title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1286 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Plant density and life history traits of Aconitum spicatum in North-central Nepal: effects of elevation and anthropogenic disturbances link: https://peerj.com/articles/7574 last-modified: 2019-09-10 description: 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. creator: Deep J. Chapagain creator: Henrik Meilby creator: Suresh K. Ghimire uri: https://doi.org/10.7717/peerj.7574 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chapagain et al. title: Technical emptiability of dairy product packaging and its environmental implications in Austria link: https://peerj.com/articles/7578 last-modified: 2019-09-10 description: BackgroundFood 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).MethodsIn 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.ResultsTechnical 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.DiscussionThe 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. creator: Bernhard Wohner creator: Nicole Schwarzinger creator: Ulla Gürlich creator: Victoria Heinrich creator: Manfred Tacker uri: https://doi.org/10.7717/peerj.7578 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wohner et al. title: Allergic rhinitis, rather than asthma, might be associated with dental caries, periodontitis, and other oral diseases in adults link: https://peerj.com/articles/7643 last-modified: 2019-09-10 description: BackgroundThe 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.MethodsData 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.ResultsThe 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.ConclusionAR, rather than AS, may be associated with oral diseases in young adults. creator: Sai-Wai Ho creator: Ko-Huang Lue creator: Min-Sho Ku uri: https://doi.org/10.7717/peerj.7643 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ho et al. title: Histological changes of female reproductive organs subjected to different jumping exercise intensities and honey supplementation in rats link: https://peerj.com/articles/7646 last-modified: 2019-09-10 description: BackgroundWe 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.MethodsA 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).ResultsThe 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.ConclusionThis 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. creator: Maryam Mosavat creator: Mahaneem Mohamed creator: Foong Kiew Ooi creator: Mitra Mirsanjari creator: Anani Aila Mat Zin creator: Aminah Che Romli uri: https://doi.org/10.7717/peerj.7646 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mosavat et al. title: Rate and success of study replication in ecology and evolution link: https://peerj.com/articles/7654 last-modified: 2019-09-10 description: 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. creator: Clint D. Kelly uri: https://doi.org/10.7717/peerj.7654 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kelly title: Diets with and without edible cricket support a similar level of diversity in the gut microbiome of dogs link: https://peerj.com/articles/7661 last-modified: 2019-09-10 description: 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. creator: Jessica K. Jarett creator: Anne Carlson creator: Mariana Rossoni Serao creator: Jessica Strickland creator: Laurie Serfilippi creator: Holly H. Ganz uri: https://doi.org/10.7717/peerj.7661 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jarett et al. title: 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 link: https://peerj.com/articles/7481 last-modified: 2019-09-09 description: BackgroundHepatitis 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.MaterialsNon-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.ResultsA 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.ConclusionThe 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. creator: Yu-Fen Tsai creator: Ching-I Yang creator: Jeng-Shiun Du creator: Ming-Hui Lin creator: Shih-Hao Tang creator: Hui-Ching Wang creator: Shih-Feng Cho creator: Yi-Chang Liu creator: Yu-Chieh Su creator: Chia-Yen Dai creator: Hui-Hua Hsiao uri: https://doi.org/10.7717/peerj.7481 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tsai et al. title: Characterization of ceRNA network to reveal potential prognostic biomarkers in triple-negative breast cancer link: https://peerj.com/articles/7522 last-modified: 2019-09-09 description: Triple-negative breast cancer (TNBC) is a particular subtype of breast malignant tumor with poorer prognosis than other molecular subtypes. Previous studies have demonstrated that some abnormal expression of non-coding RNAs including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) were closely related to tumor cell proliferation, apoptosis, invasion, migration and drug sensitivity. However, the role of non-coding RNAs in the pathogenesis of TNBC is still unclear. In order to characterize the molecular mechanism of non-coding RNAs in TNBC, we downloaded RNA data and miRNA data from the cancer genome atlas database. We successfully identified 686 message RNAs (mRNAs), 26 miRNAs and 50 lncRNAs as key molecules for high risk of TNBC. Then, we hypothesized that the lncRNA–miRNA–mRNA regulatory axis positively correlates with TNBC and constructed a competitive endogenous RNA (ceRNA) network of TNBC. Our series of analyses has shown that five molecules (TERT, TRIML2, PHBP4, mir-1-3p, mir-133a-3p) were significantly associated with the prognosis of TNBC, and there is a prognostic ceRNA sub-network between those molecules. We mapped the Kaplan–Meier curve of RNA on the sub-network and also suggested that the expression level of the selected RNA is related to the survival rate of breast cancer. Reverse transcription-quantitative polymerase chain reaction showed that the expression level of TRIML2 in TNBC cells was higher than normal. In general, our findings have implications for predicting metastasis, predicting prognosis and discovering new therapeutic targets for TNBC. creator: Xiang Song creator: Chao Zhang creator: Zhaoyun Liu creator: Qi Liu creator: Kewen He creator: Zhiyong Yu uri: https://doi.org/10.7717/peerj.7522 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Song et al. title: The new ichthyosauriform Chaohusaurus brevifemoralis (Reptilia, Ichthyosauromorpha) from Majiashan, Chaohu, Anhui Province, China link: https://peerj.com/articles/7561 last-modified: 2019-09-09 description: A new species of ichthyosauriform is recognized based on 20 specimens, including nearly complete skeletons, and named Chaohusaurus brevifemoralis. A part of the specimens was previously identified as Chaohusaurus chaoxianensis and is herein reassigned to the new species. The new species differs from existing species of Chaohusaurus in a suite of features, such as the bifurcation of the caudal peak neural spine and a short femur relative to trunk length. The specimens include both complete and partially disarticulated skulls, allowing rigorous scrutiny of cranial sutures. For example, the squamosal does not participate in the margin of the upper temporal fenestra despite previous interpretations. Also, the frontal unequivocally forms a part of the anterior margin of the upper temporal fenestra, forming the most medial part of the anterior terrace. The skull of the holotype largely retains three-dimensionality with the scleral rings approximately in situ, revealing that the eyeball was uncovered in two different directions, that is, laterally and slightly dorsally through the main part of the orbit, and dorsally through the medial extension of the orbit into the skull roof. This skull construction is likely a basal feature of Ichthyosauromorpha. Phylogenetic analyses place the new species as a sister taxon of Chaohusaurus chaoxianensis. creator: Jian-dong Huang creator: Ryosuke Motani creator: Da-yong Jiang creator: Andrea Tintori creator: Olivier Rieppel creator: Min Zhou creator: Xin-Xin Ren creator: Rong Zhang uri: https://doi.org/10.7717/peerj.7561 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Huang et al. title: Correlation between 18F-FDG maximum standardized uptake value with CD147 expression in lung adenocarcinomas: a retrospective study link: https://peerj.com/articles/7635 last-modified: 2019-09-09 description: BackgroundThe pro-tumoral action of the cluster of differentiation 147 (CD147), which is associated with the chemotherapy resistance of lung adenocarcinoma, is partly due to accelerated tumor cell glycolysis. 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) metabolic parameters included maximal standardized uptake value (SUVmax), mean standardized uptake value (SUVmean), metabolic tumor volume (MTV), and total lesion glycolysis (TLG), which are non-invasive markers of the glucose metabolism of tumor cells in vivo. This study aimed to clarify the correlation between PET metabolic parameters and CD147 expression, and to evaluate the prognostic value of CD147 expression in resectable lung adenocarcinoma patients.MethodsA total of 89 lung adenocarcinoma chemotherapy-naive patients who underwent 18F-fluorodeoxyglucose positron emission tomography and computerized tomography scan before pulmonary surgery were retrospectively analyzed. The PET metabolic parameters were calculated by 18F-FDG PET imaging, and CD147 expression was analyzed by immunohistochemistry. SUVmax, SUVmean, MTV, and TLG compared for their performance in predicting the expression of CD147 were illustrated with statistical analysis. All patients were then followed-up for survival analysis.ResultsThe SUVmax was significantly correlated with the CD147 expression and was the primary predictor for the CD147 expression of lung adenocarcinoma. A cut-off value of the SUVmax, 9.77 allowed 85.1% sensitivity and 64.3% specificity for predicting the CD147 positive lung adenocarcinoma. CD147 expression was correlated with tumor differentiation and metastasis. Univariate survival analysis showed that CD147 expression was significantly associated with a shorter overall survival (OS) time. Multivariate analysis revealed that CD147 was an independent prognostic factor of lung adenocarcinoma patients.ConclusionThe SUVmax of a primary tumor measured with 18F-FDG PET may be a simple and non-invasive marker for predicting CD147 expression in lung adenocarcinoma. CD147 is an independent prognostic factor related to OS of postoperative lung adenocarcinoma patients. creator: Fei Guo creator: Xueyan Li creator: Guodong Yao creator: Guangchun Zeng creator: Lijuan Yu uri: https://doi.org/10.7717/peerj.7635 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Guo et al.