab increases the risk of hepatitis B virus reactivation in non-Hodgkin lymphoma patients who are hepatitis B surface antigen-positive or have resolved hepatitis B virus infection in a real-world setting: a retrospective study
Background Hepatitis B virus (HBV) reactivation with a hepatitis flare is a common complication in lymphoma patients treated with immunotherapy and/or chemotherapy. Anti-HBV prophylaxis is suggested for non-Hodgkin lymphoma (NHL) patients undergoing rituximab therapy, even those with resolved HBV infection. Since anti-HBV prophylaxis for patients with resolved HBV infection is not covered by national health insurance in Taiwan, a proportion of these patients receive no prophylaxis. In addition, late HBV reactivation has emerged as a new issue in recent reports, and no consensus has been reached for the optimal duration of antiviral prophylaxis. Thus, the aim of our study was to investigate the incidence and outcomes of HBV reactivation in NHL patients in a real-world setting and to study the frequency of late HBV reactivation. Materials Non-Hodgkin lymphoma patients who received rituximab and/or chemotherapy at our institute between January 2011 and December 2015 and who were hepatitis B surface antigen (HBsAg)- or hepatitis B core antibody (HBcAb)-positive were reviewed retrospectively. Results A total of 388 patients were screened between January 2011 and December 2015. In total, 196 patients were excluded because HBsAg was not assessed, HBcAb was negative or not assessed, or they were not treated with immunosuppressive therapy. Finally, the retrospective study included 62 HBsAg-positive NHL patients and 130 NHL patients with resolved HBV infection (HBsAg-negative and HBcAb-positive). During a median 30.5-month follow-up period, seven patients experienced HBV reactivation, five of whom had a hepatitis flare. The incidence of HBV reactivation did not significantly differ between the HBsAg-positive patients and the resolved HBV infection population without anti-HBV prophylaxis (4.8% vs. 3.1%, P = 0.683). All patients with HBV reactivation were exposed to rituximab. Notably, late HBV reactivation was not uncommon (two of seven patients with HBV reactivation events, 28.6%). Hepatitis B virus reactivation did not influence the patients’ overall survival. An age ≥65 years and an advanced disease stage were independent risk factors for poorer overall survival. Conclusion The incidence of HBV reactivation was similar between the HBsAg-positive patients with antiviral prophylaxis and the resolved HBV infection population without anti-HBV prophylaxis. All HBV reactivation events occurred in NHL patients exposed to rituximab. Late reactivation was not uncommon. The duration of regular liver function monitoring for more than 1 year after immunosuppressive therapy or after withdrawal of prophylactic antiviral therapy should be prolonged. Determining the exact optimal duration of anti-HBV prophylaxis is warranted in a future prospective study for NHL patients treated with rituximab-containing therapy.
Tsai et al. (2019) Rituximab increases the risk of hepatitis B virus reactivation in non-Hodgkin lymphoma patients who are hepatitis B surface antigen-positive or have resolved hepatitis B virus infection in a real-world setting: a retrospective study. PeerJ 7:e7481 https://doi.org/10.7717/peerj.7481