title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2022-07 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Fighting ability, personality and melanin signalling in free-living Eurasian tree sparrows (Passer montanus) link: https://peerj.com/articles/13660 last-modified: 2022-07-29 description: BackgroundIndividuals’ access to resources is often decided during dyadic contests the outcome of which is determined by the fighting (or competitive) ability of the participants. Individuals’ fighting ability (termed also as resource-holding power or potential, RHP) is usually associated with individual features (e.g., sex, age, body size) and is also frequently signalled through various ornaments like the black throat patch (bib) in many birds. Individual personality is a behavioural attribute often linked to fighting ability as well. Based on earlier studies, however, the relationship between personality and fighting ability is far from being straightforward. While accounting for sex and body size, we studied whether exploratory behaviour, an aspect of personality, predicts fighting ability when competing for food during winter in free-living Eurasian tree sparrows (Passer montanus). We also investigated whether the bib can serve as a potential indicator of individual competitiveness in this species.MethodsWe captured adult tree sparrows, marked them with a unique combination of colour rings, and collected data about the individuals’ sex, body size, bib size and exploratory behaviour. Birds were then released and the agonistic behaviour of the marked individuals was recorded while foraging in groups on bird feeding platforms.ResultsThe probability of winning a fight, a proxy for fighting ability of individuals, was not related to exploratory behaviour, in either of the sexes. However, bib size was positively related to probability of winning in females, but not in males. Body size was not associated with probability of winning neither in males, nor in females.ConclusionsOur results suggest that, at least in tree sparrows, the outcome of dyadic encounters over food during the non-breeding period are not determined by the exploratory personality of individuals. However, our findings provide further support for a status signalling role of the black bib in tree sparrows, and hint for the first time that bib size might function as a status signal in females as well. Finally, our results do not confirm that body size could serve as an indicator of fighting ability (i.e., RHP) in this species. creator: Attila Fülöp creator: Zoltán Németh creator: Bianka Kocsis creator: Bettina Deák-Molnár creator: Tímea Bozsoky creator: Gabriella Kőmüves creator: Zoltán Barta uri: https://doi.org/10.7717/peerj.13660 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Fülöp et al. title: Blood glucose, insulin and glycogen profiles in Sprague-Dawley rats co-infected with Plasmodium berghei ANKA and Trichinella zimbabwensis link: https://peerj.com/articles/13713 last-modified: 2022-07-29 description: BackgroundPlasmodium falciparum and tissue dwelling helminth parasites are endemic in sub-Saharan Africa (SSA). The geographical overlap in co-infection is a common phenomenon. However, there is continued paucity of information on how the co-infection influence the blood glucose and insulin profiles in the infected host. Animal models are ideal to elucidate effects of co-infection on disease outcomes and hence, blood glucose, insulin and glycogen profiles were assessed in Sprague-Dawley rats co-infected with P. berghei ANKA (Pb) and Trichinella zimbabwensis (Tz), a tissue-dwelling nematode.MethodsOne-hundred-and-sixty-eight male Sprague-Dawley rats (weight range 90–150 g) were randomly divided into four separate experimental groups: Control (n = 42), Pb-infected (n = 42), Tz-infected (n = 42) and Pb- + Tz-infected group (n = 42). Measurement of Pb parasitaemia was done daily throughout the experimental study period for the Pb and the Pb + Tz group. Blood glucose was recorded every third day in all experimental groups throughout the experimental study period. Liver and skeletal muscle samples were harvested, snap frozen for determination of glycogen concentration.ResultsResults showed that Tz mono-infection and Tz + Pb co-infection did not have blood glucose lowering effect in the host as expected. This points to other possible mechanisms through which tissue-dwelling parasites up-regulate the glucose store without decreasing the blood glucose concentration as exhibited by the absence of hypoglycaemia in Tz + Pb co-infection group. Hypoinsulinemia and an increase in liver glycogen content was observed in Tz mono-infection and Tz + Pb co-infection groups of which the triggering mechanism remains unclear.ConclusionsTo get more insights into how glucose, insulin and glycogen profiles are affected during plasmodium-helminths co-infections, further studies are recommended where other tissue-dwelling helminths such as Taenia taeniformis which has strobilocercus as the metacestode in the liver to mimic infections such as hydatid disease in humans are used. creator: Pretty Murambiwa creator: Achasih Quinta Nkemzi creator: Samson Mukaratirwa uri: https://doi.org/10.7717/peerj.13713 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Murambiwa et al. title: Screening of ferroptosis-related genes in sepsis-induced liver failure and analysis of immune correlation link: https://peerj.com/articles/13757 last-modified: 2022-07-29 description: PurposeSepsis-induced liver failure is a kind of liver injury with a high mortality, and ferroptosis plays a key role in this disease. Our research aims to screen ferroptosis-related genes in sepsis-induced liver failure as targeted therapy for patients with liver failure.MethodsUsing the limma software, we analyzed the differentially expressed genes (DEGs) in the GSE60088 dataset downloaded from the Gene Expression Omnibus (GEO) database. Clusterprofiler was applied for enrichment analysis of DEGs enrichment function. Then, the ferroptosis-related genes of the mice in the FerrDb database were crossed with DEGs. Sepsis mice model were prepared by cecal ligation and perforation (CLP). ALT and AST in the serum of mice were measured using detection kit. The pathological changes of the liver tissues in mice were observed by hematoxylin-eosin (H & E) staining. We detected the apoptosis of mice liver tissues using TUNEL. The expression of Hmox1, Epas1, Sirt1, Slc3a2, Jun, Plin2 and Zfp36 were detected by qRT-PCR.ResultsDEGs analysis showed 136 up-regulated and 45 down-regulated DEGs. Meanwhile, we found that the up-regulated DEGs were enriched in pathways including the cytokine biosynthesis process while the down-regulated DEGs were enriched in pathways such as organic hydroxy compound metabolic process. In this study, seven genes (Hmox1, Epas1, Sirt1, Slc3a2, Jun, Plin2 and Zfp36) were obtained through the intersection of FerrDb database and DEGs. However, immune infiltration analysis revealed that ferroptosis-related genes may promote the development of liver failure through B cells and natural killer (NK) cells. Finally, it was confirmed by the construction of septic liver failure mice model that ferroptosis-related genes of Hmox1, Slc3a2, Jun and Zfp36 were significantly correlated with liver failure and were highly expressed.ConclusionThe identification of ferroptosis-related genes Hmox1, Slc3a2, Jun and Zfp36 in the present study contribute to our understanding of the molecular mechanism of sepsis-induced liver failure, and provide candidate targets for the diagnosis and treatment of the disease. creator: Qingli Chen creator: Luxiang Liu creator: Shuangling Ni uri: https://doi.org/10.7717/peerj.13757 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: LncRNA/miRNA/mRNA ceRNA network analysis in spinal cord injury rat with physical exercise therapy link: https://peerj.com/articles/13783 last-modified: 2022-07-29 description: Noncoding RNAs have been implicated in the pathophysiology of spinal cord injury (SCI), including cell death, glial scar formation, axonal collapse and demyelination, and inflammation. The evidence suggests that exercise therapy is just as effective as medical treatment in SCI. However, studies of competing endogenous RNA (ceRNA)-mediated regulation mechanisms in the therapy of SCI with exercise are rare. The focus of this research was to investigate the effect of exercise therapy on the expression levels of long noncoding RNA (lncRNA), microRNA (miRNA), and mRNA in rats with SCI. The RNA-seq technology has been used to examine the differentially expressed circRNAs (DECs), lncRNAs (DELs), miRNAs (DEMs), and genes (DEGs) between SCI and exercise therapy rats. The ceRNA network was established using interactions between miRNAs and mRNAs, as well as between miRNAs and lncRNAs/circRNAs. The Database for Annotation, Visualization, and Integrated Discovery was used to anticipate the underlying functions of mRNAs. Our current study identified 76 DELs, 33 DEMs, and 30 DEGs between groups of SCI rats and exercise therapy rats. Subsequently, these newly discovered ceRNA interaction axes could be important targets for the exercise treatment of SCI. creator: Jiahuan Wu creator: Xiangzhe Li creator: Qinghua Wang creator: Sheng Wang creator: Wenhua He creator: Qinfeng Wu creator: Chuanming Dong uri: https://doi.org/10.7717/peerj.13783 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wu et al. title: Algae from Aiptasia egesta are robust representations of Symbiodiniaceae in the free-living state link: https://peerj.com/articles/13796 last-modified: 2022-07-29 description: Many cnidarians rely on their dinoflagellate partners from the family Symbiodiniaceae for their ecological success. Symbiotic species of Symbiodiniaceae have two distinct life stages: inside the host, in hospite, and outside the host, ex hospite. Several aspects of cnidarian-algal symbiosis can be understood by comparing these two life stages. Most commonly, algae in culture are used in comparative studies to represent the ex hospite life stage, however, nutrition becomes a confounding variable for this comparison because algal culture media is nutrient rich, while algae in hospite are sampled from hosts maintained in oligotrophic seawater. In contrast to cultured algae, expelled algae may be a more robust representation of the ex hospite state, as the host and expelled algae are in the same seawater environment, removing differences in culture media as a confounding variable. Here, we studied the physiology of algae released from the sea anemone Exaiptasia diaphana (commonly called Aiptasia), a model system for the study of coral-algal symbiosis. In Aiptasia, algae are released in distinct pellets, referred to as egesta, and we explored its potential as an experimental system to represent Symbiodiniaceae in the ex hospite state. Observation under confocal and differential interference contrast microscopy revealed that egesta contained discharged nematocysts, host tissue, and were populated by a diversity of microbes, including protists and cyanobacteria. Further experiments revealed that egesta were released at night. In addition, algae in egesta had a higher mitotic index than algae in hospite, were photosynthetically viable for at least 48 hrs after expulsion, and could competently establish symbiosis with aposymbiotic Aiptasia. We then studied the gene expression of nutrient-related genes and studied their expression using qPCR. From the genes tested, we found that algae from egesta closely mirrored gene expression profiles of algae in hospite and were dissimilar to those of cultured algae, suggesting that algae from egesta are in a nutritional environment that is similar to their in hospite counterparts. Altogether, evidence is provided that algae from Aiptasia egesta are a robust representation of Symbiodiniaceae in the ex hospite state and their use in experiments can improve our understanding of cnidarian-algal symbiosis. creator: Shumpei Maruyama creator: Julia R. Unsworth creator: Valeri Sawiccy creator: Virginia M. Weis uri: https://doi.org/10.7717/peerj.13796 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Maruyama et al. title: Baseline scenarios of heat-related ambulance transportations under climate change in Tokyo, Japan link: https://peerj.com/articles/13838 last-modified: 2022-07-29 description: BackgroundPredictive scenarios of heatstroke over the long-term future have yet to be formulated. The purpose of the present study was to generate baseline scenarios of heat-related ambulance transportations using climate change scenario datasets in Tokyo, Japan.MethodsData on the number of heat-related ambulance transportations in Tokyo from 2015 to 2019 were examined, and the relationship between the risk of heat-related ambulance transportations and the daily maximum wet-bulb globe temperature (WBGT) was modeled using three simple dose–response models. To quantify the risk of heatstroke, future climatological variables were then retrieved to compute the WBGT up to the year 2100 from climate change scenarios (i.e., RCP2.6, RCP4.5, and RCP8.5) using two scenario models. The predicted risk of heat-related ambulance transportations was embedded onto the future age-specific projected population.ResultsThe proportion of the number of days with a WBGT above 28°C is predicted to increase every five years by 0.16% for RCP2.6, 0.31% for RCP4.5, and 0.68% for RCP8.5. In 2100, compared with 2000, the number of heat-related ambulance transportations is predicted to be more than three times greater among people aged 0–64 years and six times greater among people aged 65 years or older. The variance of the heatstroke risk becomes greater as the WBGT increases.ConclusionsThe increased risk of heatstroke for the long-term future was demonstrated using a simple statistical approach. Even with the RCP2.6 scenario, with the mildest impact of global warming, the risk of heatstroke is expected to increase. The future course of heatstroke predicted by our approach acts as a baseline for future studies. creator: Marie Fujimoto creator: Hiroshi Nishiura uri: https://doi.org/10.7717/peerj.13838 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Fujimoto and Nishiura title: Drug resistant Mycobacterium tuberculosis in Oman: resistance-conferring mutations and lineage diversity link: https://peerj.com/articles/13645 last-modified: 2022-07-28 description: BackgroundThe Sultanate of Oman is country a low TB-incidence, with less than seven cases per 105 population detected in 2020. Recent years have witnessed a persistence in TB cases, with sustained incidence rate among expatriates and limited reduction among Omanis. This pattern suggests transmission from the migrant population. The present study examined the genetic profile and drug resistance-conferring mutations in Mycobacterium tuberculosis collected from Omanis and expatriates to recognise possible causes of disease transmission.MethodsWe examined M. tuberculosis cultured positive samples, collected from Omanis (n = 1,344) and expatriates (n = 1,203) between 2009 and 2018. These isolates had a known in vitro susceptibility profile to first line anti-TB, Streptomycin (SM), Isoniazid (INH), Rifampicin (RIF), Ethambutol (EMB) and Pyrazinamide (PZA). The diversity of the isolates was assessed by spacer oligo-typing (spoligotyping). Drug resistance-conferring mutations resulted from full-length sequence of nine genes (katG, inhA, ahpc, rpoB, rpsL, rrs, embB, embC, pncA) and their phenotypic relationship were analysed.ResultsIn total, 341/2192 (13.4%), M. tuberculosis strains showed resistance to any drug, comprising mono-resistance (MR) (242, 71%), poly-resistance (PR) (40, 11.7%) and multi-drug resistance (MDR) (59, 17.3%). The overall rate of resistance among Omanis and expatriates was similar; however, MDR and PZAR were significantly higher among Omanis, while INHR was greater among expatriates. Mutations rpsL K43R and rpoB S450L were linked to Streptomycin (SMR) and Rifampicin resistance (RIFR) respectively. Whereas, katG S315T and inhA –C15T/G–17T were associated with Isoniazid resistance (INHR). The resistance patterns (mono-resistant, poly-resistant and MDR) and drug resistance-conferring mutations were found in different spoligo-lineages. rpsL K43R, katG S315T and rpoB S450L mutations were significantly higher in Beijing strains.ConclusionsDiverse drug resistant M. tuberculosis strains exist in Oman, with drug resistance-conferring mutations widespread in multiple spoligo-lineages, indicative of a large resistance reservoir. Beijing’s M. tuberculosis lineage was associated with MDR, and multiple drug resistance-conferring mutations, favouring the hypothesis of migration as a possible source of resistant lineages in Oman. creator: Sara Al Mahrouqi creator: Amal Gadalla creator: Saleh Al Azri creator: Salama Al-Hamidhi creator: Amina Al-Jardani creator: Abdullah Balkhair creator: Amira Al-fahdi creator: Laila Al Balushi creator: Samiya Al Zadjali creator: Asmahan Mohammed Nasser Al Marhoubi creator: Hamza A. Babiker uri: https://doi.org/10.7717/peerj.13645 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Al Mahrouqi et al. title: Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea link: https://peerj.com/articles/13730 last-modified: 2022-07-28 description: Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-SerAGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-SerAGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea. creator: Shao’e Sun creator: Ning Xiao creator: Zhongli Sha uri: https://doi.org/10.7717/peerj.13730 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sun et al. title: Fuel trait effects on flammability of native and invasive alien shrubs in coastal fynbos and thicket (Cape Floristic Region) link: https://peerj.com/articles/13765 last-modified: 2022-07-28 description: In June 2017, extreme fires along the southern Cape coast of South Africa burnt native fynbos and thicket vegetation and caused extensive damage to plantations and residential properties. Invasive alien plants (IAPs) occur commonly in the area and were thought to have changed the behaviour of these fires through their modification of fuel properties relative to that of native vegetation. This study experimentally compared various measures of flammability across groups of native and alien invasive shrub species in relation to their fuel traits. Live plant shoots of 30 species (10 species each of native fynbos, native thicket, and IAPs) were sampled to measure live fuel moisture, dry biomass, fuel bed porosity and the proportions of fine-, coarse- and dead fuels. These shoots were burnt experimentally, and flammability measured in terms of maximum temperature (combustibility), completeness of burn (consumability), and time-to-ignition (ignitability). Multiple regression models were used to assess the relationships between flammability responses and fuel traits, while the Kruskal-Wallis H test was used to establish if differences existed in flammability measures and fuel traits among the vegetation groups. Dry biomass significantly enhanced, while live fuel moisture significantly reduced, maximum temperature, whereas the proportion of fine fuels significantly increased completeness of burn. Unlike other similar studies, the proportion of dead fuels and fuel bed porosity were not retained by any of the models to account for variation in flammability. Species of fynbos and IAPs generally exhibited greater flammability in the form of higher completeness of burn and more rapid ignition than species of thicket. Little distinction in flammability and fuel traits could be made between species of fynbos and IAPs, except that fynbos species had a greater proportion of fine fuels. Thicket species had higher proportions of coarse fuels and greater dry biomass (~fuel loading) than species of fynbos and IAPs. Live fuel moisture did not differ among the vegetation groups, contrary to the literature often ascribing variation in flammability to fuel moisture differences. The fuel traits investigated only explained 21–53% of the variation in flammability and large variation was evident among species within vegetation groups suggesting that species-specific and in situ community-level investigations are warranted, particularly in regard fuel moisture and chemical contents. creator: Tineke Kraaij creator: Samukelisiwe T. Msweli creator: Alastair J. Potts uri: https://doi.org/10.7717/peerj.13765 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kraaij et al. title: Autotoxicity effect of water extracts from rhizosphere soil of Elymus sibiricus in different planting years on seed germination, physiological characteristics and phytohormones of seedlings link: https://peerj.com/articles/13768 last-modified: 2022-07-28 description: Elymus sibiricus is a highly valuable perennial forage that is widely planted in the Qinghai-Tibet Plateau (QTP) region. However, E. sibiricus artificial grasslands have a short utilization lifespan, and reach the highest yield in the 2nd and 3rd year of plantation, then rapidly drop its productivity. We hypothesized that autotoxicity is one of the mechanisms for the reduction of the productivity. To test this hypothesis, we prepared the water extract from rhizosphere soils of E. sibiricus planted for 3, 4, 5, and 8 years and examined the effects of the extract concentrations at 0.05, 0.1, 0.2, and 0.5 g/mL on seed germination, seedling growth, physiological characteristics and phytohormones in the aboveground and roots of E. sibiricus. The results showed that the soil extract concentration, planting years, and their interaction had significant influences on the most of these indices. The soil extract inhibited the seed germination and growth of seedlings, and the inhibitory effects appeared to be stronger at the 0.5 g/mL rhizosphere soil extract for 5 and 8 years. The superoxide dismultase and peroxide activities, the free proline concentration, soluble sugar concentration were altered. The malondialdehyde concentration was, in general, increased, especially in 8 years soil extract. The indole acetic acid and gibberellic acids concentrations were lowered, while the abscisic acid concentration varied. These changes were depending on the extract concentration and the years of planting, without clear patterns in some of them in response to the extract concentration and planting years. In summary, autotoxicity can be a contributor to the retardation of the growth and development of artificial E. sibiricus grasslands. The inhibitory effects could be attribute to impaired antioxidant capacity and disturbance of osmortic-regulatory substances and plant hormones, and are more profound on the root than on the aboveground part of the seedlings. creator: Hang Yang creator: Jinglong Su creator: Juan Qi uri: https://doi.org/10.7717/peerj.13768 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: Maize-peanut rotational strip intercropping improves peanut growth and soil properties by optimizing microbial community diversity link: https://peerj.com/articles/13777 last-modified: 2022-07-28 description: Rotational strip intercropping (RSI) of cereals and legumes has been developed and widely carried out to alleviate continuous cropping obstacles, to control erosion and to improve field use efficiency. In this study, a four-year fixed-field experiment was carried out in northeast China with three treatments: continuous cropping of maize, continuous cropping of peanuts and rotational strip intercropping of maize and peanut. The results show that crop rotation improved the main-stem height, branch number, lateral branch length, and yield and quality of peanuts; the yield was the highest in 2018, when it was increased by 39.5%. RSI improved the contents of total N, available N, total P, available P, total K and available K; the content of available N was the highest in 2018, with an increase of 70%. Rhizosphere soil urease and catalase activities were significantly increased and were the highest in 2017, reaching 183.13% and 91.21%, respectively. According to a high-throughput sequencing analysis, the rhizosphere soil bacterial richness and specific OTUs decreased in peanut rhizosphere soil, while the fungal increased. There were differences in the bacterial and fungal community structures; specifically, the abundance of Acidobacteria and Planctomycetes increased among bacteria and the abundance of beneficial microorganisms such as Ascomycota increased among fungi. In conclusion, rotational strip intercropping of maize and peanut increased the yield and quality of peanuts and conducive to alleviating the obstacles facing the continuous cropping of peanuts. Among then, soil physicochemical properties, enzyme activity and microbial diversity were significantly affected the yield of peanut. creator: Yi Han creator: Qiqi Dong creator: Kezhao Zhang creator: Dejian Sha creator: Chunji Jiang creator: Xu Yang creator: Xibo Liu creator: He Zhang creator: Xiaoguang Wang creator: Feng Guo creator: Zheng Zhang creator: Shubo Wan creator: Xinhua Zhao creator: Haiqiu Yu uri: https://doi.org/10.7717/peerj.13777 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Han et al. title: Quality of care and prescription patterns among patients with diabetic kidney disease—a large-scale cohort study from Taiwanese clinics link: https://peerj.com/articles/13636 last-modified: 2022-07-27 description: AimsTo investigate the quality of care and prescription patterns of patients with diabetic kidney disease (DKD) receiving primary care at local clinics in Taiwan.MethodsA retrospective chart review was conducted in 43 primary care clinics in Taiwan. The patients’ baseline characteristics, laboratory tests, presence of complications and antidiabetic agents prescribed were analyzed.Results7,200 patients with type 2 diabetes mellitus were enrolled. Percentage of HbA1c, blood pressure (BP), and low density lipoprotein cholesterol (LDL-C) goals reached were 52.5% in HbA1c < 7%, 40.9% in BP < 130/80 mmHg and 79.7% in LDL-C < 2.59 mmol/L. 18.3% achieved all three ABC goals. However, patients with DKD had a lower rate of ABC goal attainment and higher rate of complications. Among DKD patients with eGFR ≥ 30 ml/min/1.73 m2 and on monotherapy, metformin was most frequently prescribed. As for dual therapy, the most common combinations were metformin with sulfonylurea and metformin with DPP-4 inhibitors.ConclusionsDiabetes patients in Taiwan receiving primary diabetes care at local clinics had generally satisfactory management performance. However, more aggressive HbA1c, BP, and LDL-C management among DKD patients should be emphasized. Contrary to current recommendations, SGLT-2 inhibitors and GLP-1 receptor agonists as frontline therapy were under-prescribed. creator: Kun-Yuan Tsai creator: Samuel Chen creator: Chien-Wen Chou creator: Thing-Fong Tzeng creator: Yau-Jiunn Lee creator: Min-ling Chen uri: https://doi.org/10.7717/peerj.13636 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Tsai et al. title: Spatial variation in diatom abundance and composition in Biwase Bay and Hamanaka Bay (Eastern Hokkaido, Japan), with reference to environmental features link: https://peerj.com/articles/13705 last-modified: 2022-07-27 description: This study aims to examine the spatial variation of diatom abundance and composition along the nearshore areas of Biwase Bay and Hamanaka Bay, eastern Hokkaido. Terrestrial input via Kiritappu Wetland is expected to affect variation and composition differently depending on the position of the two bays. We conducted an oceanographic survey in June 2014 to measure seawater temperature, salinity, colored dissolved organic matter (CDOM) absorption, nutrient concentrations, and total and size-fractionated chlorophyll (Chl) a concentration at 11 stations of the shallowest (<5 m) parts of the bays. These were grouped into four areas (Areas 1 and 2 in Biwase Bay, and Areas 3 and 4 in Hamanaka Bay) based on the distance of the location from the wetland outlet (nearest in Area 1 to the farthest in Area 4). Diatoms are the major primary producers in the water column. Therefore, we also determined genus level cell abundance and diversity of diatoms to compare similarity among areas. Sea surface temperature was the lowest at Area 4, whereas sea surface salinity was the lowest at Area 1. The contribution of CDOM absorption, an indicator of wetland-influenced river discharge, and silica concentration was highest at Area 1. Total amount of nitrite and nitrate concentrations was the highest at Area 4. Total amount of Chl a concentration was also lowest in Area 1. Our size-fractionated Chl a results revealed that while the size composition of phytoplankton varied among areas, micro-sized (>10 µm) phytoplankton were predominant in Area 4. Finally, diatom composition at the genus level differed greatly among areas. Pennate diatoms were predominant in Areas 1 and 2, but centric diatoms dominated in Areas 3 and 4. Our results suggested great spatial variability in oceanographic conditions among areas, with less influence of wetland and more influence of Coastal Oyashio Water based on distance from the wetland outlet. Diatom composition showed geographical division between Biwase and Hamanaka Bays. creator: Hyojin Ahn creator: Miho Ito creator: Naoko Kouchi creator: Kentaro Watanabe creator: Hiroya Abe creator: Tomonori Isada creator: Masahiro Nakaoka uri: https://doi.org/10.7717/peerj.13705 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ahn et al. title: Postoperative pain intensity and incidence following single visit root canal treatment with different obturation techniques: a randomized clinical trial link: https://peerj.com/articles/13756 last-modified: 2022-07-27 description: BackgroundThere are few studies in the literature about the effect of obturation techniques on postoperative pain. Besides, GuttaFlow2 was used for the first time in this study regarding postoperative pain. This study aimed to compare the postoperative pain levels and incidence following single-visit root canal treatment with different canal filling techniques; cold lateral compaction (CLC), thermoplasticised solid-core carrier (GuttaCore) based filling and cold free-flow compaction (GuttaFlow2) technique.MethodsThe patients (n = 93) having single-rooted teeth with a single canal diagnosed with asymptomatic irreversible pulpitis or single-rooted vital teeth with a single canal requiring endodontic treatment because of prosthetic reasons were enrolled in this study. Patients were randomized into three groups (n = 31) according to the obturation technique. A single operator performed all the treatments in a single visit. Data on obturation levels, postoperative pain and analgesic intake frequency were recorded at postoperative 6, 12 and 24 h and daily afterward until the 7th day. Postoperative pain was measured by visual analogue scale (VAS). The date were statistically analyzed with chi-squared tests (for the analyses of the categorical data), the nonparametric Kruskal-Wallis test (for the comparisons of VAS score) and with the Friedman test (for the assessments of the changes in VAS scores over time).ResultsThe GuttaCore group recorded the higher pain levels, except first 12 h, on the other hand, the GuttaFlow2 group recorded the lower pain levels at all time periods. Significant differences occurred among the groups during the first 4 days (p < 0.05), except at 12 h (p = 0.054). The patients in the CLC and GuttaFlow2 groups did not need to use the prescribed analgesic; however, one patient in the GuttaCore group used it once.ConclusionsPostoperative pain levels following root canal therapy were affected by the obturation technique especially first 4 days following obturation. creator: Aliye Koçer creator: Hicran Dönmez Özkan creator: Tugba Turk uri: https://doi.org/10.7717/peerj.13756 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Koçer et al. title: Effects of bone morphogenetic protein 4 on TGF-β1-induced cell proliferation, apoptosis, activation and differentiation in mouse lung fibroblasts via ERK/p38 MAPK signaling pathway link: https://peerj.com/articles/13775 last-modified: 2022-07-27 description: Fibroblasts, in particular myofibroblasts, are the critical effector cells in idiopathic pulmonary fibrosis (IPF), a deadly lung disease characterized by abnormal lung remodeling and the formation of “fibroblastic foci”. Aberrant activation of TGF-β1 is frequently encountered and promotes fibroblast proliferation, activation, and differentiation in pulmonary fibrosis. Hence, the inhibition of TGF-β1-induced lung fibroblast activation holds promise as a therapeutic strategy for IPF. The present study aimed to investigate the potential effect and underlying mechanisms of bone morphogenetic protein 4 (BMP4) on TGF-β1-induced proliferation, apoptosis, activation and myofibroblast differentiation of adult lung fibroblasts. Here, we demonstrated that BMP4 expression was significantly decreased in TGF-β1-stimulated mouse primary lung fibroblasts (PLFs). BMP4 inhibited proliferation and apoptosis resistance of TGF-β1-stimulated mouse PLFs. BMP4 suppressed TGF-β1-induced fibroblast activation and differentiation in mouse PLFs. We also found that BMP4 inhibited TGF-β1-induced ERK and p38 MAPK phosphorylation. Our findings indicate that BMP4 exerts its anti-fibrotic effects by regulating fibroblast proliferation, apoptosis, activation and differentiation via the inhibition of the ERK/p38 MAPK signaling pathway, and thus has a potential for the treatment of pulmonary fibrosis. creator: Zhou Cai creator: Hua Guo creator: Jing Qian creator: Wei Liu creator: Yuanyuan Li creator: Liang Yuan creator: You Zhou creator: Ran Lin creator: Xiaohui Xie creator: Qiong Yang creator: Guoying Wu creator: Qiongqiong Li creator: Li Zhao creator: Fei Liu creator: Jian Wang creator: Wenju Lu uri: https://doi.org/10.7717/peerj.13775 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cai et al. title: Effects of six weeks outdoor versus treadmill running on physical fitness and body composition in recreationally active young males: a pilot study link: https://peerj.com/articles/13791 last-modified: 2022-07-27 description: BackgroundRunning as exercise may be performed either on an outdoor surface or treadmill surface. However, previous research has indicated that the nature of both the surfaces differ significantly and therefore the training outcomes from running in these surfaces may also vary.AimTherefore, the aim of this pilot study was to compare the effects of 6-weeks of supervised outdoor running (OT) vs treadmill running (TT) on physical fitness and body composition in recreationally active young males.MethodsParticipants (age: 19.82 ± 1.28 years, height: 172.6 ± 4.9 cm, body mass: 64.3 ± 8.7 kg) were randomly assigned to OT (n = 14) or TT (n = 14), and assessed for physical fitness, i.e., 50 m sprint, cardiorespiratory endurance (i.e., 1,600 m run time-trial), standing long jump (SLJ), flexibility (i.e., sit-and-reach test), and upper-body muscle endurance (i.e., push-ups repetitions), alongside body composition, i.e., body mass, body mass index (BMI), fat percentage, fat free mass, and leg skeletal muscle mass (SMM). A two (pre-post intervention) by two (OT, TT) mixed ANOVA analysed exercise-specific effects. For significant group-by-time interactions, Bonferroni adjusted paired (within-group) and independent (between-group comparisons at post) t-tests were used for post-hoc analyses.ResultsSignificant time-effect was found in all physical fitness variables (all p < 0.001, ηp2 = 0.67–0.91), body mass (p = 0.23, ηp2 = 0.18), BMI (p = 0.009, ηp2 = 0.24), body fat percentage (p = 0.001, ηp2 = 0.38), and leg SMM (p = 0.002–0.007, ηp2 = 0.25–0.33). Significant group-by-time interaction was found for 50 m sprint (p = < 0.001, ηp2 = 0.74), 1,600 m run (p = 0.001, ηp2 = 0.35), and SLJ (p < 0.001, ηp2 = 0.43), favouring OT. Group-specific post-hoc tests showed improvements in all physical fitness variables after OT (p = < 0.001–0.001, g = 0.69–2.32, %Δ = 3.0–12.4) and TT (p = < 0.001–0.017, g = 0.15–0.65, %Δ = 0.9–11.7), and fat percentage after OT and TT (p = 0.002–0.041, g = 0.14–0.26, %Δ = 4.3–6.0). However, leg SMM decreased in TT (p = 0.001–0.004, g = 0.14–0.15, %Δ = 6.2–6.7).ConclusionsBoth OT and TT improved physical fitness and decreased fat percentage. However, compared to TT, the OT intervention preserved leg SMM and induced greater physical fitness improvements. creator: Gaurav Singh creator: Gaurav Kushwah creator: Tanvi Singh creator: Rodrigo Ramírez-Campillo creator: Rohit K. Thapa uri: https://doi.org/10.7717/peerj.13791 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Singh et al. title: Weight change-related factors during the COVID-19 pandemic: a population-based cross-sectional study using social cognitive theory link: https://peerj.com/articles/13829 last-modified: 2022-07-27 description: BackgroundPublished studies during the Coronavirus-19 (COVID-19) pandemic have focused on eating and exercise behaviors and failed to portray a comprehensive understanding of the factors associated with weight change in a setting of a behavioral change framework. This study explores factors associated with weight change during the COVID-19 pandemic among Lebanese residents using the Social Cognitive Theory (SCT) framework, integrating behavioral, environmental, and cognitive factors.Materials & MethodsThis study uses a cross-sectional design using an anonymous online survey. Participants were recruited from a tertiary hospital patient portal and social media posts. The survey included four domains: demographics, cognitive, behavioral, psychological, and environmental factors. Multiple validated self-reported instruments were included Generalized Anxiety Disorder-2 items (GAD-2), Patient Health Questionnaire-2 (PHQ-2), General Self Efficacy Scale (GSES), Alcohol Use Disorders Identification Test-Concise (AUDIT-C), and the dietary pattern evaluation tool.ResultsA sample of 335 complete responses was obtained. Mean age was 39.0 ± 13.4 years old. Participants were mostly females (n = 224, 66.9%), employed (n = 191, 57.4%), nonsmokers (n = 227, 70.5%), reporting depression (n = 224, 80.3%) and anxiety (n = 242, 84.3%). Mean weight change was −7.0 ± 6.0 kg in the decrease weight group and 6.4 ± 5.0 kg in the increase group. When compared to stable weight, the multinomial logistic model factors that were found to correlate significantly to weight gain were: overeating/binge eating (p-value = 0.001) and unbalanced food pattern (p-value = 0.012). Baseline BMI (p-value = 0.003), anxiety (p-value = 0.020) and smoking (p-value = 0.004) were significant factors of weight loss as compared to stable weight.ConclusionsCOVID-19-related weight change is multifactorial and is associated with specific behavior and individual characteristics. Hence, addressing people’s behaviors and relationship to food is vital to control weight change during this continuing and future pandemic or natural occurrence. creator: Roxane Assaf creator: Jumana Antoun uri: https://doi.org/10.7717/peerj.13829 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Assaf and Antoun title: Suicidal ideation and suicide attempts among university students in South Korea during the COVID-19 pandemic: the application of interpersonal-psychological theory and early maladaptive schema link: https://peerj.com/articles/13830 last-modified: 2022-07-27 description: BackgroundThis study examined the application of interpersonal-psychological theory and early maladaptive schema of suicidal ideation and suicide attempts in South Korean university students.MethodsIn this cross-sectional study, data from 367 university students were surveyed using the Interpersonal Needs Questionnaire, Early Maladaptive Schema, Suicide Ideation Scale, and the Acquired Capability for Suicide Scale. Data were collected between June 21 and July 21, 2021.ResultsUniversity students’ interpersonal needs and early maladaptive schema were significantly associated with suicidal ideation, and influencing suicide attempts. The acquired capability for suicide moderated the relationship between suicidal ideation and attempts.ConclusionsIn suicide prevention programs for university students, it is critical to consider their interpersonal needs and early maladaptive schema, and the acquired capability for suicide, to prevent suicidal ideation and attempts among them. creator: Jeongmin Ha creator: Dahye Park uri: https://doi.org/10.7717/peerj.13830 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ha and Park title: Distribution and phylogeography of the genus Mattirolomyces with a focus on the Asian M. terfezioides haplotypes link: https://peerj.com/articles/13511 last-modified: 2022-07-26 description: Mattirolomyces is an edible commercial sequestrate genus that is globally distributed. From the five described taxa of this genus, Mattirolomyces terfezioides is the most common species in Asia. Our recent attempts to locate M. terfezioides outside its current distribution area in China documented its first records in areas of poplar trees with the lowest known temperature and precipitation averages ever recorded for this species. This peculiar ecology was not reflected on the species-morphological features nor on its phylogenetic position in the genus. The first attempt to apply the phylogenetic network approach to Mattirolomyces revealed its geographic origin in the Asian-Pacific areas prior to frequent long-distance migration events. Based on data from recent study areas, we found that the collections from Inner Mongolia and the Shanxi province were similar to European collections. Asian haplotypes were less distant from the outgroup comparing to collections from Europe, supporting the hypothesis that M. terfezioides was originated from this Chinese area and was subsequently transported to Europe. Exploring M. terfezioides ecology and its mycorrhiza potential to grow in association with poplars would be of great importance for planning cultivation projects of this valuable desert truffle species in Central and Eastern China, a currently underexploited economic sector that deserves further ecological and M. terfezioides mycorrhizal synthesis investigations. creator: Jie Wei creator: Tine Grebenc creator: Xuan Zhang creator: SiMin Xiang creator: Yongjun Fan uri: https://doi.org/10.7717/peerj.13511 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wei et al. title: Biogas slurry application alters soil properties, reshapes the soil microbial community, and alleviates root rot of Panax notoginseng link: https://peerj.com/articles/13770 last-modified: 2022-07-26 description: BackgroundPanax notoginseng is an important herbal medicine in China, where this crop is cultivated by replanting of seedlings. Root rot disease threatens the sustainability of P. notoginseng cultivation. Water flooding (WF) is widely used to control numerous soilborne diseases, and biogas slurry shows positive effects on the soil physiochemical properties and microbial community structure and has the potential to suppress soilborne pathogens. Hence, biogas slurry flooding (BSF) may be an effective approach for alleviating root rot disease of P. notoginseng; however, the underlying mechanism needs to be elucidated.MethodsIn this study, we conducted a microcosm experiment to determine if BSF can reduce the abundance of pathogens in soil and, alleviate root rot of P. notoginseng. Microcosms, containing soil collected from a patch of P. notoginseng showing symptoms of root rot disease, were subjected to WF or BSF at two concentrations for two durations (15 and 30 days), after which the changes in their physicochemical properties were investigated. Culturable microorganisms and the root rot ratio were also estimated. We next compared changes in the microbial community structure of soils under BSF with changes in WF and untreated soils through high-throughput sequencing of bacterial 16S rRNA (16S) and fungal internal transcribed spacer (ITS) genes amplicon.ResultsWF treatment did not obviously change the soil microbiota. In contrast, BSF treatment significantly altered the physicochemical properties and reshaped the bacterial and fungal communities, reduced the relative abundance of potential fungal pathogens (Fusarium, Cylindrocarpon, Alternaria, and Phoma), and suppressed culturable fungi and Fusarium. The changes in the microbial community structure corresponded to decreased root rot ratios. The mechanisms of fungal pathogen suppression by BSF involved several factors, including inducing anaerobic/conductive conditions, altering the soil physicochemical properties, enriching the anaerobic and culturable bacteria, and increasing the phylogenetic relatedness of the bacterial community.ConclusionsBSF application can reshape the soil microbial community, reduce the abundance of potential pathogens, and alleviate root rot in P. notoginseng. Thus, it is a promising practice for controlling root rot disease in P. notoginseng. creator: Chengxian Wang creator: Jianfeng Liu creator: Changmei Wang creator: Xingling Zhao creator: Kai Wu creator: Bin Yang creator: Fang Yin creator: Wudi Zhang uri: https://doi.org/10.7717/peerj.13770 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: RNA-binding protein CELF6 modulates transcription and splicing levels of genes associated with tumorigenesis in lung cancer A549 cells link: https://peerj.com/articles/13800 last-modified: 2022-07-26 description: CELF6 (CUGBP Elav-Like Family Member 6), a canonical RNA binding protein (RBP), plays important roles in post-transcriptional regulation of pre-mRNAs. However, the underlying mechanism of lower expressed CELF6 in lung cancer tissues is still unclear. In this study, we increased CELF6 manually in lung cancer cell line (A549) and utilized transcriptome sequencing (RNA-seq) technology to screen out differentially expressed genes (DEGs) and alternative splicing events (ASEs) after CELF6 over-expression (CELF6-OE). We found that CELF6-OE induced 417 up-regulated and 1,351 down-regulated DEGs. Functional analysis of down-regulated DEGs showed that they were highly enriched in immune/inflammation response- related pathways and cell adhesion molecules (CAMs). We also found that CELF6 inhibited the expression of many immune-related genes, including TNFSF10, CCL5, JUNB, BIRC3, MLKL, PIK3R2, CCL20, STAT1, MYD88, and CFS1, which mainly promote tumorigenesis in lung cancer. The dysregulated DEGs were also validated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) experiment. In addition, CELF6 regulates the splicing pattern of large number of genes that are enriched in p53 signaling pathway and apoptosis, including TP53 and CD44. In summary, we made an extensive analysis of the transcriptome profile of gene expression and alternative splicing by CELF6-OE, providing a global understanding of the target genes and underlying regulation mechanisms mediated by CELF6 in the pathogenesis and development of lung cancer. creator: HuSai Ma creator: GuoWei Liu creator: Bin Yu creator: Joshua Wang creator: YaLi Qi creator: YiYing Kou creator: Ying Hu creator: ShunJun Wang creator: Fei Wang creator: Dong Chen uri: https://doi.org/10.7717/peerj.13800 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ma et al. title: Incipient speciation, high genetic diversity, and ecological divergence in the alligator bark juniper suggest complex demographic changes during the Pleistocene link: https://peerj.com/articles/13802 last-modified: 2022-07-26 description: The most recent glacial cycles of the Pleistocene affected the distribution, population sizes, and levels of genetic structure of temperate-forest species in the main Mexican mountain systems. Our objective was to investigate the effects these cycles had on the genetic structure and distribution of a dominant species of the “mexical” vegetation across North and Central America. We studied the genetic diversity of Juniperus deppeana, a conifer distributed from the Southwestern United States to the highlands of Central America. We combined information of one plastid marker and two nuclear markers to infer phylogeographic structure, genetic diversity and demographic changes. We also characterized the climatic niche for each variety to infer the plausible area of suitability during past climatic conditions and to evaluate climatic niche discontinuities along with the species distribution. We found a marked phylogeographic structure separating the populations North and South of the Isthmus of Tehuantepec, with populations to the South of this barrier forming a distinct genetic cluster corresponding to Juniperus deppeana var. gamboana. We also found signals of population expansion in the Northern genetic cluster. Ecological niche modeling results confirmed climatic niche differences and discontinuities among J. deppeana varieties and heterogeneous responses to climatic oscillations. Overall, J. deppeana’s genetic diversity has been marked by distribution shifts, population growth and secondary contact the North, and in situ permanence in the South since the last interglacial to the present. High genetic variation suggests a wide and climatically diverse distribution during climatic oscillations. We detected the existence of two main genetic clusters, supporting previous proposals that Juniperus deppeana and Juniperus gamboana may be considered two separate species. creator: Rodrigo Martínez de León creator: Gabriela Castellanos-Morales creator: Alejandra Moreno-Letelier uri: https://doi.org/10.7717/peerj.13802 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Martínez de León et al. title: Slower maximal walking speed is associated with poorer global cognitive function among older adults residing in China link: https://peerj.com/articles/13809 last-modified: 2022-07-26 description: BackgroundMaintaining both walking speed and cognitive function is essential for active, healthy aging. This study investigated age-related differences in walking speed and global cognitive function with aging and the association between them among older adults residing in the developing country of China.MethodsThis cross-sectional study measured usual (UWS) and maximal walking speed (MWS) of participants for six meters. The Chinese version of the Montreal Cognitive Assessment was used to evaluate global cognition through in-person interviews. Analyses of variance were used to compare the differences in UWS, MWS, and global cognition between genders and age groups. Multiple linear regression models were used to determine the association between walking speed and global cognitive function.ResultsIn total, 791 Chinese adults (252 men and 539 women) aged 60–89 years were included in this study. Markedly slowed UWS and worse global cognitive function scores were observed for both genders among adults ≥80 years of age. MWS slowed considerably in men ≥85 years of age and in women ≥80 years of age. There was a significant gender difference in MWS—with men walking faster than women—but not in UWS. Linear regression analysis adjusted for the confounding factors of gender, height, weight, years of education, and chronic disease indicated that MWS, but not UWS, was significantly associated with global cognitive function (β = 0.086, [0.177, 1.657], P = 0.015) such that slower maximal walking speed was associated with poorer cognitive performance. This association was statistically significant only for adults aged 75-79 years (β = 0.261 [0.647, 4.592], P = 0.010).ConclusionWalking speed was slower in the older age groups. Global cognitive function deteriorated markedly after 80 years of age. After controlling for confounding variables, slower MWS, but not UWS, was associated with poorer global cognitive function. MWS may serve as a potential indicator for earlier identification of poor cognition and motoric cognitive risk syndrome in an older Chinese population. creator: Guiping Jiang creator: Xueping Wu uri: https://doi.org/10.7717/peerj.13809 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Jiang and Wu title: A new istiodactylid pterosaur, Lingyuanopterus camposi gen. et sp. nov., from the Jiufotang Formation of western Liaoning, China link: https://peerj.com/articles/13819 last-modified: 2022-07-26 description: The Istiodactylidae is a group of pterodactyloids characterised by large nasoantorbital fenestrae and labiolingually compressed teeth, with several records reported from the Early Cretaceous of northeastern China and western Europe. Here we report a new istiodactylid, Lingyuanopterus camposi gen. et sp. nov. from the Jiufotang Formation of Lingyuan, Liaoning, northeastern China. The holotype is represented by a near-complete skull, mandible and atlas-axis complex. It is distinguished from other istiodactylids by several characters, including two autapomorphies: short triangular tooth crowns with sharp mesial and distal carinae limited to the distal teeth, mandibular symphysis occupying approximately a quarter the mandible length. We also report the presence of helical jaw joints in istiodactylids, and provide a revised diagnosis of the clade Istiodactylidae, which includes five genera: Istiodactylus, Liaoxipterus, Nurhachius, Luchibang and Lingyuanopterus. Four pellets containing fish fragments were observed and are tentatively interpreted as bromalites of Lingyuanopterus. Although members of this clade possess similar skull morphologies, istiodactylids vary in terms of their dentition, with at least three forms from the Jiufotang Formation alone. This may represent different feeding strategies, and also indicate a similarity between the pterosaur assemblages of northeastern China and Britain during the Early Cretaceous. creator: Yizhi Xu creator: Shunxing Jiang creator: Xiaolin Wang uri: https://doi.org/10.7717/peerj.13819 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xu et al. title: Factors associated with non-attendance at appointments in the gastroenterology endoscopy unit: a retrospective cohort study link: https://peerj.com/articles/13518 last-modified: 2022-07-25 description: Background and AimsGastrointestinal (GI) endoscopy is a limited health resource because of a scarcity of qualified personnel and limited availability of equipment. Non-adherence to endoscopy appointments therefore wastes healthcare resources and may compromise the early detection and treatment of GI diseases. We aimed to identify factors affecting non-attendance at scheduled appointments for GI endoscopy and thus improve GI healthcare outcomes.MethodsThis was a single-center retrospective cohort study performed at a tertiary hospital gastroenterology endoscopy unit, 12 months before and 12 months after the start of the COVID-19 pandemic. We used multiple logistic regression analysis to identify variables associated with non-attendance at scheduled appointments.ResultsOverall, 5,938 appointments were analyzed, and the non-attendance rate was 18.3% (1,088). The non-attendance rate fell significantly during the pandemic (22.6% vs. 11.6%, p < 0.001). Multivariable regression analysis identified the absence of deep sedation (OR: 3.253, 95% CI [2.386–4.435]; p < 0.001), a referral from a physician other than a gastroenterologist (OR: 1.891, 95% CI [1.630–2.193]; p < 0.001), a longer lead time (OR: 1.006, 95% CI [1.004–1.008]; p < 0.001), and female gender (OR: 1.187, 95% CI [1.033–1.363]; p = 0.015) as associated with appointment non-attendance.ConclusionsFemale patients, those undergoing endoscopic procedures without deep sedation, those referred by physicians other than gastroenterologists, and with longer lead time were less likely to adhere to appointments. Precautions should be directed at patients with one or more of these risk factors, and for those scheduled for screening procedures during the COVID-19 pandemic. creator: Hasan Yılmaz creator: Burcu Kocyigit uri: https://doi.org/10.7717/peerj.13518 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yılmaz and Kocyigit title: The immunomodulatory potential of phage therapy to treat acne: a review on bacterial lysis and immunomodulation link: https://peerj.com/articles/13553 last-modified: 2022-07-25 description: BackgroundCharacterized by an inflammatory pathogenesis, acne is the most common skin disorder worldwide. Altered sebum production, abnormal proliferation of keratinocytes, and microbiota dysbiosis represented by disbalance in Cutibacterium acnes population structure, have a synergic effect on inflammation of acne-compromised skin. Although the role of C. acnes as a single factor in acne development is still under debate, it is known that skin and skin-resident immune cells recognize this bacterium and produce inflammatory markers as a result. Control of the inflammatory response is frequently the target for acne treatment, using diverse chemical or physical agents including antibiotics. However, some of these treatments have side effects that compromise patient adherence and drug safety and in the case of antibiotics, it has been reported C. acnes resistance to these molecules. Phage therapy is an alternative to treat antibiotic-resistant bacterial strains and have been recently proposed as an immunomodulatory therapy. Here, we explore this perspective about phage therapy for acne, considering the potential immunomodulatory role of phages.MethodologyLiterature review was performed using four different databases (Europe PubMed Central-ePMC, Google Scholar, PubMed, and ScienceDirect). Articles were ordered and selected according to their year of publication, number of citations, and quartile of the publishing journal.ResultsThe use of lytic bacteriophages to control bacterial infections has proven its promising results, and anti-inflammatory effects have been found for some bacteriophages and phage therapy. These effects can be related to bacterial elimination or direct interaction with immune cells that result in the regulation of pro-inflammatory cytokines. Studies on C. acnes bacteriophages have investigated their lytic activity, genomic structure, and stability on different matrices. However, studies exploring the potential of immunomodulation of these bacteriophages are still scarce.ConclusionsC. acnes bacteriophages, as well as other phages, may have direct immunomodulatory effects that are yet to be fully elucidated. To our knowledge, to the date that this review was written, there are only two studies that investigate anti-inflammatory properties for C. acnes bacteriophages. In those studies, it has been evidenced reduction of pro-inflammatory response to C. acnes inoculation in mice after bacteriophage application. Nevertheless, these studies were conducted in mice, and the interaction with the immune response was not described. Phage therapy to treat acne can be a suitable therapeutic alternative to C. acnes control, which in turn can aid to restore the skin’s balance of microbiota. By controlling C. acnes colonization, C. acnes bacteriophages can reduce inflammatory reactions triggered by this bacterium. creator: Juan Farfán creator: John M. Gonzalez creator: Martha Vives uri: https://doi.org/10.7717/peerj.13553 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Farfán et al. title: Genome-wide identification of long non-coding (lncRNA) in Nilaparvata lugens’s adaptability to resistant rice link: https://peerj.com/articles/13587 last-modified: 2022-07-25 description: BackgroundThe brown planthopper (BPH), Nilaparvata lugens (Stål), is a very destructive pest that poses a major threat to rice plants worldwide. BPH and rice have developed complex feeding and defense strategies in the long-term co-evolution.MethodsTo explore the molecular mechanism of BPH’s adaptation to resistant rice varieties, the lncRNA expression profiles of two virulent BPH populations were analyzed. The RNA-seq method was used to obtain the lncRNA expression data in TN1 and YHY15.ResultsIn total, 3,112 highly reliable lncRNAs in TN1 and YHY15 were identified. Compared to the expression profiles between TN1 and YHY15, 157 differentially expressed lncRNAs, and 675 differentially expressed mRNAs were identified. Further analysis of the possible regulation relationships between differentially expressed lncRNAs and differentially expressed mRNAs, identified three pair antisense targets, nine pair cis-regulation targets, and 3,972 pair co-expressed targets. Function enriched found arginine and proline metabolism, glutathione metabolism, and carbon metabolism categories may significantly affect the adaptability in BPH when it is exposed to susceptible and resistant rice varieties. Altogether, it provided scientific data for the study of lncRNA regulation of brown planthopper resistance to rice. These results are helpful in the development of new control strategies for host defense against BPH and breeding rice for high yield. creator: Wenjun Zha creator: Sanhe Li creator: Huashan Xu creator: Junxiao Chen creator: Kai Liu creator: Peide Li creator: Kai Liu creator: Guocai Yang creator: Zhijun Chen creator: Shaojie Shi creator: Lei Zhou creator: Aiqing You uri: https://doi.org/10.7717/peerj.13587 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zha et al. title: Microbial communities associated with mounds of the Orange-footed scrubfowl Megapodius reinwardt link: https://peerj.com/articles/13600 last-modified: 2022-07-25 description: Megapodius reinwardt, the orange-footed scrubfowl, belongs to a small family of birds that inhabits the Indo-Australian region. Megapodes are unique in incubating their eggs in mounds using heat from microbial decomposition of organic materials and solar radiation. Little is known about the microorganisms involved in the decomposition of organic matter in mounds. To determine the source of microbes in the mounds, we used 16S and 18S rRNA gene sequencing to characterize the microbial communities of mound soil, adjacent soil and scrubfowl faeces. We found that the microbial communities of scrubfowl faeces were substantially different from those of the mounds and surrounding soils, suggesting that scrubfowls probably do not use their faeces to inoculate their mounds although a few microbial sequence variants were present in both faeces and mound samples. Further, the mound microbial community structure was significantly different to the adjacent soils. For example, mounds had a high relative abundance of sequence variants belonging to Thermomonosporaceae, a thermophilic soil bacteria family able to degrade cellulose from plant residues. It is not clear whether members of Thermomonosporaceae disproportionately contribute to the generation of heat in the mound, or whether they simply thrive in the warm mound environment created by the metabolic activity of the mound microbial community. The lack of clarity in the literature between designations of heat-producing (thermogenic) and heat-thriving (thermophilic) microbes poses a challenge to understanding the role of specific bacteria and fungi in incubation. creator: Karla Cardenas Gomez creator: Alea Rose creator: Karen Susanne Gibb creator: Keith A. Christian uri: https://doi.org/10.7717/peerj.13600 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cardenas Gomez et al. title: Pollution caused by nanoplastics: adverse effects and mechanisms of interaction via molecular simulation link: https://peerj.com/articles/13618 last-modified: 2022-07-25 description: The continuous increase in the production of synthetic plastics for decades and the inadequate disposal of plastic waste have resulted in a considerable increase of these materials in aquatic environments, which has developed into a major environmental concern. In addition to conventional parameters, the relevance of the environmental monitoring of microplastics (MPs) and nanoplastics (NPs) has been highlighted by the scientific community due to the potential adverse effects these materials pose to the ecosystem as well as to human health. The literature has registered an increasing interest in understanding the mechanisms, at the molecular level, of the interaction between NPs and other compounds using molecular simulation techniques. The present review aims to: (i) summarize the force fields conventionally used to describe NPs by molecular simulations; (ii) discuss the effects of NPs in the structural and dynamical properties of biological membranes; (iii) evaluate how NPs affect the folding of proteins; (iv) discuss the mechanisms by which NPs adsorb contaminants from the environment. NPs can affect the secondary structure of proteins and change the lateral organization and diffusion of lipid membranes. As a result, they may alter the lipid digestion in the gastrointestinal system representing a risk to the assimilation of the nutrients by humans. The adsorption of contaminants on MPs and NPs can potentiate their harmful effects on human health, due to a possible synergism. Therefore, understanding the mechanisms involved in these interactions is crucial to predict dangerous combinations and outline action strategies that reduce negative impacts on ecosystems and human health. Depending on the chemical properties of contaminants and NPs, electrostatic and/or van der Waals interactions can be more relevant in explaining the adsorption process. Finally, we conclude by highlighting gaps in the literature and the critical aspects for future investigations. creator: Yamara Matos Oliveira creator: Nathalia Salles Vernin creator: Daniele Maia Bila creator: Marcia Marques creator: Frederico Wanderley Tavares uri: https://doi.org/10.7717/peerj.13618 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Oliveira et al. title: Adaptation of a clinical reasoning model for use in inflammatory conditions of the lactating breast: a retrospective mixed-methods study link: https://peerj.com/articles/13627 last-modified: 2022-07-25 description: Background:Many potential factors associated with Inflammatory Conditions of the Lactating Breast (ICLB) have been reported in the literature, by lactating mothers and clinicians. Clinicians, including general practitioners, lactation consultants and physiotherapists, require a clinical reasoning model that summarises associated or linked factors, to aid in the assessment, treatment, and prevention of ICLB. Thus, we aimed to adapt the existing Breastfeeding Pain Reasoning Model (BPRM), for use in the management of ICLB, using prior research and clinical audit data to guide adaptation. The existing BPRM categorises contributing factors for breastfeeding nipple pain, rather than ICLB.Methods:Factors linked with ICLB were identified from prior research and considered for inclusion into the existing model. Clinical data from a retrospective audit of ICLB patient notes at a private physiotherapy practice were also examined. Any factors identified from prior research that could not be identified in the clinical notes were not considered for inclusion into the existing model. Additional factors from the clinical notes that appeared repeatedly were considered for inclusion into the adaptation of the BPRM. A draft adapted model was created comprising all eligible factors, considering their counts and percentages as calculated from the clinical data. The research team iteratively examined all factors for appropriate categorisation and modification within the adapted model.Results:Prior research and data from 160 clinical notes were used to identify factors for inclusion in the adapted model. A total of 57 factors, 13 pre-existing in the BPRM and 44 extra identified from the prior research or clinical audit, comprised the draft adapted model. Factor consolidation and terminology modification resulted in a total of 34 factors in the final proposed adapted ICLB model. The three main categories, CNS modulation, External influences and Local stimulation, from the existing model were maintained, with one minor terminology change to the former Local stimulation category, resulting in ‘Local influences’ category. Terminology for five subcategories were modified to better reflect the types of factors for ICLB. The most common factors in the adapted model, calculated from the clinical audit population of mothers with ICLB, were employment (85%), high socioeconomic status (81%), antibiotic use during breastfeeding (61%), history of an ICLB (56%), any breast pump use (45%), multiparity (43%), birth interventions (35%), decreased milk transfer (33%), breastfeeding behaviour and practices (33%), nipple pain (30%) and fit and hold (attachment and positioning) difficulty (28%).Conclusion:An ICLB-specific linked factors model is proposed in this paper. Clinicians treating mothers with ICLB can use this model to identify influencing and determining factors of ICLB clinical presentations and provide targeted education and effective treatment plans. creator: Emma Heron creator: Adelle McArdle creator: Melinda Cooper creator: Donna Geddes creator: Leanda McKenna uri: https://doi.org/10.7717/peerj.13627 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Heron et al. title: Recent deterioration of coral reefs in the South China Sea due to multiple disturbances link: https://peerj.com/articles/13634 last-modified: 2022-07-25 description: More frequent global warming events, biological disasters, and anthropogenic activities have caused extensive damage to coral reefs around the world. Coral reefs in the Xisha Islands (also known as the Paracel Islands) have been damaged following rounds of heatwaves and crown-of-thorns starfish (CoTS) outbreaks over recent decades. Based on a comprehensive community survey in 2020, we determined a diagnosis for the present state of six coral regions in the Xisha Islands. The findings suggested that these regions had a total of 213 species of scleractinian corals belonging to 43 genera and 16 families. Living coral coverage across sites was widely divergent and ranged from 0.40% (IQR: 7.74–0.27%) in Panshi Yu to 38.20% (IQR: 43.00–35.90%) in Bei Jiao. Coral bleaching prevalence was 23.90% (IQR: 41.60–13.30%) overall and topped out at 49.30% (IQR: 50.60–48.10%) in Bei Jiao. Five of the coral regions (all but Yongxing Dao) were under threat of CoTS outbreaks. High mortality combined with excellent recruitment rates suggested potential rehabilitation after recent deterioration. We employed a quantifiable Deterioration Index (DI) to evaluate the intensity of deterioration of coral reefs in the Xisha Islands. The results showed that Yongxing Dao and Langhua Jiao had low recent deterioration (DIrecent = 0.05, IQR: 0.07–0.02 and 0.04, IQR: 0.11–0.01, respectively), while Bei Jiao, Yongle Atoll, Yuzhuo Jiao, and Panshi Yu had high recent deterioration (DIrecent > 0.16). Different monitoring sites within the same coral region were heterogeneous with regards to all above indexes. Moreover, we reviewed and discussed potential disturbances that threaten the health of the Xisha Islands’ corals. It is crucial to identify severely afflicted areas and find successful methods to better manage coral reef health in this region. creator: Jiaguang Xiao creator: Wei Wang creator: Xiaolei Wang creator: Peng Tian creator: Wentao Niu uri: https://doi.org/10.7717/peerj.13634 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Xiao et al. title: Insights on the evolution of Coronavirinae in general, and SARS-CoV-2 in particular, through innovative biocomputational resources link: https://peerj.com/articles/13700 last-modified: 2022-07-25 description: The structural proteins of coronaviruses portray critical information to address issues of classification, assembly constraints, and evolutionary pathways involving host shifts. We compiled 173 complete protein sequences from isolates belonging to the four genera of the subfamily Coronavirinae. We calculate a single matrix of viral distance as a linear combination of protein distances. The minimum spanning tree (MST) connecting the individuals captures the structure of their similarities. The MST re-capitulates the known phylogeny of Coronovirinae. Hosts were mapped onto the MST and we found a non-trivial concordance between host phylogeny and viral proteomic distance. We also study the chimerism in our dataset through computational simulations. We found evidence that structural units coming from loosely related hosts hardly give rise to feasible chimeras in nature. This work offers a fresh way to analyze features of SARS-CoV-2 and related viruses. creator: Daniel Andrés Dos Santos creator: María Celina Reynaga creator: Juan Cruz González creator: Gabriela Fontanarrosa creator: María de Lourdes Gultemirian creator: Agustina Novillo creator: Virginia Abdala uri: https://doi.org/10.7717/peerj.13700 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Dos Santos et al. title: Identifying DUSP-1 and FOSB as hub genes in immunoglobulin A nephropathy by WGCNA and DEG screening and validation link: https://peerj.com/articles/13725 last-modified: 2022-07-25 description: BackgroundThe mechanism of immunoglobulin A nephropathy (IgAN) is still unknown. A bioinformatics analysis is a powerful method to identify the biomarkers and possible therapeutic targets of a certain disease from related datasets.MethodsThe GSE93973 dataset, obtained from the Gene Expression Omnibus (GEO) database, was used to construct a weighted gene co-expression network (WGCNA) and filter differentially expressed genes (DEGs). The biological process (BP) enrichment among all the genes in the key modules was analyzed through a Gene Ontology (GO) enrichment analysis. We selected the overlap of hub genes in the WGCNA and Protein-Protein Interaction (PPI) network as the final hub genes in IgAN. We verified the final hub genes in two other datasets and in clinical kidney tissue specimens. A receiver operating characteristic (ROC) curve was used to evaluate the diagnostic efficacy of hub genes for IgAN.ResultsThe turquoise module, which contained 1,806 genes, was the module with the highest correlation coefficient with IgAN in the GSE93973 dataset. The GO enrichment analysis showed that these 1,806 genes were mainly enriched in inflammation and immune responses. There were five hub genes identified by WGCNA and 34 hub genes identified in a DEG analysis in the GSE93973 dataset. DUSP1 and FOSB were identified as the final hub genes in IgAN. The validation results of the final hub genes in two other databases and clinical kidney tissue specimens validated the result that, compared to the control group, FOSB and DUSP1 were expressed at lower levels in the glomerulus of IgAN patients. The ROC curve indicated that DUSP1 and FOSB were good diagnostic indicators for IgAN.ConclusionsOur analysis identified two hub genes that might be potential targets for the intervention and treatment of IgAN. creator: Wu Jianping creator: Xiaona Wei creator: Jiajia Li creator: Rui Zhang creator: Qianqian Han creator: Qiongqiong Yang uri: https://doi.org/10.7717/peerj.13725 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Jianping et al. title: Forest tree species distribution for Europe 2000–2020: mapping potential and realized distributions using spatiotemporal machine learning link: https://peerj.com/articles/13728 last-modified: 2022-07-25 description: This article describes a data-driven framework based on spatiotemporal machine learning to produce distribution maps for 16 tree species (Abies alba Mill., Castanea sativa Mill., Corylus avellana L., Fagus sylvatica L., Olea europaea L., Picea abies L. H. Karst., Pinus halepensis Mill., Pinus nigra J. F. Arnold, Pinus pinea L., Pinus sylvestris L., Prunus avium L., Quercus cerris L., Quercus ilex L., Quercus robur L., Quercus suber L. and Salix caprea L.) at high spatial resolution (30 m). Tree occurrence data for a total of three million of points was used to train different algorithms: random forest, gradient-boosted trees, generalized linear models, k-nearest neighbors, CART and an artificial neural network. A stack of 305 coarse and high resolution covariates representing spectral reflectance, different biophysical conditions and biotic competition was used as predictors for realized distributions, while potential distribution was modelled with environmental predictors only. Logloss and computing time were used to select the three best algorithms to tune and train an ensemble model based on stacking with a logistic regressor as a meta-learner. An ensemble model was trained for each species: probability and model uncertainty maps of realized distribution were produced for each species using a time window of 4 years for a total of six distribution maps per species, while for potential distributions only one map per species was produced. Results of spatial cross validation show that the ensemble model consistently outperformed or performed as good as the best individual model in both potential and realized distribution tasks, with potential distribution models achieving higher predictive performances (TSS = 0.898, R2logloss = 0.857) than realized distribution ones on average (TSS = 0.874, R2logloss = 0.839). Ensemble models for Q. suber achieved the best performances in both potential (TSS = 0.968, R2logloss = 0.952) and realized (TSS = 0.959, R2logloss = 0.949) distribution, while P. sylvestris (TSS = 0.731, 0.785, R2logloss = 0.585, 0.670, respectively, for potential and realized distribution) and P. nigra (TSS = 0.658, 0.686, R2logloss = 0.623, 0.664) achieved the worst. Importance of predictor variables differed across species and models, with the green band for summer and the Normalized Difference Vegetation Index (NDVI) for fall for realized distribution and the diffuse irradiation and precipitation of the driest quarter (BIO17) being the most frequent and important for potential distribution. On average, fine-resolution models outperformed coarse resolution models (250 m) for realized distribution (TSS = +6.5%, R2logloss = +7.5%). The framework shows how combining continuous and consistent Earth Observation time series data with state of the art machine learning can be used to derive dynamic distribution maps. The produced predictions can be used to quantify temporal trends of potential forest degradation and species composition change. creator: Carmelo Bonannella creator: Tomislav Hengl creator: Johannes Heisig creator: Leandro Parente creator: Marvin N. Wright creator: Martin Herold creator: Sytze de Bruin uri: https://doi.org/10.7717/peerj.13728 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bonannella et al. title: The determinants of patient care manager role and the implementation of COVID-19 clinical pathway: a cross-sectional study link: https://peerj.com/articles/13764 last-modified: 2022-07-25 description: ObjectiveThis study aims to determine the factors associated with patient care manager role and the implementation of the clinical pathway among nurses in private hospitals.MethodsThis study was conducted from January–July 2021 using the cross-sectional approach. The sample consisted of 168 nurses working in a private hospital in Surabaya City, East Java, Indonesia. Meanwhile, the data were collected using the Patient Care Manager Role Scale (PCMRS) and analyzed by multiple logistic regression to find the correlation between the variables.ResultsA higher percentage of nurses namely 64.3% had compliance in COVID-19 clinical pathways with an average PCMRS score of 27.81 ± 2.43. Nurses with a high-level patient care manager role level had a significant compliance risk with odds ratio [OR] 440.137, 95% confidence interval [CI] [51.850–3736.184], and p-value = 0.000 compared to those with a low role.ConclusionThe role of patient care manager and compliance with COVID-19 clinical pathways correlated significantly. Based on the results, several actions are needed for the early identification of patient service managers’ roles to ensure compliance with COVID-19 clinical pathways and reduce the number of cases in Indonesia. creator: Abdul Aziz Alimul Hidayat creator: Wen-Ling Chen creator: Rahimah Mohd Nor creator: Musrifatul Uliyah creator: Fatin Lailatul Badriyah creator: Masunatul Ubudiyah uri: https://doi.org/10.7717/peerj.13764 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Aziz Alimul Hidayat et al. title: Wedelolactone facilitates the early development of parthenogenetically activated porcine embryos by reducing oxidative stress and inhibiting autophagy link: https://peerj.com/articles/13766 last-modified: 2022-07-25 description: Wedelolactone (WDL) is a coumaryl ether compound extracted from the traditional Chinese medicinal plant, Eclipta prostrata L. It is a natural polyphenol that exhibits a variety of pharmacological activities, such as anti-inflammatory, anti-free radical, and antioxidant activities in the bone, brain, and ovary. However, its effect on embryonic development remains unknown. The present study explored the influence of WDL supplementation of porcine oocytes culture in vitro on embryonic development and the underlying mechanisms and its effect on the levels of Kelch-like ECH-associated protein 1/nuclear factor-erythroid 2-related factor 2/antioxidant response element (Keap1/Nrf2/ARE). The results showed that WDL (2.5 nM) significantly increased the blastocyst formation rate, mitochondrial activity, and proliferation ability while reducing the reactive oxygen species accumulation, apoptosis, and autophagy. These findings suggested that WDL can enhance the growth and development of early porcine embryos to alleviate oxidative stress and autophagy through regulating NRF2 and microtubule-associated protein 1 light chain 3 (MAP1LC3) gene expression levels. creator: Xin-Qin Wang creator: Rong-Ping Liu creator: Jing Wang creator: Dan Luo creator: Ying-Hua Li creator: Hao Jiang creator: Yong-Nan Xu creator: Nam-Hyung Kim uri: https://doi.org/10.7717/peerj.13766 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Nuclear energy transition and CO2 emissions nexus in 28 nuclear electricity-producing countries with different income levels link: https://peerj.com/articles/13780 last-modified: 2022-07-25 description: BackgroundNuclear energy carries the least environmental effects compared to fossil fuels and most other renewable energy sources. Therefore, nuclear energy transition (NET) would reduce pollution emissions. The present study investigates the role of the NET on CO2 emissions and tests the environmental Kuznets curve (EKC) in the 28 nuclear electricity-producing countries from 1996–2019.MethodsAlong with a focus on the whole panel, countries are divided into three income groups using the World Bank classification, i.e., three Lower-Middle-Income (LMI), eight Upper-Middle-Income (UMI), and 17 High-Income (HI) countries. The cross-sectional dependence panel data estimation techniques are applied for the long and short run analyses.ResultsIn the long run, the EKC is corroborated in HI countries’ panel with estimated positive and negative coefficients of economic growth and its square variable. The Netherlands, Sweden, Switzerland, and the USA are found in the 2nd stage of the EKC. However, the remaining HI economies are facing 1st phase of the EKC. Moreover, economic growth has a monotonic positive effect on CO2 emissions in LMI and UMI economies. NET reduces CO2 emissions in UMI and HI economies. On the other hand, NET has an insignificant effect on CO2 emissions in LMI economies. In the short run, the EKC is validated and NET has a negative effect on CO2 emissions in HI countries and the whole panel. However, NET could not affect CO2 emissions in LMI and UMI countries. Based on the long-run results, we recommend enhancing nuclear energy transition in UMI and HI economies to reduce CO2 emissions. In addition, the rest of the world should also build capacity for the nuclear energy transition to save the world from global warming. creator: Haider Mahmood uri: https://doi.org/10.7717/peerj.13780 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mahmood title: Rare earth element geochemistry of Middle Devonian reefal limestones of the Dianqiangui Basin, South China: implications for nutrient sources and expansion of the reef ecosystem link: https://peerj.com/articles/13663 last-modified: 2022-07-22 description: The Givetian Age witnessed the greatest expansion of stromatoporoid-coral reefs from low to higher latitudes of the Phanerozoic. Multi-proxy seawater surface temperature reconstruction suggests the establishment of a super-greenhouse climate as a major reason for reef expansion, yet many questions remain. This article presents the results of a rare earth element and yttrium (herein referred to as REY, derived from REE + Y) geochemical study as well as mineralogy and oxygen isotope values of two well-documented Middle Givetian reefal carbonate sections (Jiwozhai and Buzhai) of the Jiwozhai Formation of South China. The nearshore Jiwozhai patch reef succession displays greater biodiversity and more abundant coral than the marginal platform Upper Buzhai reef. Reefal and micritic carbonates of the Jiwozhai section are characterized by shale-like post-Archean Australian Shale (PAAS)-normalized REY patterns, by very weak negative Ce anomaly values (Ce/Ce* 0.80–0.96; average = 0.89), slightly elevated Y/Ho values (28.9–39.1; average = 34.1), and near-unity values of (Pr/Yb)N (average = 0.87), (Pr/Tb)N (average = 0.80), and (Tb/Yb)N (average = 1.09). Moreover, REY patterns of deposits of the Jiwozhai section differ markedly from those of modern seawater. The described geochemical aspects of the Jiwozhai section and the positive correlation of REY and Th contents displayed by the section point to a terrestrial siliciclastic contribution contemporaneous with reef-building. In contrast, REY patterns of the Upper Buzhai reef section samples are similar to those of modern seawater characterized by light rare earth element (LREE) depletion (average (Pr/Yb)N = 0.76), negative Ce anomalies (average Ce/Ce* = 0.88), and average super-chondritic Y/Ho ratios (average = 45.4)). Slightly positive Eu anomalies (Eu/Eu* = 0.93–1.94; average = 1.36) of the Upper Buzhai reef section samples are attributed to the negligible effect of hydrothermal fluids. Middle REE (MREE) enrichment (average (Tb/Yb)N = 1.48) of Buzhai section carbonate samples and positive correlation of REY and Th suggest a riverine input. Combined with siliciclastic mineralogy, oxygen isotope values, and reef-building biota morphology of the studied two sections, we suggest that terrestrial nutrients delivered by rivers far outweighed upwelling as a source of nutrients supplied to the Givetian reef ecosystem of South China. Coral and stromatoporoid in tropic oceans thrived in turbid water containing abundant terrestrial sediment and the nutrient-laden water helped expand reef-builder habitats during the Givetian time. creator: Qi Mao creator: Shangyi Gu creator: Huan Li creator: Gary G. Lash creator: Tianyi Zhang creator: Xiaofeng Xie creator: Zidong Guo uri: https://doi.org/10.7717/peerj.13663 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mao et al. title: Analysis of microRNA expression profiles in exosomes derived from acute myeloid leukemia by p62 knockdown and effect on angiogenesis link: https://peerj.com/articles/13498 last-modified: 2022-07-22 description: ObjectivesIn this study, we aimed to investigate the effect of p62 on angiogenesis and microRNA (miRNA) expression profiles in acute myeloid leukemia (AML) exosomes.MethodsAn Exiqon v19.0 microRNA MicroArray was used to profile miRNAs in exosomes derived from parental and p62-knockdown U937 cells. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to predict the biological functions and potential mechanisms of differentially expressed miRNAs in AML exosomes. Endothelial cell tube formation assays using human umbilical vein endothelial cells (HUVECs) were performed to investigate the effect of AML exosomes on angiogenesis.ResultsWe demonstrated that 2,080 miRNAs were expressed in exosomes derived from our cultured cell samples, of which 215 and 208 miRNAs were upregulated and downregulated, respectively, in p62-knockdown U937 cells (fold change ≥ 2, P < 0.05). GO analysis indicated that miRNAs were most enriched in the intercellular pathways. Biological process analysis revealed that 1460 biological processes were associated with downregulated transcripts, including 19 pathways related to vesicles, and 1,515 pathways were upregulated, including 8 pathways related to vesicles. Molecular function analysis indicated that protein binding, transcription regulator activity, and DNA-binding transcription factor activity were enriched (P < 0.05). Pathway analysis indicated that 84 pathways corresponded to upregulated transcripts, and 55 pathways corresponded to downregulated transcripts (P < 0.05). We also found that exosomes derived from U937 cells promoted angiogenesis in HUVECs.ConclusionsOur data suggest that exosomal miRNAs may play important roles in the pathogenesis of AML, which may be treated by p62 knockdown with exosomal miRNAs to inhibit angiogenesis. creator: Chuan Li creator: Xinyi Long creator: Peiqi Liang creator: Zhuogang Liu creator: Chen Wang creator: Rong Hu uri: https://doi.org/10.7717/peerj.13498 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Genetic dissection of grain iron concentration in hexaploid wheat (Triticum aestivum L.) using a genome-wide association analysis method link: https://peerj.com/articles/13625 last-modified: 2022-07-22 description: Iron (Fe) is an essential micronutrient of the body. Low concentrations of bioavailable Fe in staple food result in micronutrient malnutrition. Wheat (Triticum aestivum L.) is the most important global food crop and thus has become an important source of iron for people. Breeding nutritious wheat with high grain-Fe content has become an effective means of alleviating malnutrition. Understanding the genetic basis of micronutrient concentration in wheat grains may provide useful information for breeding for high Fe varieties through marker-assisted selection (MAS). Hence, in the present study, genome-wide association studies (GWAS) were conducted for grain Fe. An association panel of 207 accessions was genotyped using a 660K SNP array and phenotyped for grain Fe content at three locations. The genotypic and phenotypic data obtained thus were used for GWAS. A total of 911 SNPs were significantly associated with grain Fe concentrations. These SNPs were distributed on all 21 wheat chromosomes, and each SNP explained 5.79–25.31% of the phenotypic variations. Notably, the two significant SNPs (AX-108912427 and AX-94729264) not only have a more significant effect on grain Fe concentration but also have the reliability under the different environments. Furthermore, candidate genes potentially associated with grain Fe concentration were predicted, and 10 candidate genes were identified. These candidate genes were related to transport, translocation, remobilization, and accumulationof ironin wheat plants. These findings will not only help in better understanding the molecular basis of Fe accumulation in grains, but also provide elite wheat germplasms to develop Fe-rich wheat varieties through breeding. creator: Jiansheng Wang creator: Xia Shi creator: Zhengfu Zhou creator: Maomao Qin creator: Yahuan Wang creator: Wenxu Li creator: Pan Yang creator: Zhengqing Wu creator: Zhensheng Lei uri: https://doi.org/10.7717/peerj.13625 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Blood transcriptome analysis revealing aging gene expression profiles in red panda link: https://peerj.com/articles/13743 last-modified: 2022-07-22 description: The red panda is an endangered forest species distributed on the edge of the Qinghai Tibet Plateau. The species has been conserved in ex-situ in many countries and its survival is threatened by many diseases. Its immune system is vulnerable to age-associated alterations, which accumulate and result in a progressive deterioration that leads to an increased incidence of diseases. We identified 2,219 differentially expressed genes (DEGs) between geriatric (11–16 years) and adult individuals (4–8 years), and 1690 DEGs between adults and juveniles (1 year). The gene expression and functional annotation results showed that the innate immunity of red pandas increases significantly in geriatric individuals, whereas its change remains unclear when comparing adults and juveniles. We found that the adaptive immunity of red pandas first increased and then decreased with age. We identified CXCR3, BLNK, and CCR4 as the hub genes in the age-related protein–protein interaction network, which showed their central role in age-related immune changes. Many DNA repair genes were down-regulated in geriatric red pandas, suggesting that the DNA repair ability of the blood tissue in geriatric red pandas is significantly reduced. The significantly up-regulated TLR5 in geriatric individuals also suggests the possibility of enhancing the vaccination immune response by incorporating flagellin, which could be used to address decreased vaccine responses caused by age-related declines in immune system function. This work provides an insight into gene expression changes associated with aging and paves the way for effective disease prevention and treatment strategies for red pandas in the future. creator: Jing Luo creator: Liang Zhang creator: Fujun Shen creator: Li Luo creator: Lei Chen creator: Zhenxin Fan creator: Rong Hou creator: Bisong Yue creator: Xiuyue Zhang uri: https://doi.org/10.7717/peerj.13743 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Luo et al. title: Genome-wide identification and expression pattern analysis of lipoxygenase gene family in turnip (Brassica rapa L. subsp. rapa) link: https://peerj.com/articles/13746 last-modified: 2022-07-22 description: Turnip (Brassica rapa L. subsp. rapa) is an important crop with edible and medicinal values, and various stresses, especially salt stress and drought stress, seriously threaten the yield of turnips. LOXs play important roles in regulating plant growth and development, signal transduction, and biotic and abiotic stress responses through secondary metabolites produced by the oxylipin metabolic pathway, and although the turnip genome has been published, however, the role of LOX family genes in various abiotic stress responses has not been systematically studied in turnips. In this study, a total of 15 LOX genes (BrrLOX) were identified in turnip, distributed on six chromosomes. Phylogenetic tree analysis classified these LOX genes into two classes: three 9-LOX proteins and 12 13-LOX type II proteins. Gene duplication analysis showed that tandem and segmental duplication were the main pathways for the expansion of the BrrLOX gene family. The Ka and Ks values of the duplicated genes indicate that the BrrLOX gene underwent strong purifying selection. Further analysis of the cis-acting elements of the promoters suggested that the expression of the BrrLOX gene may be influenced by stress and phytohormones. Transcriptome data analysis showed that 13 BrrLOX genes were expressed at one or more stages of turnip tuber development, suggesting that LOX genes may be involved in the formation of turnip fleshy roots. The qRT-PCR analysis showed that four stresses (salt stress, drought stress, cold stress, and heat stress) and three hormone treatments (methyl jasmonate, salicylic acid, and abscisic acid) affected the expression levels of BrrLOX genes and that different BrrLOX genes responded differently to these stresses. In addition, weighted gene co-expression network analysis (WGCNA) of BrrLOX revealed seven co-expression modules, and the genes in these co-expression modules are collectively involved in plant growth and development and stress response processes. Thus, our results provide valuable information for the functional identification and regulatory mechanisms of BrrLOX in turnip growth and development and stress response. creator: Cunyao Yan creator: Kai Jia creator: Jing Zhang creator: Zhonglin Xiao creator: Xiaomei Sha creator: Jie Gao creator: Huizhuan Yan uri: https://doi.org/10.7717/peerj.13746 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yan et al. title: Comparison of sagittal plane gait characteristics between the overground and treadmill approach for gait analysis in typically developing children link: https://peerj.com/articles/13752 last-modified: 2022-07-22 description: BackgroundInstrumented treadmills have become more mainstream in clinical assessment of gait disorders in children, and are increasingly being applied as an alternative to overground gait analysis. Both approaches differ in multiple elements of set-up (e.g., overground versus treadmill, Pug-in Gait versus Human Body Model-II), workflow (e.g., limited amount of steps versus many successive steps) and post-processing of data (e.g., different filter techniques). These individual elements have shown to affect gait. Since the approaches are used in parallel in clinical practice, insight into the compound effect of the multiple different elements on gait is essential. This study investigates whether the outcomes of two approaches for 3D gait analysis are interchangeable in typically developing children.MethodsSpatiotemporal parameters, sagittal joint angles and moments, and ground reaction forces were measured in typically developing children aged 3–17 years using the overground (overground walking, conventional lab environment, Plug-In Gait) and treadmill (treadmill walking in virtual environment, Human Body Model-II) approach. Spatiotemporal and coefficient of variation parameters, and peak values in kinematics and kinetics of both approaches were compared using repeated measures tests. Kinematic and kinetic waveforms from both approaches were compared using statistical parametric mapping (SPM). Differences were quantified by mean differences and root mean square differences.ResultsChildren walked slower, with lower stride and stance time and shorter and wider steps with the treadmill approach than with the overground approach. Mean differences ranged from 0.02 s for stride time to 3.3 cm for step width. The patterns of sagittal kinematic and kinetic waveforms were equivalent for both approaches, but significant differences were found in amplitude. Overall, the peak joint angles were larger during the treadmill approach, showing mean differences ranging from 0.84° (pelvic tilt) to 6.42° (peak knee flexion during swing). Mean difference in peak moments ranged from 0.02 Nm/kg (peak knee extension moment) to 0.32 Nm/kg (peak hip extension moment), showing overall decreased joint moments with the treadmill approach. Normalised ground reaction forces showed mean differences ranging from 0.001 to 0.024.ConclusionThe overground and treadmill approach to 3D gait analysis yield different sagittal gait characteristics. The systematic differences can be due to important changes in the neuromechanics of gait and to methodological choices used in both approaches, such as the biomechanical model or the walkway versus treadmill. The overview of small differences presented in this study is essential to correctly interpret the results and needs to be taken into account when data is interchanged between approaches. Together with the research/clinical question and the context of the child, the insight gained can be used to determine the best approach. creator: Rachel Senden creator: Rik Marcellis creator: Kenneth Meijer creator: Paul Willems creator: Ton Lenssen creator: Heleen Staal creator: Yvonne Janssen creator: Vincent Groen creator: Roland Jeroen Vermeulen creator: Marianne Witlox uri: https://doi.org/10.7717/peerj.13752 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Senden et al. title: A diagnostic model for overweight and obesity from untargeted urine metabolomics of soldiers link: https://peerj.com/articles/13754 last-modified: 2022-07-22 description: Soldiers in active military service need optimal physical fitness for successfully carrying out their operations. Therefore, their health status is regularly checked by army doctors. These inspections include physical parameters such as the body-mass index (BMI), functional tests, and biochemical studies. If a medical exam reveals an individual’s excess weight, further examinations are made, and corrective actions for weight lowering are initiated. The collection of urine is non-invasive and therefore attractive for frequent metabolic screening. We compared the chemical profiles of urinary samples of 146 normal weight, excess weight, and obese soldiers of the Mexican Army, using untargeted metabolomics with liquid chromatography coupled to high-resolution mass spectrometry (LC-MS). In combination with data mining, statistical and metabolic pathway analyses suggest increased S-adenosyl-L-methionine (SAM) levels and changes of amino acid metabolites as important variables for overfeeding. We will use these potential biomarkers for the ongoing metabolic monitoring of soldiers in active service. In addition, after validation of our results, we will develop biochemical screening tests that are also suitable for civil applications. creator: Exsal M. Albores-Mendez creator: Alexis D. Aguilera Hernández creator: Alejandra Melo-González creator: Marco A. Vargas-Hernández creator: Neptalí Gutierrez de la Cruz creator: Miguel A. Vazquez-Guzman creator: Melchor Castro-Marín creator: Pablo Romero-Morelos creator: Robert Winkler uri: https://doi.org/10.7717/peerj.13754 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Albores-Mendez et al. title: Effects of self-selected versus motivational music on lower limb muscle strength and affective state in middle-aged adults link: https://peerj.com/articles/13795 last-modified: 2022-07-22 description: BackgroundStrength training plays a crucial role in promoting healthy ageing and music might affect how individuals perform and perceive strength exercises. This study aimed to investigate the effects of self-selected music (SSM) on muscle strength and affective states during maximal isometric contractions on a customized leg extension.MethodsTwenty-six healthy middle-aged males (50.8 ± 8.4 years) performed maximal and endurance isometric strength tests under three different conditions: SSM, motivational music (MM), and control condition (CC). Peak force and Rate of Force Development (RFD) were assessed during the maximal isometric strength test. The isometric endurance test evaluated the mean force and a fatigue index. Moreover, Felt Arousal Scale (FAS) was administered before the strength protocol, whereas the Rate of Perceived Exertion (RPE) and Feeling Scale (FS) at the end of it.ResultsMean force was significantly higher in the SSM (507.3 ± 132.2 N) than MM (476.3 ± 122.4 N, p < 0.01) and CC (484.6 ± 119.2 N, p = 0.03). FAS was significantly higher in the SSM (4.0 [1.3] than MM (3.0 [2.3], p < 0.01) and CC (3.0 [1.3], p < 0.01) conditions. FS was significantly higher in the SSM (4.0 [2.0] than MM (3.0 [1.3], p < 0.01) and CC (3.0 [1.3], p < 0.01) conditions. No significant differences were found for peak force, RFD, fatigue index, and RPE.ConclusionsListening to SSM seems to influence isometric endurance strength performance in middle-aged adults positively. Moreover, listening to SSM might improve individuals’ affective states without affecting the level of perceived exertion. creator: Francesca Greco creator: Luca Rotundo creator: Elisa Grazioli creator: Attilio Parisi creator: Attilio Carraro creator: Carolina Muscoli creator: Antonio Paoli creator: Giuseppe Marcolin creator: Gian Pietro Emerenziani uri: https://doi.org/10.7717/peerj.13795 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Greco et al. title: Identification and characterization of auxin response factor (ARF) family members involved in fig (Ficus carica L.) fruit development link: https://peerj.com/articles/13798 last-modified: 2022-07-22 description: The auxin response factor (ARF) combines with AuxREs cis-acting elements in response to auxin to regulate plant development. To date, no comprehensive analysis of ARF genes expressed during fruit development has been conducted for common fig (Ficus carica L.). In this study, members of the FcARF gene family were screened, identified in the fig genome database and their features characterized using bioinformatics. Twenty FcARF genes were clustered into three classes, with almost similar highly conserved DBD (B3-like DNA binding domain), AUX/IAA (auxin/indole-3-acetic acid gene family) and MR domain structure among class members. Analysis of amino acid species in MR domain revealed 10 potential transcription activators and 10 transcription inhibitors, and 17 FcARF members were predicted to be located in the nucleus. DNA sequence analysis showed that the ARF gene family consisted of 4–25 exons, and the promoter region contained 16 cis-acting elements involved in stress response, hormone response and flavonoid biosynthesis. ARF genes were expressed in most tissues of fig, especially flower and peel. Transcriptomics analysis results showed that FcARF2, FcARF11 and FcARF12, belonging to class-Ia, were stably and highly expressed in the early development stage of flower and peel of ‘Purple peel’ fig. However, their expression levels decreased after maturity. Expression of class-Ic member FcARF3 conformed to the regularity of fig fruit development. These four potential transcription inhibitors may regulate fruit growth and development of ‘Purple Peel’ fig. This study provides comprehensive information on the fig ARF gene family, including gene structure, chromosome position, phylogenetic relationship and expression pattern. Our work provides a foundation for further research on auxin-mediated fig fruit development. creator: Haomiao Wang creator: Hantang Huang creator: Yongkai Shang creator: Miaoyu Song creator: Huiqin Ma uri: https://doi.org/10.7717/peerj.13798 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: A spatiotemporal ensemble machine learning framework for generating land use/land cover time-series maps for Europe (2000–2019) based on LUCAS, CORINE and GLAD Landsat link: https://peerj.com/articles/13573 last-modified: 2022-07-21 description: A spatiotemporal machine learning framework for automated prediction and analysis of long-term Land Use/Land Cover dynamics is presented. The framework includes: (1) harmonization and preprocessing of spatial and spatiotemporal input datasets (GLAD Landsat, NPP/VIIRS) including five million harmonized LUCAS and CORINE Land Cover-derived training samples, (2) model building based on spatial k-fold cross-validation and hyper-parameter optimization, (3) prediction of the most probable class, class probabilities and model variance of predicted probabilities per pixel, (4) LULC change analysis on time-series of produced maps. The spatiotemporal ensemble model consists of a random forest, gradient boosted tree classifier, and an artificial neural network, with a logistic regressor as meta-learner. The results show that the most important variables for mapping LULC in Europe are: seasonal aggregates of Landsat green and near-infrared bands, multiple Landsat-derived spectral indices, long-term surface water probability, and elevation. Spatial cross-validation of the model indicates consistent performance across multiple years with overall accuracy (a weighted F1-score) of 0.49, 0.63, and 0.83 when predicting 43 (level-3), 14 (level-2), and five classes (level-1). Additional experiments show that spatiotemporal models generalize better to unknown years, outperforming single-year models on known-year classification by 2.7% and unknown-year classification by 3.5%. Results of the accuracy assessment using 48,365 independent test samples shows 87% match with the validation points. Results of time-series analysis (time-series of LULC probabilities and NDVI images) suggest forest loss in large parts of Sweden, the Alps, and Scotland. Positive and negative trends in NDVI in general match the land degradation and land restoration classes, with “urbanization” showing the most negative NDVI trend. An advantage of using spatiotemporal ML is that the fitted model can be used to predict LULC in years that were not included in its training dataset, allowing generalization to past and future periods, e.g. to predict LULC for years prior to 2000 and beyond 2020. The generated LULC time-series data stack (ODSE-LULC), including the training points, is publicly available via the ODSE Viewer. Functions used to prepare data and run modeling are available via the eumap library for Python. creator: Martijn Witjes creator: Leandro Parente creator: Chris J. van Diemen creator: Tomislav Hengl creator: Martin Landa creator: Lukáš Brodský creator: Lena Halounova creator: Josip Križan creator: Luka Antonić creator: Codrina Maria Ilie creator: Vasile Craciunescu creator: Milan Kilibarda creator: Ognjen Antonijević creator: Luka Glušica uri: https://doi.org/10.7717/peerj.13573 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Witjes et al. title: Variability within a clonal population of Erwinia amylovora disclosed by phenotypic analysis link: https://peerj.com/articles/13695 last-modified: 2022-07-21 description: BackgroundFire blight is a destructive disease of pome trees, caused by Erwinia amylovora, leading to high losses of chain-of-values fruits. Major outbreaks were registered between 2010 and 2017 in Portugal, and the first molecular epidemiological characterization of those isolates disclosed a clonal population with different levels of virulence and susceptibility to antimicrobial peptides.MethodsThis work aimed to further disclose the genetic characterization and unveil the phenotypic diversity of this E. amylovora population, resorting to MLSA, growth kinetics, biochemical characterization, and antibiotic susceptibility.ResultsWhile MLSA further confirmed the genetic clonality of those isolates, several phenotypic differences were recorded regarding their growth, carbon sources preferences, and chemical susceptibility to several antibiotics, disclosing a heterogeneous population. Principal component analysis regarding the phenotypic traits allows to separate the strains Ea 630 and Ea 680 from the remaining.DiscussionRegardless the genetic clonality of these E. amylovora strains isolated from fire blight outbreaks, the phenotypic characterization evidenced a population diversity beyond the genotype clonality inferred by MLSA and CRISPR, suggesting that distinct sources or environmental adaptations of this pathogen may have occurred.ConclusionAttending the characteristic clonality of E. amylovora species, the data gathered here emphasizes the importance of phenotypic assessment of E. amylovora isolates to better understand their epidemiological behavior, namely by improving source tracking, make risk assessment analysis, and determine strain-specific environmental adaptations, that might ultimately lead to prevent new outbreaks. creator: Rafael J. Mendes creator: Conceição Amaro creator: João Pedro Luz creator: Fernando Tavares creator: Conceição Santos uri: https://doi.org/10.7717/peerj.13695 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mendes et al. title: Identification and validation of immune related core transcription factors GTF2I in NAFLD link: https://peerj.com/articles/13735 last-modified: 2022-07-21 description: BackgroundNonalcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide that endangers human health. Transcription factors (TFs) have gradually become hot spots for drug development in NAFLD for their impacts on metabolism. However, the specific TFs that regulate immune response in the development of NAFLD is not clear. This study aimed to investigate the TFs involved in the immune response of NAFLD and provide novel targets for drug development.MethodsMicroarray data were obtained from liver samples from 26 normal volunteers and 109 NAFLD patients using the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were analyzed by limma package. Differentially expressed transcription factors (DETFs) were obtained on DEGs combined with Cistrome Cancer database. Immune signatures and pathways hallmark were identified by ssGSSEA and GSVA. The co-regulation network was constructed by the above results. Further, quantitative Real-time Polymerase Chain Reaction (qRT-PCR), Western blot (WB) and Immunohistochemistry (IHC) were used to validate the relationship between GTF2I and NAFLD. CIBERSORT analysis was performed to identify cell types to explore the relationship between differential expression of GTF2I and immune cell surface markers.ResultsA total of 617 DEGs and six DETFs (ESR1, CHD2, GTF2I, EGR1, HCFC1, SP2) were obtained by differential analysis. Immune signatures and pathway hallmarks were identified by ssGSSEA and GSVA. GTF2I and CHD2 were screened through the co-regulatory networks of DEGs, DETFs, immune signatures and pathway hallmarks. Furthermore, qRT-PCR, WB and IHC indicated that GTF2I but not CHD2 was significantly upregulated in NAFLD. Finally, in silico, our data confirmed that GTF2I has a wide impact on the immune profile by negatively regulating the expression of the chemokine receptor family (227/261, count of significance).ConclusionGTF2I plays a role in NAFLD by negatively regulating the chemokine receptor family, which affects the immune profile. This study may provide a potential target for the diagnosis or therapy of NAFLD. creator: Minbo Zhang creator: Yu Zhang creator: Xiaoxiao Jiao creator: Linying Lai creator: Yiting Qian creator: Bo Sun creator: Wenzhuo Yang uri: https://doi.org/10.7717/peerj.13735 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: The function of small RNA in Pseudomonas aeruginosa link: https://peerj.com/articles/13738 last-modified: 2022-07-21 description: Pseudomonas aeruginosa, the main conditional pathogen causing nosocomial infection, is a gram-negative bacterium with the largest genome among the known bacteria. The main reasons why Pseudomonas aeruginosa is prone to drug-resistant strains in clinic are: the drug-resistant genes in its genome and the drug resistance easily induced by single antibiotic treatment. With the development of high-throughput sequencing technology and bioinformatics, the functions of various small RNAs (sRNA) in Pseudomonas aeruginosa are being revealed. Different sRNAs regulate gene expression by binding to protein or mRNA to play an important role in the complex regulatory network. In this article, first, the importance and biological functions of different sRNAs in Pseudomonas aeruginosa are explored, and then the evidence and possibilities that sRNAs served as drug therapeutic targets are discussed, which may introduce new directions to develop novel disease treatment strategies. creator: Pei Liu creator: Changwu Yue creator: Lihua Liu creator: Can Gao creator: Yuhong Lyu creator: Shanshan Deng creator: Hongying Tian creator: Xu Jia uri: https://doi.org/10.7717/peerj.13738 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Soil carbon sequestration potential in global croplands link: https://peerj.com/articles/13740 last-modified: 2022-07-21 description: Improving the amount of organic carbon in soils is an attractive alternative to partially mitigate climate change. However, the amount of carbon that can be potentially added to the soil is still being debated, and there is a lack of information on additional storage potential on global cropland. Soil organic carbon (SOC) sequestration potential is region-specific and conditioned by climate and management but most global estimates use fixed accumulation rates or time frames. In this study, we model SOC storage potential as a function of climate, land cover and soil. We used 83,416 SOC observations from global databases and developed a quantile regression neural network to quantify the SOC variation within soils with similar environmental characteristics. This allows us to identify similar areas that present higher SOC with the difference representing an additional storage potential. We estimated that the topsoils (0–30 cm) of global croplands (1,410 million hectares) hold 83 Pg C. The additional SOC storage potential in the topsoil of global croplands ranges from 29 to 65 Pg C. These values only equate to three to seven years of global emissions, potentially offsetting 35% of agriculture’s 85 Pg historical carbon debt estimate due to conversion from natural ecosystems. As SOC store is temperature-dependent, this potential is likely to reduce by 14% by 2040 due to climate change in a “business as usual” scenario. The results of this article can provide a guide to areas of focus for SOC sequestration, and highlight the environmental cost of agriculture. creator: José Padarian creator: Budiman Minasny creator: Alex McBratney creator: Pete Smith uri: https://doi.org/10.7717/peerj.13740 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Padarian et al. title: Growth parameters and responses of green algae across a gradient of phototrophic, mixotrophic and heterotrophic conditions link: https://peerj.com/articles/13776 last-modified: 2022-07-21 description: Many studies have shown that algal growth is enhanced by organic carbon and algal mixotrophy is relevant for physiology and commercial cultivation. Most studies have tested only a single organic carbon concentration and report different growth parameters which hampers comparisons and improvements to algal cultivation methodology. This study compared growth of green algae Chlorella vulgaris and Chlamydomonas reinhardtii across a gradient of photoautotrophic-mixotrophic-heterotrophic culture conditions, with five acetate concentrations. Culture growth rates and biomass achieved were compared using different methods of biomass estimation. Both species grew faster and produced the most biomass when supplied with moderate acetate concentrations (1–4 g L−1), but light was required to optimize growth rates, biomass yield, cell size and cell chlorophyll content. Higher acetate concentration (10 g L−1) inhibited algal production. The choice of growth parameter and method to estimate biomass (optical density (OD), chlorophyll a fluorescence, flow cytometry, cell counts) affected apparent responses to organic carbon, but use of OD at 600, 680 or 750 nm was consistent. There were apparent trade-offs among exponential growth rate, maximum biomass, and culture time spent in exponential phase. Different cell responses over 1–10 g L−1 acetate highlight profound physiological acclimation across a gradient of mixotrophy. In both species, cell size vs cell chlorophyll relationships were more constrained in photoautotrophic and heterotrophic cultures, but under mixotrophy, and outside exponential growth phase, these relationships were more variable. This study provides insights into algal physiological responses to mixotrophy but also has practical implications for choosing parameters for monitoring commercial algal cultivation. creator: Erica B. Young creator: Lindsay Reed creator: John A. Berges uri: https://doi.org/10.7717/peerj.13776 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Young et al. title: FastANI, Mash and Dashing equally differentiate between Klebsiella species link: https://peerj.com/articles/13784 last-modified: 2022-07-21 description: Bacteria of the genus Klebsiella are among the most important multi-drug resistant human pathogens, though they have been isolated from a variety of environments. The importance and ubiquity of these organisms call for quick and accurate methods for their classification. Average Nucleotide Identity (ANI) is becoming a standard for species delimitation based on whole genome sequence comparison. However, much faster genome comparison tools have been appearing in the literature. In this study we tested the quality of different approaches for genome-based species delineation against ANI. To this end, we compared 1,189 Klebsiella genomes using measures calculated with Mash, Dashing, and DNA compositional signatures, all of which run in a fraction of the time required to obtain ANI. Receiver Operating Characteristic (ROC) curve analyses showed equal quality in species discrimination for ANI, Mash and Dashing, with Area Under the Curve (AUC) values above 0.99, followed by DNA signatures (AUC: 0.96). Accordingly, groups obtained at optimized cutoffs largely agree with species designation, with ANI, Mash and Dashing producing 15 species-level groups. DNA signatures broke the dataset into more than 30 groups. Testing Mash to map species after adding draft genomes to the dataset also showed excellent results (AUC above 0.99), producing a total of 26 Klebsiella species-level groups. The ecological niches of Klebsiella strains were found to neither be related to species delimitation, nor to protein functional content, suggesting that a single Klebsiella species can have a wide repertoire of ecological functions. creator: Julie E. Hernández-Salmerón creator: Gabriel Moreno-Hagelsieb uri: https://doi.org/10.7717/peerj.13784 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hernández-Salmerón and Moreno-Hagelsieb title: Cross-sectional associations between effort-reward imbalance at work and oral diseases in Japan link: https://peerj.com/articles/13792 last-modified: 2022-07-21 description: BackgroundPsychological stress is a potential risk factor for oral diseases. However, evidence for the association between work stress and oral diseases is scarce. We aimed to examine the associations of work stress, according to the effort-reward imbalance model, with dental caries, periodontal status, and tooth loss.MethodsThis cross-sectional study included 184 regular employees at a medical university and 435 registrants of a web research company. Work stress was assessed using the effort-reward imbalance (ERI) ratio. Dental caries and tooth loss were assessed according to the number of decayed, filled, and missing teeth (DMFT) among the set of 28 teeth. Periodontal status was assessed using a self-administered questionnaire. For the DMFT, a linear regression model was used to estimate the unstandardised coefficients. A Poisson regression model was used to estimate the prevalence ratios (PRs) of poor periodontal status.ResultsAmong medical university employees and employees enrolled from among the registrants of an online research company, a one-unit increase in the ERI ratio was associated with −2.81 (95% CI [−4.70 to −0.92]; p-value = 0.004) and −0.84 (95% CI [−1.80 to 0.12]; p-value = 0.085) changes in the DMFT from adjusted linear regression models, respectively. In employees enrolled from among the registrants of an online research company, a one-unit increase in the ERI ratio was also associated with 1.55 (95% CI [1.04–2.32]; p-value = 0.032) of the PR for poor periodontal status based on Poisson regression models.ConclusionERI at work was associated with an increased risk of poor periodontal status. creator: Yukihiro Sato creator: Eiji Yoshioka creator: Masanori Takekawa creator: Yasuaki Saijo uri: https://doi.org/10.7717/peerj.13792 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sato et al. title: Effects of growing Coptis chinensis Franch in the natural understory vs. under a manmade scaffold on its growth, alkaloid contents, and rhizosphere soil microenvironment link: https://peerj.com/articles/13676 last-modified: 2022-07-20 description: BackgroundThe main planting modes currently used for the production of Coptis chinensis Franch are under the shade of a manmade scaffold or a natural understory. In this study, we analysed changes in the growth, development, and alkaloids of C. chinensis when grown in a natural understory compared with under a manmade scaffold. We also clarified the differences in the rhizosphere soil microenvironment, represented by soil physicochemical factors, enzyme activity, and microbial community structure of 1- to 5-year-old C. chinensis between the different planting modes. These results will provide theoretical guidance and scientific evidence for the development, application, and extension of ecological planting technologies for C. chinensis.ResultsThe results of this study showed that rhizome length, rhizome diameter, and rhizome weight all increased over time in both planting modes. The greatest rhizome length was reached in 4-year-old C. chinensis, while the greatest rhizome diameter and rhizome weight were obtained in 5-year-old C. chinensis. There was no significant difference in rhizome biomass between the two planting modes. The alkaloid content of the four common alkaloids in the rhizome of 5-year-old C. chinensis at the harvest stage met the standards found in the Pharmacopoeia of the People’s Republic of China; the berberine content and total alkaloids in the rhizomes were significantly higher with natural understory planting compared to planting under a manmade scaffold. A redundancy analysis revealed that the physicochemical factors and enzyme activity of rhizosphere soil were significantly correlated with variation in microbial community structure. Soil pH, available potassium, bulk density, available nitrogen, catalase, and peroxidase were all significantly correlated with bacterial and fungal community structures. Among these, soil pH was the most important factor influencing the structures of the fungal and bacterial community. In the two planting modes, the differences in soil enzyme activity and microbial community structure mainly manifested in the rhizosphere soil of C. chinensis between different growth years, as there was little difference between the rhizosphere soil of C. chinensis in a given growth year under different planting modes. The levels of nitrogen, phosphorus, potassium, and organic matter in the rhizosphere soil under either planting mode were closely associated with the type and amount of fertiliser applied to C. chinensis. Investigating the influence of different fertilisation practices on nutrient cycling in farmland and the relationship between fertilisation and the soil environment will be key to improving the yield and quality of C. chinensis medicinal materials while maintaining the health of the soil microenvironment. creator: Yu Wang creator: Yu R. Mo creator: Jun Tan creator: Li X. Wu creator: Yuan Pan creator: Xia D. Chen uri: https://doi.org/10.7717/peerj.13676 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Evaluating the readability, quality and reliability of online patient education materials on post-covid pain link: https://peerj.com/articles/13686 last-modified: 2022-07-20 description: BackgroundThe use of the Internet to access healthcare-related information is increasing day by day. However, there are concerns regarding the reliability and comprehensibility of this information. This study aimed to investigate the readability, reliability, and quality of Internet-based patient educational materials (PEM) related to “post-COVID-19 pain.”MethodsOne-hundred websites that fit the purposes of the study were identified by searching for the terms “post-COVID-19 pain” and “pain after COVID-19” using the Google search engine on February 24, 2022. The website readability was assessed using the Flesch Reading Ease Score (FRES), Flesch–Kincaid Grade Level (FKGL), Simple Measure of Gobbledygook (SMOG), and Gunning FOG (GFOG). The reliability, quality, and popularity of the websites were assessed using the JAMA score, DISCERN score/Health on the Net Foundation code of conduct, and Alexa, respectively.ResultsUpon investigation of the textual contents, the mean FRES was 51.40 ± 10.65 (difficult), the mean FKGL and SMOG were 10.93 ± 2.17 and 9.83 ± 1.66 years, respectively, and the mean GFOG was 13.14 ± 2.16 (very difficult). Furthermore, 24.5% of the websites were highly reliable according to JAMA scores, 8% were of high quality according to GQS values, and 10% were HONcode-compliant. There was a statistically significant difference between the website types and reliability (p = 0.003) and quality scores (p = 0.002).ConclusionThe readability level of PEM on post-COVID-19 pain was considerably higher than grade 6 educational level, as recommended by the National Institutes of Health, and had low reliability and poor quality. We suggest that Internet-based PEM should have a certain degree of readability that is in accordance with the educational level of the general public and feature reliable content. creator: Erkan Ozduran creator: Sibel Büyükçoban uri: https://doi.org/10.7717/peerj.13686 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ozduran and Büyükçoban title: Baleen whale inhalation variability revealed using animal-borne video tags link: https://peerj.com/articles/13724 last-modified: 2022-07-20 description: Empirical metabolic rate and oxygen consumption estimates for free-ranging whales have been limited to counting respiratory events at the surface. Because these observations were limited and generally viewed from afar, variability in respiratory properties was unknown and oxygen consumption estimates assumed constant breath-to-breath tidal volume and oxygen uptake. However, evidence suggests that cetaceans in human care vary tidal volume and breathing frequency to meet aerobic demand, which would significantly impact energetic estimates if the findings held in free-ranging species. In this study, we used suction cup-attached video tags positioned posterior to the nares of two humpback whales (Megaptera novaeangliae) and four Antarctic minke whales (Balaenoptera bonaerensis) to measure inhalation duration, relative nares expansion, and maximum nares expansion. Inhalation duration and nares expansion varied between and within initial, middle, and terminal breaths of surface sequences between dives. The initial and middle breaths exhibited the least variability and had the shortest durations and smallest nares expansions. In contrast, terminal breaths were highly variable, with the longest inhalation durations and the largest nares expansions. Our results demonstrate breath-to-breath variability in duration and nares expansion, suggesting differential oxygen exchange in each breath during the surface interval. With future validation, inhalation duration or nares area could be used alongside respiratory frequency to improve oxygen consumption estimates by accounting for breath-to-breath variation in wild whales. creator: Emily C. Nazario creator: David E. Cade creator: K.C. Bierlich creator: Max F. Czapanskiy creator: Jeremy A. Goldbogen creator: Shirel R. Kahane-Rapport creator: Julie M. van der Hoop creator: Merceline T. San Luis creator: Ari S. Friedlaender uri: https://doi.org/10.7717/peerj.13724 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nazario et al. title: Experiencing the impossible and creativity: a targeted literature review link: https://peerj.com/articles/13755 last-modified: 2022-07-20 description: Previous work suggests that unexpected and surprising experiences (e.g., living in another culture or looking at surreal images) promotes creative thinking. This targeted literature review examines whether the inherent cognitive disruption associated with experiencing the seemingly impossible has a similar effect. Correlational and experimental research across six domains (entertainment magic, fantasy play, virtual reality and computer gaming, dreaming, science fiction/fantasy, and anomalous experiences) provided consistent support for the hypothesis. In addition, anecdotal evidence illustrated the possible impact that the creative output associated with each of these areas may have had on technology, science, and the arts. It is argued that impossible experiences are an important driver of creative thinking, thus accounting for reports of such experiences across the lifespan and throughout history. The theoretical and practical implications of this work are discussed, along with recommendations for future research. creator: Richard Wiseman creator: Caroline Watt uri: https://doi.org/10.7717/peerj.13755 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wiseman and Watt title: Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships link: https://peerj.com/articles/13772 last-modified: 2022-07-20 description: Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history. creator: Isabel Duarte-Velázquez creator: Javier de la Mora creator: Jorge Humberto Ramírez-Prado creator: Alondra Aguillón-Bárcenas creator: Fátima Tornero-Gutiérrez creator: Eugenia Cordero-Loreto creator: Fernando Anaya-Velázquez creator: Itzel Páramo-Pérez creator: Ángeles Rangel-Serrano creator: Sergio Rodrigo Muñoz-Carranza creator: Oscar Eduardo Romero-González creator: Luis Rafael Cardoso-Reyes creator: Ricardo Alberto Rodríguez-Ojeda creator: Héctor Manuel Mora-Montes creator: Naurú Idalia Vargas-Maya creator: Felipe Padilla-Vaca creator: Bernardo Franco uri: https://doi.org/10.7717/peerj.13772 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Duarte-Velázquez et al. title: Knowledge, attitude and practice towards bio-medical waste management among healthcare workers: a northern Saudi study link: https://peerj.com/articles/13773 last-modified: 2022-07-20 description: BackgroundHealth care workers (HCWs) involved in day-to-day care and other healthcare activities play a significant role in biomedical waste (BMW) management. The World Health Organization stated some of the causes for the failure of BMW management, namely, lack of awareness of the health hazards related to BMW and inadequate trained HCWs in BMW management. The present study assessed knowledge, attitude, and practice (KAP) towards BMW management among the HCWs in northern Saudi Arabia.MethodologyThe present study assessed KAP through a self-administered and validated questionnaire. Using a multistage probability sampling method, 384 HCWs from different healthcare facilities participated in this survey. We performed binomial logistic regression analysis to find association between KAP subscales and sociodemographic characteristics. Spearman’s correlation test was performed to find the strength and direction of correlation (rho) between KAP scores.ResultsOf the population studied, high knowledge, attitude, and practice scores were found in 47.1%, 65.1%, and 49.5% of the HCWs, respectively. The present study found that knowledge score was significantly higher among the age group from 30 to 39 years (ref: age less than 30 years: AOR = 2.25, 95% CI [1.05–4.85], p = 0.04) and non- Saudi nationals (ref: Saudi: AOR = 2.84, 95% CI [1.63–4.94], p < 0.001) The attitude score towards BMW management was significantly lower among the HCWs working in tertiary care settings (ref: PHC: AOR = 0.38, 95% CI [0.12–0.69], p = 0.01). Regarding the practice score, the male categories had a significantly higher score (ref: female: AOR = 1.82, 95% CI [1.19 –2.99], p = 0.02), while pharmacist (ref: physicians: AOR = 0.39, 95% CI [0.18–0.58], p = 0.02) and lab technicians (ref: physicians: AOR = 0.31, 95% CI [0.11–0.53], p = 0.02) had a significant lower practice score. The test results revealed a weak positive correlation of knowledge with the attitude scores (rho = 0.249, p = 0.001), and a moderately strong positive correlation was found between attitude and practice scores (rho = 0.432, p = 0.001).ConclusionThis study suggests that a regular training program for the HCWs on BMW management is necessary through symposiums, role play, interactive lectures, and other feasible training methods. Furthermore, a multicentric prospective exploratory study is to be conducted in other regions of the KSA to understand the region-specific training needs of HCWs. creator: Ashokkumar Thirunavukkarasu creator: Ahmad Homoud Al-Hazmi creator: Umar Farooq Dar creator: Ahmed Mohammed Alruwaili creator: Saleh Dhifallah Alsharari creator: Fahad Adel Alazmi creator: Saif Farhan Alruwaili creator: Abdullah Mohammed Alarjan uri: https://doi.org/10.7717/peerj.13773 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Thirunavukkarasu et al. title: Engineering a tunable bicistronic TetR autoregulation expression system in Gluconobacter oxydans link: https://peerj.com/articles/13639 last-modified: 2022-07-19 description: Acetic acid bacteria are well-known for their ability to incompletely oxidize their carbon sources. Many of the products of these oxidations find industrial uses. Metabolic engineering of acetic acid bacteria would improve production efficiency and yield by allowing controllable gene expression. However, the molecular tools necessary for regulating gene expression have only recently started being explored. To this end the ability of the activation-dependent Plux system and two constitutive repression Ptet systems were examined for their ability to modulate gene expression in Gluconobacter oxydans. The activation-dependent Plux system increased gene expression approximately 5-fold regardless of the strength of the constitutive promoter used to express the luxR transcriptional activator. The Ptet system was tunable and had a nearly 20-fold induction when the tetR gene was expressed from the strong constitutive promoters P0169 and P264, but only had a 4-fold induction when a weak constitutive promoter (P452) was used for tetR expression. However, the Ptet system was somewhat leaky when uninduced. To mitigate this background activity, a bicistronic TetR expression system was constructed. Based on molecular modeling, this system is predicted to have low background activity when not induced with anhydrotetracycline. The bicistronic system was inducible up to >3,000-fold and was highly tunable with almost no background expression when uninduced, making this bicistronic system potentially useful for engineering G. oxydans and possibly other acetic acid bacteria. These expression systems add to the newly growing repertoire of suitable regulatable promoter systems in acetic acid bacteria. creator: Monica Bertucci creator: Ky Ariano creator: Meg Zumsteg creator: Paul Schweiger uri: https://doi.org/10.7717/peerj.13639 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bertucci et al. title: Ubiquitin-proteasome system in diabetic retinopathy link: https://peerj.com/articles/13715 last-modified: 2022-07-19 description: Diabetic retinopathy (DR) is the most common complication of diabetes, being the most prevalent reason for blindness among the working-age population in the developed world. Despite constant improvement of understanding of the pathogenesis of DR, identification of novel biomarkers of DR is needed for improvement of patient risk stratification and development of novel prevention and therapeutic approaches. The ubiquitin-proteasome system (UPS) is the primary protein quality control system responsible for recognizing and degrading of damaged proteins. This review aims to summarize literature data on modifications of UPS in diabetes and DR. First, we briefly review the structure and functions of UPS in physiological conditions. We then describe how UPS is involved in the development and progression of diabetes and touch upon the association of UPS genetic factors with diabetes and its complications. Further, we focused on the effect of diabetes-induced hyperglycemia, oxidative stress and hypoxia on UPS functioning, with examples of studies on DR. In other sections, we discussed the association of several other mechanisms of DR (endoplasmic reticulum stress, neurodegeneration etc) with UPS modifications. Finally, UPS-affecting drugs and remedies are reviewed. This review highlights UPS as a promising target for the development of therapies for DR prevention and treatment and identifies gaps in existing knowledge and possible future study directions. creator: Zane Svikle creator: Beate Peterfelde creator: Nikolajs Sjakste creator: Kristine Baumane creator: Rasa Verkauskiene creator: Chi-Juei Jeng creator: Jelizaveta Sokolovska uri: https://doi.org/10.7717/peerj.13715 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Svikle et al. title: When does self-report of pain occur?: A study of older adults link: https://peerj.com/articles/13716 last-modified: 2022-07-19 description: Technologies for self-care can drive participatory health and promote independence of older adults. One self-care activity is regularly measuring and registering personal health indicators (self-reporting). Older adults may benefit from this practice, as they are more likely to have chronic health issues and have specific self-monitoring needs. However, self-reporting technologies are usually not designed specifically for them. Pain is usually measured using patient reports compiled during medical appointments, although this process may be affected by memory bias and under reporting of fluctuating pain. To address these issues, we introduced a simple tangible interface to self-report pain levels and conducted a three-hour evaluation with 24 older adults. The goal of this study was to identify whether specific activities, activity levels or pain levels trigger older adults to self-report their pain level, besides to understand how older adults would use such a device. Within the limited time frame of the experiment, the majority of our participants chose to report pain when they felt it most, not reporting lower levels of pain. No evidence was found to suggest a relationship between the reporting of pain and the activity (or activity level). Several design insights intended to improve the design of technologies are provided. creator: Iyubanit Rodríguez creator: Gabriela Cajamarca creator: Valeria Herskovic uri: https://doi.org/10.7717/peerj.13716 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Rodríguez et al. title: Diversity and distribution of air-breathing sea slug genus Peronia Fleming, 1822 (Gastropoda: Onchidiidae) in southern Japanese waters link: https://peerj.com/articles/13720 last-modified: 2022-07-19 description: Species of the genus Peronia Fleming, 1822, are air-breathing onchidiid sea slugs that inhabit intertidal reef flats of temperate to tropical zones. In the Ryukyu Islands of southern subtropical Japan, Peronia species are a traditional food source for local people. To date, there have been three species recorded around Okinawajima Island; P. verruculata and P. peronii, along with recently described P. okinawensis, which was described as possibly endemic to Okinawajima Island. This study aimed to map the distribution ranges of these three Peronia species within the Ryukyu Islands using molecular analyses in order to understand the specific distribution of each species. Since Peronia species are generally indistinguishable by gross external morphology, a DNA barcoding approach was employed to identify specimens. The molecular data showed that there are four species present in the Ryukyu Islands. P. verruculata (unit #1 sensuDayrat et al., 2020) was dominant at almost all locations, while P. peronii was present in much lower numbers than P. verruculata, but found across a relatively wide range in the Ryukyu Islands. We newly record P. okinawensis and P. setoensis from Amami Oshima Island and from several places around Okinawajima Island, and also identified high levels of genetic variation within P. setoensis. Peronia okinawensis and P. setoensis have been thought to be endemic to Okinawajima Island and to Honshu, mainland Japan, respectively. However, as both species were observed around Okinawajima and Amami Oshima islands, other islands of the Ryukyus are also likely to harbor these species, and their distribution ranges are wider than previously thought. Based on the results from molecular analyses, we provide general descriptions of each species. Sizes of specimens were consistently smaller for P. setoensis and relatively larger for P. peronii specimens. On the other hand, P. verruculata and P. okinawensis had similar size ranges, but P. okinawensis had comparatively much more distinct papillae. This study revealed that the Ryukyu Islands are the only region currently known with four sympatric Peronia species, and this work provides a basis for future research on these Peronia species throughout the northwest Pacific Ocean, representing the first step in more effective management of the local Peronia fisheries in the Ryukyu Islands. creator: Iori Mizukami creator: Chloé Julie Loïs Fourreau creator: Sakine Matsuo creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.13720 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mizukami et al. title: Comparative genomic analysis of the COBRA genes in six Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri) link: https://peerj.com/articles/13723 last-modified: 2022-07-19 description: COBRA-Like (COBL) genes encode a glycosylphosphatidylinositol (GPI) anchoring protein unique to plants. In current study, 87 COBRA genes were identified in 6 Rosaceae species, including Pyrus bretschneideri (16 genes), Malus domestica (22 genes), Fragaria vesca (13 genes), Prunus mume (11 genes), Rubus occidentalis (13 genes) and Prunus avium (12 genes). We revealed the evolution of the COBRA gene in six Rosaceae species by phylogeny, gene structure, conservative sequence, hydrophobicity analysis, gene replication events and sliding window analysis. In addition, based on the analysis of expression patterns in pear fruit combined with bioinformatics, we identified PbCOBL12 and PbCOBL13 as potential genes regulating secondary cell wall (SCW) formation during pear stone cell development. This study aimed to understand the evolutionary relationship of the COBRA gene in Rosaceae species, clarify the potential function of COBRA in pear fruit development, and provide essential theoretical basis and gene resources for improving pear fruit quality through genetical modification mechanism. creator: Yu Zhao creator: Xueqiang Su creator: Xinya Wang creator: Mengna Wang creator: Xiaofeng Feng creator: Muhammad Aamir Manzoor creator: Yongping Cai uri: https://doi.org/10.7717/peerj.13723 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhao et al. title: Adaptive multi-paddock grazing management’s influence on soil food web community structure for: increasing pasture forage production, soil organic carbon, and reducing soil respiration rates in southeastern USA ranches link: https://peerj.com/articles/13750 last-modified: 2022-07-19 description: BackgroundMeasurement of two grazing management’s influence on pasture productivity, soil food web structure, soil organic carbon and soil microbial respiration efficiency was conducted on five southeastern US, across-the-fence ranch pairs to compare adaptive multi-paddock grazing (AMP) management, using short grazing events with planned, adaptive recovery periods, to conventional grazing (CG) management, with continuous grazing at low stock density.MethodologyA point-in-time experimental field analysis was conducted to compare five AMP or CG ranch pairs to better understand the influence of grazing management on (a) standing crop biomass productivity; (b) soil food web community population, structure and functionality; (c) soil organic carbon accrual; and d) soil-C (CO2) respiration kinetics.ResultsAMP grazing systems outperformed CG systems by generating: (a) 92.68 g m−2 more standing crop biomass (SCB), promoting 46% higher pasture photosynthetic capacity (Two sample Mann-Whitney; Z = 6.1836; no DF in MW; p = 6.26 × 10−10; Effect size = 0.35) (b) a strong positive linear relationship of SCB with fungal biomass (R = 0.9915; F(1,3) = 175.35; p = 0.015); fungal to bacterial (F:B) biomass ratio (R = 0.9616; F(1,3) = 36.75; p = 0.009) and a soil food web proxy (R = 0.9616; F(1,3) = 36.75; p = 0.009) and a concurrent very strong inverse relationship with bacteria biomass (R = −0.946; F(1,3) = 25.56; p = 0.015); (c) significant predator/prey interactions with an inverse relationship with bacterial population biomass (R =  − 0.946; F(1,3) = 25.56; p = 0.015) and a positive relationship with total protozoa enumeration (R = 0.9826; F(1,3) = 83.68; p = 0.003) when compared to SCB; (d) a 19.52% reduction in soil C (CO2) respiration rates (Two sample t-test; T = −2.3581; DF = 52.3541; p = 0.0221; Effect size = 0.59); and (e) a 20.6% increase in soil organic carbon (SOC) in the top 10 cm of soil profile (Two sample Mann–Whitney; Z = 2.6507; no DF in MW; p = 0.008; Effect size = 0.24). Rancher conversion to AMP grazing strategies would appear to regenerate soil food web population, structure, diversity and biological functionality helping to improve: carbon flow into plant biomass, buildup of soil carbon, predator/prey nutrient cycling and soil microbial respiration efficiency while offering improved climate resilience and a strategy to increase the capture and storage of atmospheric CO2 in soils of the world’s rangeland. creator: David C. Johnson creator: Richard Teague creator: Steven Apfelbaum creator: Ry Thompson creator: Peter Byck uri: https://doi.org/10.7717/peerj.13750 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Johnson et al. title: Plastic debris in plastic-mulched soil—a screening study from western Germany link: https://peerj.com/articles/13781 last-modified: 2022-07-19 description: BackgroundAgricultural plastic mulches offer great benefits such as higher yields and lower pesticide use. Yet, plastic mulches may disintegrate over time and fragment into smaller debris. Such plastic debris is expected to remain in the field after removal of the plastic mulch and thus contributes to soil contamination with plastics.MethodTo investigate this, we collected soil samples at 0–10 cm and 10–40 cm depth from three fields covered with black mulch film for three consecutive years. Three fields without any reported plastic use served as control. Visual plastic debris > 1 cm (macroplastics) was collected from the soil surface. Mesoplastics between 2 mm and 1 cm were density separated from the sampled soil using saturated NaCl solution and analyzed by Fourier-transform infrared spectroscopy. Debris ≤ 2 mm (microplastics) was dispersed from 50 g soil using sodium hexametaphosphate solution followed by the aforementioned density separation. The separated polyethylene (PE), polypropylene (PP), and polystyrene (PS) were quantified via solvent-based pyrolysis–gas chromatography/mass spectrometry (Py–GC/MS).ResultsWith 89–206 fragments ha−1, the majority of macroplastics were located in fields previously covered with mulch films. 80% of the collected specimen were identified as black PE film. The number of mesoplastics in plastic-mulched soil was 2.3 particles kg−1, while only 1.0 particles kg−1 were found in the reference fields. Py–GC/MS revealed microplastic levels of up to 13 mg kg−1. The PE content was significantly higher in plastic-mulched fields than in reference fields.DiscussionAlthough the identified plastic levels are lower than those reported in comparable studies, our results still suggest that plastic mulching functions as a source of plastic debris in agricultural systems. Due to its severely restricted degradability, these plastics are likely to accumulate in soil in the long term and further fragment into smaller and smaller debris. creator: Zacharias Steinmetz creator: Heike Schröder uri: https://doi.org/10.7717/peerj.13781 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Steinmetz and Schröder title: Coral micro-fragmentation assays for optimizing active reef restoration efforts link: https://peerj.com/articles/13653 last-modified: 2022-07-18 description: The global decline of coral reefs has driven considerable interest in active coral restoration. Despite their importance and dominance on mature reefs, relatively few coral restoration projects use slower growth forms like massive and encrusting coral species. Micro-fragmentation can increase coral cover by orders of magnitude faster than natural growth, which now allows cultivation of slow growing massive forms and shows promise and flexibility for active reef restoration. However, the major causes of variation in growth and survival of outplanted colonies remain poorly understood. Here, we report simple outplanting assays to aid in active reef restoration of slower growing species and increase the likelihood of restoration success. We used two different micro-fragmentation assays. Pyramid assays were used to examine variation associated with fragment size (ranging from ≈1–9 cm2), nursery residence time (for both in-situ and ex-situ nurseries), and 2D vs. 3D measurements of growth. Block assays were used to examine spatial variation among individual performance at outplanting sites in the field. We found 2D and 3D measurements correlated well, so measured survivorship and growth using top-down planar images for two of the main Hawaiian reef building corals, the plating Montipora capitata and the massive Porites compressa. Pyramid assays housed and outplanted from the in-situ nursery showed no effect of residence time or size on overall survivorship or growth for either species. Results from the ex-situ nursery, however, varied by species, with P. compressa again showing no effect of nursery residence time or size on survivorship or growth. In contrast, nursery culture resulted in improved survivorship of small M. capitata fragments, but net growth showed a weak positive effect of nursery time for medium fragments. Small fragments still suffered higher mortality than either medium or large fragments. Due to their lower mortality, medium fragments (≈3 cm2) appear to be the best compromise between growth and survivorship for outplanting. Likewise, given weak positive gains relative to the investment, our results suggest that it could be more cost-effective to simply outplant medium fragments as soon as possible, without intermediate culture in a nursery. Furthermore, the block assay revealed significant differences in survivorship and growth among sites for individuals of both species, emphasizing the importance of considering spatial variation in coral survival and growth following outplanting. These results highlight the value of using short-term micro-fragmentation assays prior to outplanting to assess size, and location specific performance, optimizing the efficiency of active reef restoration activities and maximizing the probability of success for active coral restoration projects. creator: Ingrid S.S. Knapp creator: Zac H. Forsman creator: Austin Greene creator: Erika C. Johnston creator: Claire E. Bardin creator: Norton Chan creator: Chelsea Wolke creator: David Gulko creator: Robert J. Toonen uri: https://doi.org/10.7717/peerj.13653 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Knapp et al. title: Active ingredients and molecular targets of Taraxacum mongolicum against hepatocellular carcinoma: network pharmacology, molecular docking, and molecular dynamics simulation analysis link: https://peerj.com/articles/13737 last-modified: 2022-07-18 description: BackgroundTaraxacum mongolicum (TM) is a widely used herb. Studies have reported that TM exhibits growth-inhibitory and apoptosis-inducing on multiple tumors, including hepatocellular carcinoma (HCC). The active ingredients, targets, and molecular mechanisms of TM against HCC need to be further elucidated.MethodsWe identified the active ingredients and targets of TM via HERB, PubChem, SwissADME, SwissTargetPrediction, and PharmMapper. We searched HCC targets from GeneCards, Comparative Toxicogenomics Database (CTD), and DisGeNET. Then, the intersection of drug targets and disease targets was uploaded to the STRING database to construct protein-protein interactions (PPI) networking whose topology parameters were analyzed in Cytoscape software to screen hub targets. Next, we used Metascape for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and we employed AutoDock vina, AMBER18 and PyMOL software along with several auxiliary tools for molecular docking and molecular dynamics (MD) simulation. Finally, based on the in silico findings, cellular experiments were conducted to investigate the effect of TM on HSP90AA1 gene expression.ResultsA total of 228 targets and 35 active ingredients were identified. Twenty two hub targets were selected through PPI networking construction for further investigation. The enrichment analysis showed that protein kinase binding, mitogenactivated protein kinase (MAPK) and phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathways were mainly involved. Molecular docking and MD simulation results supported good interaction between HSP90 protein and Austricin/Quercetin. The in vitro assay showed that TM inhibited the proliferation of HepG2 cells and the expression of HSP90AA1 gene.ConclusionsThis study is the first to use network pharmacology, molecular docking, MD simulation and cellular experiments to elucidate the active ingredients, molecular targets, and key biological pathways responsible for TM anti-HCC, providing a theoretical basis for further research. creator: Yanfeng Zheng creator: Shaoxiu Ji creator: Xia Li creator: Quansheng Feng uri: https://doi.org/10.7717/peerj.13737 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zheng et al. title: Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris) link: https://peerj.com/articles/13753 last-modified: 2022-07-18 description: The gut microbiota has key physiological functions in host adaptation, although little is known about the seasonal changes in the composition and diversity of the gut microbiota in deer. In this study, seasonal variations (grassy and withering season) in the gut microbiota of white-lipped deer (Cervus albirostris), which lives in alpine environments, were explored through 16S rRNA high-throughput sequencing based on sixteen fecal samples collected from Gansu Qilian Mountain National Nature Reserve in China. At the phylum level, Firmicutes, Bacteroidota, and Actinobacteriota dominated the grassy season, while Firmicutes, Proteobacteria, and Actinobacteriota dominated the withering season. At the genus level, Carnobacterium dominated the grassy season, while Arthrobacter and Acinetobacter dominated the withering season. Alpha diversity results (Shannon: P = 0.01, ACE: P = 0.00, Chao1: P = 0.00) indicated that there was a difference in the diversity and richness of the gut microbiota between the two seasons, with higher diversity in the grassy season than in the withering season. Beta diversity results further indicated that there was a significant difference in the community structure between the two seasons (P = 0.001). In summary, the composition, diversity, and community structure of the gut microbiota showed significant seasonal variations, which could be explained by variations in the seasonal food availability, composition, diversity, and nutrition due to phenological alternations. The results of this study indicate that the gut microbiota can adapt to changes in the environment and provide the scientific basis for health assessment of white-lipped deer. creator: Zhangqiang You creator: Jing Deng creator: Jialin Liu creator: Junhua Fu creator: Huan Xiong creator: Wei Luo creator: Jianli Xiong uri: https://doi.org/10.7717/peerj.13753 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 You et al. title: Structural and functional characteristics of soil microbial community in a Pinus massoniana forest at different elevations link: https://peerj.com/articles/13504 last-modified: 2022-07-15 description: Shifts in forest soil microbial communities over altitudinal gradients have long been attracting scientific interest. The distribution patterns of different soil microbial communities along altitudinal gradients in subtropical mountain forest ecosystems remain unclear. To better understand the changes in soil microbial communities along an altitude gradient, we used Illumina MiSeq metagenome sequencing technology to survey the soil microbial communities in a Pinus massoniana forest at four elevations (Mp1000, Mp1200, Mp1400, Mp1600) and in a tea garden in Guizhou Leigong Mountain in Southwestern China. We observed that the richness of bacteria, fungi, and viruses in the soil microbial community changed in a unimodal pattern with increasing elevation while that of Archaea first increased significantly, then decreased, and finally increased again. Euryarchaeota and Thaumarchaeota were the predominant Archaea, Proteobacteria and Acidobacteria were the predominant bacterial groups, Ascomycota and Basidiomycota were the predominant fungal groups, and Myoviridae, Podoviridae, and Siphoviridae were the predominant virus groups. Amino acid transport and metabolism, energy production and conversion, signal transduction mechanisms, and DNA replication, restructuring and repair were the predominant categories as per NOG function gene-annotation. Carbohydrate metabolism, global and overview map, amino acid metabolism, and energy metabolism were predominant categories in the KEGG pathways. Glycosyl transferase and glycoside hydrolase were predominant categories among carbohydrate enzyme-functional genes. Cluster, redundancy, and co-occurring network analyses showed obvious differences in the composition, structure, and function of different soil microbial communities along the altitudinal gradient studied. Our findings indicate that the different soil microbial communities along the altitudinal gradient have different distribution patterns, which may provide a better understanding of the mechanisms that determine microbial life in a mid-subtropical mountain forest ecosystem. creator: Jian Zhang creator: Ming Xu creator: Xiao Zou creator: Jin Chen uri: https://doi.org/10.7717/peerj.13504 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Muscone improves hypoxia/reoxygenation (H/R)-induced neuronal injury by blocking HMGB1/TLR4/NF-κB pathway via modulating microRNA-142 link: https://peerj.com/articles/13523 last-modified: 2022-07-15 description: Previous reports have indicated that natural muscone has neuroprotective effects against cerebral hypoxia injury; however, little is known in regards to its pharmacological mechanism. In this study, we tried to evaluate the neuroprotective effects and mechanisms of muscone against cerebral hypoxia injury using an in vitro model. The cerebral hypoxia injury cell model was produced by hypoxia/reoxygenation (H/R). The cell viability and apoptosis were measured using the cell counting Kit-8 and the Annexin V-FITC/PI Apoptosis Detection kit, respectively. To screen microRNAs regulated by muscone, we analyzed the gene expression datasets of GSE84216 retrieved from gene expression omnibus (GEO). Here, it was demonstrated that muscone treatment significantly alleviated the cell apoptosis, oxidative stress and inflammation in H/R-exposed neurons. Subsequently, through analyzing GSE84216 from the GEO database, miR-142-5p was markedly upregulated by treatment of muscone in this cell model of cerebral hypoxia injury. Further experiments revealed that downregulation of miR-142-5p eliminated the neuroprotective effects of muscone against H/R induced neuronal injury. Additionally, high mobility group box 1 (HMGB1), an important inflammatory factor, was identified as a direct target of miR-142-5p in neurons. Meanwhile, we further demonstrated that muscone could reduce the expression of HMGB1 by upregulating miR-142-5p expression, which subsequently resulted in the inactivation of TLR4/NF-κB pathway, finally leading to the improvement of cell injury in H/R-exposed neurons. Overall, we demonstrate for the first time that muscone treatment alleviates cerebral hypoxia injury in in vitro experiments through blocking activation of the TLR4/NF-κB signaling pathway by targeting HMGB1, suggesting that muscone may serve as a potential therapeutic drug for treating cerebral hypoxia injury. creator: Weihua Ren creator: Fucheng Zhao creator: Yanru Han creator: Zhenzhou Liu creator: Jianli Zhai creator: Kui Jia uri: https://doi.org/10.7717/peerj.13523 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ren et al. title: Oral manifestations in young adults infected with COVID-19 and impact of smoking: a multi-country cross-sectional study link: https://peerj.com/articles/13555 last-modified: 2022-07-15 description: BackgroundOral manifestations and lesions could adversely impact the quality of people’s lives. COVID-19 infection may interact with smoking and the impact on oral manifestations is yet to be discovered.ObjectivesThe aim of this study was to assess the self-reported presence of oral lesions by COVID-19-infected young adults and the differences in the association between oral lesions and COVID-19 infection in smokers and non-smokers.MethodsThis cross-sectional multi-country study recruited 18-to-23-year-old adults. A validated questionnaire was used to collect data on COVID-19-infection status, smoking and the presence of oral lesions (dry mouth, change in taste, and others) using an online platform. Multi-level logistic regression was used to assess the associations between the oral lesions and COVID-19 infection; the modifying effect of smoking on the associations. ResultsData was available from 5,342 respondents from 43 countries. Of these, 8.1% reported COVID-19-infection, 42.7% had oral manifestations and 12.3% were smokers. A significantly greater percentage of participants with COVID-19-infection reported dry mouth and change in taste than non-infected participants. Dry mouth (11.1% vs 7.5%, p = 0.009) and change in taste (11.5% vs 2.7%, p < 0.001) were greater in COVID-19 infected than non-infected persons. The association between COVID-19-infection and dry mouth was stronger among smokers than non-smokers (AOR = 1.26 and 1.03, p = 0.09) while the association with change in taste was stronger among non-smokers (AOR = 1.22 and 1.13, p = 0.86).ConclusionDry mouth and changed taste may be used as an indicator for COVID-19 infection in low COVID-19-testing environments. Smoking may modify the association between some oral lesions and COVID-19-infection. creator: Maha El Tantawi creator: Heba Jafar Sabbagh creator: Nada Abubakor Alkhateeb creator: Maryam Quritum creator: Joud Abourdan creator: Nafeesa Qureshi creator: Shabnum Qureshi creator: Ahmed Hamoud creator: Nada Mahmoud creator: Ruba Odeh creator: Nuraldeen Maher Al-Khanati creator: Rawiah Jaber creator: Abdulrahman Loaie Balkhoyor creator: Mohammed Shabi creator: Morenike O. Folayan creator: Noha Gomaa creator: Raqiya Al_Nahdi creator: Nawal Mahmoud creator: Hanane El Wazziki creator: Manal Alnaas creator: Bahia Samodien creator: Rawa Mahmoud creator: Nour Abu Assab creator: Sherin Saad creator: Sondos Al-Hachim creator: Ali Alshaikh creator: Wafaa Abdelaziz uri: https://doi.org/10.7717/peerj.13555 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 El Tantawi et al. title: Morphological and olfactory tree traits influence the susceptibility and suitability of the apple species Malus domestica and M. sylvestris to the florivorous weevil Anthonomus pomorum (Coleoptera: Curculionidae) link: https://peerj.com/articles/13566 last-modified: 2022-07-15 description: The florivorous apple blossom weevil, Anthonomus pomorum (Coleoptera: Curculionidae), is the most economically relevant insect pest of European apple orchards in early spring. Neither efficient monitoring nor ecologically sustainable management of this insect pest has yet been implemented. To identify heritable traits of apple trees that might influence the host selection of A. pomorum, we compared the susceptibility of apple tree species using infestation rates of the domesticated apple, Malus domestica (Rosaceae: Pyreae), and the European crab apple, M. sylvestris. We evaluated the suitability of the two apple species for A. pomorum by quantifying the mass of weevil offspring. Because volatile organic compounds (VOCs) emitted from flower buds of the domesticated apple have previously been suggested to mediate female weevil preference via olfactory cues, we conducted bioassay experiments with blossom buds of both apple species to explore the olfactory preference of adult weevils and, furthermore, identified the headspace VOCs of blossom buds of both apple species through GC-MS analysis. The infestation analysis showed that A. pomorum infested the native European crab apple more prevalently than the domesticated apple, which originated from Central Asia. The European crab apple also appeared to be better suited for weevil larval development than the domesticated apple, as weevils emerging from M. sylvestris had a higher body mass than those emerging from M. domestica. These field observations were supported by olfactory bioassays, which showed that A. pomorum significantly preferred the odor of M. sylvestris buds compared to the odor of M. domestica buds. The analysis of headspace VOCs indicated differences in the blossom bud volatiles separating several M. domestica individuals from M. sylvestris individuals. This knowledge might be employed in further studies to repel A. pomorum from M. domestica blossom buds. creator: Benjamin Henneberg creator: Torsten Meiners creator: Karsten Mody creator: Elisabeth Obermaier uri: https://doi.org/10.7717/peerj.13566 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Henneberg et al. title: The efficacy of commercial decontamination agents differs between standardised test settings and research laboratory usage for a variety of bacterial species link: https://peerj.com/articles/13646 last-modified: 2022-07-15 description: Decontamination of surfaces and items plays an important role in reducing the spread of infectious microorganisms in many settings including hospitals and research institutes. Regardless of the location, appropriate decontamination procedures are required for maintaining biosafety and biosecurity. For example, effective decontamination of microbial cultures is essential to ensure proper biocontainment and safety within microbiological laboratories. To this end, many commercial decontamination agents are available which have been tested to a prescribed standard to substantiate their efficacy. However, these standardised tests are unlikely to accurately reflect many conditions encountered in medical and biomedical research. Despite this, laboratory workers and other users of decontamination agents may assume that all decontamination agents will work in all situations. We tested commonly used commercial decontamination agents against a range of bacterial species to determine their efficacy under real-world research laboratory conditions. As each decontamination agent has a different recommended dilution for use, to compare their efficacy we calculated their ‘effective ratio’ which reflects the difference between the manufacturer-recommended dilution and the dilution needed to achieve decontamination under real-world research laboratory conditions. Effective ratios above one indicate that the agent was effective at a dilution more dilute than recommended whereas effective ratios lower than one indicate that the agent required a higher concentration than recommended. Our results show that the quaternary ammonium agents TriGene Advance and Chemgene HLD4L were the most effective out of the agents tested, with biocidal activity measured at up to 64 times the recommended dilution. In contrast, hypochlorite (bleach) and Prevail™ (stabilised hydrogen peroxide) had the lowest effective ratios amongst the tested agents. In conclusion, our data suggests that not all decontamination agents will work at the recommended dilutions under real-world research laboratory conditions. We recommend that the protocols for the use of decontamination agents are verified under the specific conditions required to ensure they are fit for purpose. creator: Benedict Uy creator: Hannah Read creator: Shara van de Pas creator: Rebecca Marnane creator: Francesca Casu creator: Simon Swift creator: Siouxsie Wiles uri: https://doi.org/10.7717/peerj.13646 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Uy et al. title: Temperature regulation in the Balkan spadefoot (Pelobates balcanicus Karaman, 1928) at the beginning of nocturnal activity link: https://peerj.com/articles/13647 last-modified: 2022-07-15 description: On land, the amphibians interact with the environment in a complex way-even small changes in the physiological conditions may significantly impact the behaviour and vice versa. In ectothermic tetrapods, the transition from inactive to active phase may be related to important changes in their thermal status. We studied the thermal ecology of adult Balkan spadefoots (Pelobates balcanicus Karaman, 1928) in northeastern Bulgaria. These toads spend the daytime buried between 10 and 15 cm in sandy substrates, and emerge after sunset. On the substrate, their thermal energy exchange is defined by the absence of heat flow from the sun. Secondary heat sources, like stored heat and infrared radiation from the soil play an important role for the thermal balance of the active spadefoot toads. At the beginning of their daily activity, we measured substrate temperature (at a depth of 11–12 cm), toad’s surface body temperature, and also provided thermal profiles of the animals and the substrate surface in their microhabitats. In animals which recently emerged from the substrate, the temperature was comparatively higher and was closer to that of the subsoil on the spot. After that, body temperature decreased rapidly and continued to change slowly, in correlation with air temperature. We detected a temperature gradient on the dorsal surface of the toads. On the basis of our measurements and additional data, we discuss the eventual role of air humidity and the effects of surface and skin water evaporation on the water balance and activity of the investigated toads. creator: Nikolay Natchev creator: Teodora Koynova creator: Krasimir Tachev creator: Dimitar Doichev creator: Pavlina Marinova creator: Valeriya Velkova creator: Daniel Jablonski uri: https://doi.org/10.7717/peerj.13647 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Natchev et al. title: A new genus and species of frog from the Kem Kem (Morocco), the second neobatrachian from Cretaceous Africa link: https://peerj.com/articles/13699 last-modified: 2022-07-15 description: Neobatrachia, a clade representing the majority of extant anuran diversity, is thought to have emerged and diversified during the Cretaceous. Most of the early diversification of neobatrachians occurred in southern Gondwana, especially the regions that are today South America and Africa. Whereas five extinct neobatrachians have been described from the Cretaceous of South America in the last decade, only one is known from Africa. This difference in the known extinct diversity is linked to the lack of well-preserved specimens, understudy of fragmentary remains, and lack of known Cretaceous sites in Africa. Study of fragmentary anuran remains from Africa could allow for the identification of previously unknown neobatrachians, allowing for a better understanding of their early diversification. We reanalysed several previously described anuran specimens from the well-known Kem Kem beds, including using CT-scanning. Through our osteological study, we determined that several cranial bones and vertebrae represent a new hyperossified taxon for which we provide a formal description. Comparison to other hyperossified anurans revealed similarities and affinity of this new taxon with the neobatrachians Beelzebufo (extinct) and Ceratophrys (extant). Phylogenetic analyses supported this affinity, placing the new taxon within Neobatrachia in an unresolved clade of Ceratophryidae. This taxon is the oldest neobatrachian from Africa, and reveals that neobatrachians were already widespread throughout southern Gondwana during the earliest Late Cretaceous. creator: Alfred Lemierre creator: David C. Blackburn uri: https://doi.org/10.7717/peerj.13699 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lemierre and Blackburn title: Mitochondrial marker implies fishery separate management units for spotted sardinella, Amblygaster sirm (Walbaum, 1792) populations in the South China Sea and the Andaman Sea link: https://peerj.com/articles/13706 last-modified: 2022-07-15 description: The spotted sardinella, Amblygaster sirm (Walbaum, 1792), is a commercial sardine commonly caught in Malaysia. Lack of management of these marine species in Malaysian waters could lead to overfishing and potentially declining fish stock populations. Therefore, sustainable management of this species is of paramount importance to ensure its longevity. As such, molecular information is vital in determining the A. sirm population structure and management strategy. In the present study, mitochondrial DNA Cytochrome b was sequenced from 10 A. sirm populations: the Andaman Sea (AS) (two), South China Sea (SCS) (six), Sulu Sea (SS) (one), and Celebes Sea (CS) (one). Accordingly, the intra-population haplotype diversity (Hd) was high (0.91–1.00), and nucleotide diversity (π) was low (0.002–0.009), which suggests a population bottleneck followed by rapid population growth. Based on the phylogenetic trees, minimum spanning network (MSN), population pairwise comparison, and FST,and supported by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA) tests, distinct genetic structures were observed (7.2% to 7.6% genetic divergence) between populations in the SCS and its neighboring waters, versus those in the AS. Furthermore, the results defined A. sirm stock boundaries and evolutionary between the west and east coast (which shares the same waters as western Borneo) of Peninsular Malaysia. In addition, genetic homogeneity was revealed throughout the SCS, SS, and CS based on the non-significant FSTpairwise comparisons. Based on the molecular evidence, separate management strategies may be required for A. sirm of the AS and the SCS, including its neighboring waters. creator: Noorul Azliana Jamaludin creator: Jamsari Amirul Firdaus Jamaluddin creator: Masazurah A. Rahim creator: Noor Adelyna Mohammed Akib creator: Sahat Ratmuangkhwang creator: Wahidah Mohd Arshaad creator: Siti Azizah Mohd Nor uri: https://doi.org/10.7717/peerj.13706 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Jamaludin et al. title: Tumor budding of cervical squamous cell carcinoma: epithelial-mesenchymal transition-like cancer stem cells? link: https://peerj.com/articles/13745 last-modified: 2022-07-15 description: Recent evidence indicates that cancer stem cells (CSCs) are the origin of cancers. Scientists have identified CSCs in various tumors and have suggested the existence of a variety of states of CSCs. The existence of epithelial–mesenchymal transition (EMT)-like CSCs has been confirmed in vitro, but they have not been identified in vivo. Tumor budding was defined as single cell or clusters of ≤ 5 cells at the invasive front of cancers. Such tumor budding is hypothesized to be closely related to EMT and linked to CSCs, especially to those migrating at the invasive front. Therefore, tumor budding has been proposed to represent EMT-like stem cells. However, this hypothesis has not yet been proven. Thus, we studied the expression of EMT markers, certain CSC markers of tumor budding, and the tumor center of cervical squamous cell carcinoma (CxSCC). We performed tissue chip analyses of 95 primary CxSCCs from patients. Expression of EMT and CSC markers (E-cadherin, β-catenin, vimentin, Ki67, CD44, SOX2 , and ALDH1A1) in a set of tumor samples on tissue chips (87 cases of tumor budding/the main tumor body) were evaluated by immunohistochemistry. We found that the cell-membranous expression of β-catenin was stronger in the main tumor body than in tumor buds. Compared with the main tumor body, tumor buds had reduced proliferative activity as measured by Ki67. Moreover, vimentin expression was high and E-cadherin expression was low in tumor buds. Expression of EMT-related markers suggested that tumor buds were correlated with EMT. We noted that CxSCC tumor buds had a CD44negative/low/SOX2high/ALDH1A1high staining pattern, indicating that tumor buds of CxSCC present CSC-like immunophenotypic features. Taken together, our data indicate that tumor buds in CxSCC may represent EMT-like CSCs in vivo. creator: Shaoqiu Zheng creator: Jing Luo creator: Shoucheng Xie creator: Shanming Lu creator: Qinghua Liu creator: Huanqin Xiao creator: Wenjuan Luo creator: Yanfang Huang creator: Kun Liu uri: https://doi.org/10.7717/peerj.13745 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zheng et al. title: Compensatory growth and understory soil stoichiometric features of Hippophae rhamnoides at different stubble heights link: https://peerj.com/articles/13363 last-modified: 2022-07-14 description: BackgroundThis study was aimed to explore the compensatory growth ability and influence mechanism of Hippophae rhamnoides at the decaying phase in feldspathic sandstone areas of Ordos, and clarify the stubble height when the compensatory growth ability of H. rhamnoides was the strongest.MethodsThe H. rhamnoides forests in the decaying phase from an exposed feldspathic sandstone zone of Ordos were chosen. The compensatory growth ability of H. rhamnoides at stubble height of 0 cm (S1), 10 cm (S2), 15 cm (S3), 20 cm (S4) and control (CK) was investigated with H. rhamnoides forests at the decaying stage in the exposed feldspathic sandstone areas of Ordos. Relationships of compensatory growth ability of H. rhamnoides and understory soil properties with understory soil stoichiometric features as well as the response mechanism to stubble height were explored.Results(1) Overcompensatory growth of H. rhamnoides in feldspathic sandstone areas occurred at all stubble heights. Especially, the plant height compensation index (1.45) and biomass compensation index (1.25) at the stubble height of 15 cm were both larger compared with other stubbling treatments. These results indicate the stubble height of 15 cm can well promote the growth of the ground part of H. rhamnoides. (2) All stubble heights significantly affected the contents and eco-stoichiometric ratios of soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP) in understory soils, but the influence rules differed. SOC, TN, and TP contents at all stubble heights were larger than those of the control, and maximized at the stubble height of 15 cm. The carbon(C): phosphorus(P) ratio, and nitrogen (N):(P) ratio after stubbling treatments were all lower compared with the control, and minimized to 19.52 and 1.84 respectively at the stubble height of 15 cm. (3) The understory C:N:P stoichiometric ratio of H. rhamnoides in feldspathic sandstone areas is jointly affected by compensatory growth, stubble height, and soil physicochemical properties. The total explanation rate determined from RDA is 93.1%. The understory soil eco-stoichiometric ratio of H. rhamnoides is mainly affected by soil moisture content (contribution of 87.6%) and total porosity (7.9%), indicating soil moisture content is the most influential factor. The findings will offer some new clues for eco-construction and theoretically underlie soil-water loss administration. creator: Xin Wang creator: Yuefeng Guo creator: Wei Qi creator: Li Zhen creator: Yunfeng Yao creator: Fucang Qin uri: https://doi.org/10.7717/peerj.13363 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Effects of commercial beverages on the neurobehavioral motility of Caenorhabditis elegans link: https://peerj.com/articles/13563 last-modified: 2022-07-14 description: To study the effects of different types of commercially available drinks/beverages on neurobehavior using the model organism C. elegans, and critically review their potential health hazards. Eighteen kinds of beverages from the supermarket were randomly selected and grouped into seven categories namely functional beverage, tea beverage, plant protein beverage, fruit juice beverage, dairy beverage, carbonated beverage and coffee beverage. The pH value, specific gravity and osmotic pressure were also examined. The L4 stage N2 worms were exposed to different concentration of tested beverages (0, 62.5, 125, 250 and 500 µL/mL) for 24 h to measure the survival rate and locomotory behavior such as head thrashing, body bending as well as pharyngeal pumping. All the 18 beverages tested did not induce any visible lethal effects in the nematodes. However, exposure to different types of tested beverages exhibited different effects on the behavioral ability of C. elegans: (1) sports functional beverage and herbal tea drink accelerated the head thrashing and body bending of nematodes when compared to the control group (P < 0.05). (2) The vibration frequency of the pharyngeal pump of nematodes was significantly accelerated after treated with three plant protein beverages (almond milk, coconut milk and milk tea) and dairy products A and B (P < 0.05), and decelerated after treatment with other tested beverages. (3) Carbonated beverage significantly inhibits the head thrashing, body bending and pharyngeal pumping vibration (P < 0.05). Our results indicate that 18 kinds of popular beverages in the market have different influence on the neurobehavior in C. elegans, which may be related to their different components or properties. Further research would be required to conduct a systematic analysis of the effect of beverages by appropriate kinds, taking into consideration other endpoints such as reproduction, lifespan and molecular stress response, etc., and to elucidate the mechanism for its potential health hazards. creator: Wenjing Zhang creator: Nan Zhang creator: Shan Zheng creator: Wei Zhang creator: Jingjing Liu creator: Liwei He creator: Anastasia Ngozi Ezemaduka creator: Guojun Li creator: Junyu Ning creator: Bo Xian creator: Shan Gao uri: https://doi.org/10.7717/peerj.13563 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: The oldest record of Saurosphargiformes (Diapsida) from South China could fill an ecological gap in the Early Triassic biotic recovery link: https://peerj.com/articles/13569 last-modified: 2022-07-14 description: Diversification following the end-Permian mass extinction marks the initiation of Mesozoic reptile dominance and of modern marine ecosystems, yet major clades are best known from the Middle Triassic suggesting delayed recovery, while Early Triassic localities produce poorly preserved specimens or have restricted diversity. Here we describe Pomolispondylus biani gen. et sp. nov. from the Early Triassic Nanzhang-Yuan’an Fauna of China assigned to Saurosphargiformes tax. nov., a clade known only from the Middle Triassic or later, which includes Saurosphargidae, and likely is the sister taxon to Sauropterygia. Pomolispondylus biani is allied to Saurosphargidae by the extended transverse processes of dorsal vertebrae and a low, table-like dorsal surface on the neural spine; however, it does not have the typical extensive osteoderms. Rather an unusual tuberous texture on the dorsal neural spine and rudimentary ossifications lateral to the gastralia are observed. Discovery of Pomolispondylus biani extends the known range of Saurosphargiformes and increases the taxic and ecological diversity of the Nanzhang-Yuan’an Fauna. Its small size fills a different ecological niche with respect to previously found species, but the overall food web remains notably different in structure to Middle Triassic and later ecosystems, suggesting this fauna represents a transitional stage during recovery rather than its endpoint. creator: Long Cheng creator: Benjamin C. Moon creator: Chunbo Yan creator: Ryosuke Motani creator: Dayong Jiang creator: Zhihui An creator: Zichen Fang uri: https://doi.org/10.7717/peerj.13569 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cheng et al. title: Novel lncRNAs with diagnostic or prognostic value screened out from breast cancer via bioinformatics analyses link: https://peerj.com/articles/13641 last-modified: 2022-07-14 description: BackgroundRecent studies have shown that long non-coding RNAs (lncRNAs) may play key regulatory roles in many malignant tumors. This study investigated the use of novel lncRNA biomarkers in the diagnosis and prognosis of breast cancer.Materials and MethodsThe database subsets of The Cancer Genome Atlas (TCGA) by RNA-seq for comparing analysis of tissue samples between breast cancer and normal control groups were downloaded. Additionally, anticoagulant peripheral blood samples were collected and used in this cohort study. The extracellular vesicles (EVs) from the plasma were extracted and sequenced, then analyzed to determine the expressive profiles of the lncRNAs, and the cancer-related differentially expressed lncRNAs were screened out. The expressive profiles and associated downstream-mRNAs were assessed using bioinformatics (such as weighted correlation network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) enrichments, Receiver-Operating Characteristic (ROC) curve and survival analysis, etc.) to investigate the diagnostic and prognostic values of these EV lncRNAs and their effectors.ResultsIn this study, 41 breast cancer-related lncRNAs were screen out from two datasets of tissue and fresh collected plasma samples of breast cancer via the transcriptomic and bioinformatics techniques. A total of 19 gene modules were identified with WGCNA analysis, of which five modules were significantly correlated with the clinical stage of breast cancer, including 28 lncRNA candidates. The ROC curves of these lncRNAs revealed that the area under the curve (AUC) of all candidates were great than 70%. However, eight lncRNAs had an AUC >70%, indicating that the combined one has a good diagnostic value. In addition, the results of survival analysis suggested that two lncRNAs with low expressive levels may indicate the poor prognosis of breast cancer. By tissue sample verification, C15orf54, AL157935.1, LINC01117, and SNHG3 were determined to have good diagnostic ability in breast cancer lesions, however, there was no significant difference in the plasma EVs of patients. Moreover, survival analysis data also showed that AL355974.2 may serve as an independent prognostic factor and as a protective factor.ConclusionA total of five lncRNAs found in this study could be developed as biomarkers for breast cancer patients, including four diagnostic markers (C15orf54, AL157935.1, LINC01117, and SNHG3) and a potential prognostic marker (AL355974.2). creator: Hongxian Wang creator: Lirong Shu creator: Nan Niu creator: Chenyang Zhao creator: Shuqi Lu creator: Yanhua Li creator: Huanyu Wang creator: Yao Liu creator: Tianhui Zou creator: Jiawei Zou creator: Xiaoqin Wu creator: Yun Wang uri: https://doi.org/10.7717/peerj.13641 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Low-level nutrient enrichment during thermal stress delays bleaching and ameliorates calcification in three Hawaiian reef coral species link: https://peerj.com/articles/13707 last-modified: 2022-07-14 description: Terrestrial-based nutrient pollution has emerged as one of the most detrimental factors to coral health in many reef habitats. Recent studies have shown that excessive dissolved inorganic nutrients can reduce coral thermal tolerance thresholds and even exacerbate bleaching during thermal stress, yet the effects of minor nutrient enrichment under heat stress have not been extensively studied. In this study, Lobactis scutaria, Montipora capitata, and Pocillopora acuta colonies under heated conditions (~30.5 °C) were exposed to low and balanced nitrogen and phosphorous concentrations over a 31-day heating period. Coral colonies were collected from Kāne‘ohe Bay, O‘ahu, which has a unique history of nutrient pollution, and held in mesocosms that allowed for environmental manipulation yet are also influenced by local field conditions. Principal findings included delays in the bleaching of nutrient-enriched heated colonies as compared to heated-only colonies, in addition to relatively greater calcification rates and lower proportions of early-stage paling. Species-specific outcomes were prevalent, with L. scutaria demonstrating no difference in calcification with enrichment under heat stress. By the end of the heating stage, however, many heated colonies were at least partially impacted by bleaching or mortality. Despite this, our findings suggest that low levels of balanced nutrient enrichment may serve as a mitigative force during thermal events. Further field-based studies will be required to assess these results in different reef habitats. creator: Ji Hoon J. Han creator: Matthew P. Stefanak creator: Ku‘ulei S. Rodgers uri: https://doi.org/10.7717/peerj.13707 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Han et al. title: ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17 link: https://peerj.com/articles/13710 last-modified: 2022-07-14 description: BackgroundThe auxin indole-3-acetic acid (IAA) is a type of endogenous plant hormone with a low concentration in plants, but it plays an important role in their growth and development. The AUX/IAA gene family was found to be an early sensitive auxin gene with a complicated way of regulating growth and development in plants. The regulation of root growth and development by AUX/IAA family genes has been reported in Arabidopsis, rice and maize.ResultsIn this study, subcellular localization indicated that ZmIAA1-ZmIAA6 primarily played a role in the nucleus. A thermogram analysis showed that AUX/IAA genes were highly expressed in the roots, which was also confirmed by the maize tissue expression patterns. In maize overexpressing ZmIAA5, the length of the main root, the number of lateral roots, and the stalk height at the seedling stage were significantly increased compared with those of the wild type, while the EMS mutant zmiaa5 was significantly reduced. The total number of roots and the dry weight of maize overexpressing ZmIAA5 at the mature stage were also significantly increased compared with those of the wild type, while those of the mutant zmiaa5 was significantly reduced. Yeast one-hybrid experiments showed that ZmTCP15/16/17 could specifically bind to the ZmIAA5 promoter region. Bimolecular fluorescence complementation and yeast two-hybridization indicated an interaction between ZmIAA5 and ZmARF5.ConclusionsTaken together, the results of this study indicate that ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17. creator: Feiyang Yang creator: Yutian Shi creator: Manli Zhao creator: Beijiu Cheng creator: Xiaoyu Li uri: https://doi.org/10.7717/peerj.13710 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: Association between IL-1A and IL-1B gene polymorphisms with peri-implantitis in a Portuguese population—a pilot study link: https://peerj.com/articles/13729 last-modified: 2022-07-14 description: BackgroundScientific evidence indicates that biological complications in dental implants tend to be concentrated in a subset of individuals, which seems to imply that the host response may play a determining role in implant success. Over the last few decades, several polymorphisms have been studied. Polymorphisms in the interleukin (IL) 1 gene cluster have been associated with periodontitis. There are some similar features in the sequence of immunopathological events in peri-implant and periodontal infections. We aimed to investigate if individuals carrying the genetic single nucleotide polymorphism (SNP) in the IL-1A (rs1800587) and IL-1B (rs1143634) genes are more susceptible to develop peri-implantitis.MethodsA cross-sectional analytic pilot study was conducted in 20 Caucasian Portuguese subjects divided into two groups: 10 subjects with peri-implantitis and 10 subjects with peri-implant health (control group). Samples containing cells from the buccal mucosa were stored at −20 °C and later submitted to the DNA extraction process. Genetic analysis was performed using the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Data were analyzed by using descriptive and inferential statistical methodologies.ResultsFor the IL-1A (−889) gene polymorphism, it was observed that the mutated allele was present in a higher percentage in the peri-implantitis group compared to the control group (30% vs 15% respectively, Fisher’s exact test, p = 0.45). For the IL-1B (+3954) gene polymorphism, it was also observed that the altered allele was present in a higher percentage in the disease group compared to the control group (35% vs 10% respectively, Fisher’s exact test, p = 0.13). The positive genotype (at least one allele with nucleotide sequence changed in both genes) was detected in six patients, five belonging to the disease group and one to the health group.ConclusionsRegarding IL-1 gene polymorphisms, there was no statistically significant difference between the health and disease group, however a trend should be highlighted, showing a potential link between the IL-1 genotype and peri-implantitis. More studies are needed to clarify the role of genetic polymorphisms in the development of peri-implantitis. creator: José Maria Cardoso creator: Ana Clara Ribeiro creator: Constança Palos creator: Luis Proença creator: Susana Noronha creator: Ricardo Castro Alves uri: https://doi.org/10.7717/peerj.13729 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cardoso et al. title: Minimally invasive versus traditional inverted “L” approach for posterior cruciate ligament avulsion fractures: a retrospective study link: https://peerj.com/articles/13732 last-modified: 2022-07-14 description: PurposeTo evaluate the clinical efficacy of a minimally invasive arthroscopic approach and to compare it with the traditional inverted “L” approach for the treatment of posterior cruciate ligament (PCL) avulsion fractures.MethodsFrom January 2016 to January 2020, the clinical data from patients with PCL avulsion fracture of the tibial insertion were analyzed retrospectively. They were divided into two groups based on surgical approaches: minimally invasive approach group (n = 15) and traditional inverted “L” group (n = 15 cases). The operation time, incision length, intraoperative blood loss, hospitalization time and complications were all recorded and compared between the two groups. The fracture healing time, knee range of motion (ROM), and residual relaxation degree were compared between the two groups after regular follow-up. The International Knee Documentation Committee (IKDC) and Lysholm scores were used to assess knee joint function.ResultsThere were no significant differences between the two groups in terms of gender, age, side, body mass index, cause of injury, Meyers McKeever classification and time from injury to operation (P > 0.05). The incision length and intraoperative bleeding in the minimally invasive group were significantly lower (P < 0.05) than those in the traditional group. There were no significant differences between the two groups in terms of operative time, fracture healing time, or residual relaxation (P > 0.05). The Lachman test and posterior drawer test were both negative, and there were no postoperative complications. The VAS pain score within 2 weeks and ROM within 4 weeks in the minimally invasive group were significantly better (P < 0.05) than those in the traditional inverted “L” approach group. The knee joint stability of both groups was good 12 months after surgery, and there were no significant differences in IKDC score, Lysholm score and ROM (P > 0.05) between the two groups.ConclusionThe minimally invasive approaches for the treatment of PCL avulsion fractures provide adequate exposure without the surgical complications associated with traditional open surgical approaches. The procedure is safe, fast and minimally invasive, and does not need a long learning curve. creator: Yao Zhao creator: Huihui Guo creator: Liang Gao creator: Chang Liu creator: Xinzhong Xu creator: Wendan Cheng uri: https://doi.org/10.7717/peerj.13732 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhao et al. title: Land use affects the response of soil moisture and soil temperature to environmental factors in the loess hilly region of China link: https://peerj.com/articles/13736 last-modified: 2022-07-14 description: Changes in soil moisture and soil temperature result from the combined effects of several environmental factors. Scientific determination of the response characteristics of soil moisture and soil temperature to environmental factors is critical for adjusting the sloping land use structure and improving the ecological environment in China’s loess hilly region. Soybean sloping fields, maize terraced fields, jujube orchards, and grasslands in the loess hilly region were selected as the research areas. The change in characteristics of soil moisture and soil temperature, as well as their interactions and statistical relationships with meteorological factors, were analyzed using continuously measured soil moisture, soil temperature, and meteorological factors. The results revealed that air temperature and humidity were the main controlling factors affecting soil moisture changes in the 0–60 cm soil layer of soybean sloping fields and grasslands in the normal precipitation year (2014) and the dry year (2015). Humidity and wind speed were the main meteorological factors affecting soil moisture changes in the maize terraced field. Air temperature had a significant negative effect on soil moisture in the jujube orchard. Soil moisture and soil temperature were all negatively correlated under the four sloping land use types. In normal precipitation years, atmospheric humidity had the greatest direct and comprehensive effect on soil moisture in soybean sloping fields, maize terraced fields, and grasslands; soil temperature had a relatively large impact on soil moisture in jujube orchards. The direct and comprehensive effects of soil temperature on soil moisture under all sloping land use types were the largest and most negative in the dry year. Air temperature had a high correlation with soil temperature in the 0–60 cm soil layer under the four sloping land use types, and the grey relational grade decreased as the soil layer deepened. The coefficient of determination between the 0–20 cm soil temperature and air temperature in the maize terraced field was low, indicating a weak response to air temperature. The above findings can serve as a scientific foundation for optimizing sloping land use structures and maximizing the efficient and sustainable utilization of sloping land resources in China’s loess hilly region. creator: Min Tang creator: Wanning Li creator: Xiaodong Gao creator: Pute Wu creator: Hongchen Li creator: Qiang Ling creator: Chao Zhang uri: https://doi.org/10.7717/peerj.13736 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tang et al. title: Acoustic and vibrational signaling in true katydid Nesoecia nigrispina: three means of sound production in one species link: https://peerj.com/articles/13749 last-modified: 2022-07-14 description: The males of Mexican katydids Nesoecia nigrispina (Stal, 1873) produce calling songs and protest sounds using the typical stridulatory apparatus, situated, as in most of the other Ensifera, at the bases of the tegmina. It includes a stridulatory file on the upper tegmen and a plectrum on the lower one. The calling sounds, which are of two types (fast and slow), are two-syllabic series, with a repetition rate fluctuate within 3–4.5 s−1 (fast) and 1.2–2 s−1 (slow). After tactile stimulation, males produce protest signals in the form of short trills of uniform syllable duration. The syllable repetition rate is higher than that of the calling sounds: 7.7 s−1. The frequency spectra of these signals have maxima in the band of 14–15 kHz. However, in addition to the sounds described, both males and females are capable of producing protest signals of the second type, with the help of another sound apparatus, namely the hind wings. Apparently, the sound is produced by the friction of the hind wings on the lower tegmen. The dominant frequencies in the frequency spectra of these sounds are 40–60 kHz. In adults of both sexes and older nymphs, in response mainly to tactile stimulation, short clicks are recorded, which they produce, apparently, by the mandibles. Thus, N. nigrispina seems to have the most extensive acoustic repertoire among pseudophyllines and three means of emitting sound signals. Tremulatory substrate-borne vibrations are produced by individuals of both sexes during courtship and by males completing the calling signal cycle and after copulation. It is possible that vibrational signals are an additional factor in the reproductive isolation of sympatric species, since the calling sound signals in representatives of the genus Nesoecia are similar and exhibit considerable variability. The type and parameters of the calling signal used by the female during recognizing a conspecific mate remain unclear. creator: Olga S. Korsunovskaya creator: Rustem D. Zhantiev uri: https://doi.org/10.7717/peerj.13749 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Korsunovskaya and Zhantiev title: Synthesis of geological data and comparative phylogeography of lowland tetrapods suggests recent dispersal through lowland portals crossing the Eastern Andean Cordillera link: https://peerj.com/articles/13186 last-modified: 2022-07-13 description: Vicariance is the simplest explanation for divergence between sister lineages separated by a potential barrier, and the northern Andes would seem to provide an ideal example of a vicariant driver of divergence. We evaluated the potential role of the uplift of the Eastern Cordillera (EC) of the Colombian Andes and the Mérida Andes (MA) of Venezuela as drivers of vicariance between lowland populations co-distributed on both flanks. We synthesized published geological data and provided a new reconstruction showing that the EC-MA grew from north to south, reaching significant heights and separating drainages and changing sediment composition by 38–33 million years ago (Ma). A few lowland passes across the EC-MA may have reached their current heights (~1,900 m a.s.l.) at 3–5 Ma. We created a comparative phylogeographic data set for 37 lineages of lowland tetrapods. Based on molecular phylogenetic analyses, most divergences between sister populations or species across the EC-MA occurred during Pliocene and the Quaternary and a few during the latest Miocene, and coalescent simulations rejected synchronous divergence for most groups. Divergence times were on average slightly but significantly more recent in homeotherms relative to poikilotherms. Because divergence ages are mostly too recent relative to the geological history and too asynchronous relative to each other, divergence across the northern Andes may be better explained by organism-environment interactions concomitant with climate oscillations during the Pleistocene, and/or dispersal across portals through the Andes. creator: Erika Rodriguez-Muñoz creator: Camilo Montes creator: Fernando J. M. Rojas-Runjaic creator: Andrew J. Crawford uri: https://doi.org/10.7717/peerj.13186 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rodriguez-Muñoz et al. title: Postembryonic development of the tracheal system of beetles in the context of aptery and adaptations towards an arid environment link: https://peerj.com/articles/13378 last-modified: 2022-07-13 description: The tracheal system comprises one of the major adaptations of insects towards a terrestrial lifestyle. Many aspects such as the modifications towards wing reduction or a life in an arid climate are still poorly understood. To address these issues, we performed the first three-dimensional morphometric analyses of the tracheal system of a wingless insect, the desert beetle Gonopus tibialis and compared it with a flying beetle (Tenebrio molitor). Our results clearly show that the reduction of the flight apparatus has severe consequences for the tracheal system. This includes the reduction of the tracheal density, the relative volume of the trachea, the volume of the respective spiracles and the complete loss of individual tracheae. At the same time, the reduction of wings in the desert beetle allows modifications of the tracheal system that would be impossible in an animal with a functional flight apparatus such as the formation of a subelytral cavity as a part of the tracheal system, the strong elongation of the digestive tract including its tracheal system or the respiration through a single spiracle. Finally, we addressed when these modifications of the tracheal system take place during the development of the studied beetles. We can clearly show that they develop during pupation while the larvae of both species are almost identical in their tracheal system and body shape. creator: Marcin Raś creator: Benjamin Wipfler creator: Tim Dannenfeld creator: Dariusz Iwan uri: https://doi.org/10.7717/peerj.13378 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Raś et al. title: WASH regulates the oxidative stress Nrf2/ARE pathway to inhibit proliferation and promote apoptosis of HeLa cells under the action of Jolkinolide B link: https://peerj.com/articles/13499 last-modified: 2022-07-13 description: Jolkinolide B (JB), a diterpenoid compound isolated from the roots of Euphorbia fischeriana, has gained research attention for its antitumor effects. In recent years, JB reportedly displayed anti-tumor activity in solid tumors, such as breast, ovarian, and prostate cancer, and leukemia. In this study, we evaluated the effect of JB on HeLa cells with a focus on cell growth inhibition and related mechanisms. HeLa cells were cultured in vitro and divided into a blank control group, HeLa-Scramble (0, 0.25, 0.5 mM), and Wiskott-Aldrich syndrome protein and SCAR homolog (WASH) protein silenced group, HeLa-shWASH (0, 0.25, 0.5 mM). Morphological changes were observed using an inverted microscope. The inhibition rate of cell proliferation was detected using the WST-1 method. Flow cytometry Brdu+PI double standard method was used to detect cell replication ability and FITC+PI double standard method was used to detect cell apoptosis rate. Western blot was used to verify the expression of Nrf2, HO-1, WASH, Bax, Bcl-2, and PCNA. The mRNA expression of cytokines (IL-1α, IL-6, and IL-8) was detected using RT-qPCR. The results showed that JB induced cell apoptosis and arrested cells at the G2/M phase in HeLa-shWASH cells compared with HeLa-Scramble cells (P < 0.05, P < 0.01, respectively). In addition, JB upregulated IL-1α, IL-6, and IL-8 in HeLa-shWASH cells. We conclude that WASH protein participates in JB-induced regulation of the Nrf2/ARE pathway, aggravates inflammatory responses, and promotes cancer cell apoptosis, thus inhibiting the proliferation and invasion abilities of HeLa cells. JB may have anti-tumor effects and potential clinical value for the treatment of cervical cancer. creator: Yu Hong creator: Jicheng Liu creator: Wanying Kong creator: Hui Li creator: Ying Cui creator: Yuchao Liu creator: Zhihui Deng creator: Dezhi Ma creator: Keyong Zhang creator: Jinghui Li creator: Minhui Li uri: https://doi.org/10.7717/peerj.13499 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hong et al. title: Five decades of change in somatic growth of Pacific hake from Puget Sound and Strait of Georgia link: https://peerj.com/articles/13577 last-modified: 2022-07-13 description: Declines in fish body size have been reported in many populations and these changes likely have important ramifications for the sustainability of harvested species and ecosystem function. Pacific hake, Merluccius productus, have shown declines in size over the last several decades for populations located in Puget Sound (PS), Washington, USA, and Strait of Georgia (SoG), British Columbia, Canada. To examine this decrease in size, we used archived otoliths from both populations to assess when the decrease in somatic growth occurred and explored what factors and processes might explain the decline, including otolith microchemistry to infer the environment experienced by fish at different ages. Results indicated that substantial changes in juvenile somatic growth have occurred across decades. The divergence in body size occurred in the second summer, whereby SoG fish grew, on average, 18% more than PS fish. Within the PS population, somatic growth differed significantly among fish that hatched in the 1980s, 1990s, and 2010s, such that the more recently hatched fish grew 26% more in their first summer and 71% less in their second summer relative to those that hatched in the 1980s. In comparison, growth of SoG fish did not differ between those that hatched in 1970s and 1990s. For both populations growth in the first and third summer was positively and negatively related, respectively, to the abundance of harbor seals, while growth in the first and second summer was negatively related to salinity. Overall, this study highlights the complicated nature of Pacific hake population recovery under dynamic, and typically uncontrollable, variation in biotic and abiotic conditions. creator: Paul Chittaro creator: Chris Grandin creator: Robert Pacunski creator: Rich Zabel uri: https://doi.org/10.7717/peerj.13577 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chittaro et al. title: Assessing availability of European plant protection product data: an example evaluating basic area treated link: https://peerj.com/articles/13586 last-modified: 2022-07-13 description: Besides the benefits of plant protection products (PPPs) for agricultural production, there is an increasing acknowledgement of the associated potential environmental risks. Here, we examine the feasibility of summarizing the extent of PPP usage at the country level, using Ireland as a case study, as well as at the European level. We used the area over which PPPs are applied (basic area) as an example variable that is relevant to initially assess the geographic extent of environmental risk. In Irish agricultural systems, which are primarily grass-based, herbicides fluroxypyr and glyphosate are the most widely applied active substances (ASs) in terms of basic area, followed by the fungicides chlorothalonil and prothioconazole that are closely associated with arable crops. Although all EU countries are subject to Regulation (EC) No 1185/2009, which sets the obligation of PPP usage data reporting at the national level, we only found usable data that met our criteria for Estonia, Germany, Finland, and Spain (4 of 30 countries reviewed). Overall, the most widely applied fungicide and herbicide in terms of basic area were prothioconazole (20%, 7% and 5% of national cultivated areas of Germany, Estonia and Ireland) and glyphosate (11%, 8% and 5% of national cultivated areas of Spain, Estonia and Ireland) respectively, although evaluations using application frequency may result in the observation of different trends. Several recommendations are proposed to tackle current data gaps and deficiencies in accessibility and usability of pesticide usage data across the EU in order to better inform environmental risk assessment and promote evidence-based policymaking. creator: Ana López-Ballesteros creator: Aoife Delaney creator: James Quirke creator: Jane C. Stout creator: Matthew Saunders creator: James C. Carolan creator: Blánaid White creator: Dara A. Stanley uri: https://doi.org/10.7717/peerj.13586 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 López-Ballesteros et al. title: Seeds harvested during mowing from semi-natural grasslands as an ad hoc but effective solution for grassland restoration link: https://peerj.com/articles/13621 last-modified: 2022-07-13 description: Species-rich grasslands formed by local ecotypes of native species provide numerous ecosystem services both in rural areas as well as urban grasslands. Nonetheless, their area is still too small, making grasslands one of the most frequently restored habitats. Successful restoration requires high-quality seed material, which is expensive and often not easy to acquire. In this study, we tested the potential of seeds accidentally collected during the mowing of a semi-natural grassland for grassland restoration. We tested seed purity, species composition, and germination capability in both laboratory and field conditions. Ninety percent of the collected material consisted of pure seeds of numerous species. Their germination capability was relatively low but still sufficient for successful grassland restoration under a typical seed density/mass per unit area seeding ratio. The germination capacity was the highest in the first two weeks after sowing and increased with overwintering seed storage. The results suggested that the seeds could be successfully used for species-rich grassland restoration. In terms of advantages, the seed mixture had a low cost and contained native species seeds representing local ecotypes. In terms of disadvantages, there was a relatively low amount of seed material and an inability to plan the time of seed harvesting. Thus, the use of the accidentally collected seeds can be considered an effective but rather ad hoc solution. creator: Peliyagodage Chathura Dineth Perera creator: Zofia Nocoń creator: Hassanali Mollashahi creator: Malwina Wierzbicka creator: Tomasz H. Szymura creator: Magdalena Szymura uri: https://doi.org/10.7717/peerj.13621 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Perera et al. title: Genetic population structure and reproductive system of two invasive Asian earthworms, Amynthas tokioensis and Amynthas agrestis link: https://peerj.com/articles/13622 last-modified: 2022-07-13 description: The invasive Asian earthworms, Amynthas tokioensis and A. agrestis, have been successful in entering North American forests in recent decades, with significant damage to both soils and above-ground environments. This success could be driven in part by a polyploid genetic system and parthenogenetic reproduction, often suggested as benefits for invasive species. Therefore, we assessed the genetic population structure, genetic diversity, and reproductive system of both species using morphological traits and panels of microsatellite markers. A total of 216 A. tokioensis and 196 A. agrestis from six sites in Vermont USA were analyzed. Although all worms were morphologically hermaphroditic, all the A. agrestis lacked the male pore (the structure allowing pass of sperm between individuals), and only 19% of the A. tokioensis possessed the male pore. All A. tokioensis earthworms were triploid (scored for three alleles for at least 1 locus, and usually several), and A. agrestis was a mix of triploid and diploid individuals. Notable was the high proportion (80%) of A. agrestis earthworms that were diploid at one site. There was clearly clonal reproduction, with identical seven- locus genotypes observed for earthworms from each site, with as many as 45 individuals with the identical genotype at one site. However, the earthworms were also genetically diverse, with 14 genotypes observed for A. tokioensis and 54 for A. agrestis, and with many singleton genotypes (a single individual). Most genotypes (71% for A. tokioensis and 92% for A. agrestis) were found at a single site. The greatest number of genotypes was found at a commercial nursery where fully 23/26 A. agrestis earthworms were singleton genotypes. As expected for the pattern of private clone alleles at sites, several measures of geographic genetic differentiation were positive, and as expected for triploid systems, an AMOVA analysis showed high within-individual genetic diversity. The paradox of clear clonal reproduction, but with a great number of genotypes for each species, and the mix of triploid and diploid individuals could be explained if the worms have been sexually reproductive, with the switch to the uniparental system only recently (or even if sexual reproduction is episodic). Last, a large number of microsatellite loci were recovered for each species and there sequence and suggested PCR primers are provided for free use by other researchers. creator: Maryam Nouri-Aiin creator: Samantha Connolly creator: Cheryl Keough creator: Annie Jean Smigelsky creator: Yiyi Wen creator: Jeremy Howland creator: Jos. J. Schall creator: Josef H. Görres uri: https://doi.org/10.7717/peerj.13622 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nouri-Aiin et al. title: Changes in the core species of the ant-plant network of oak forest converted to grassland: replacement of its ant functional groups link: https://peerj.com/articles/13679 last-modified: 2022-07-13 description: Land-use change in terrestrial environments is one of the main threats to biodiversity. The study of ant-plant networks has increased our knowledge of the diversity of interactions and structure of these communities; however, little is known about how land-use change affects ant-plant networks. Here we determine whether the change in land use, from native oak forest to induced grassland, affected the network properties of ant-plant networks in a temperate forest in Mexico. We hypothesize that the disturbed vegetation will be more nested and generalized due to the addition of generalist species to the network. The oak forest network comprises 47 plant species and 11 ant species, while the induced grassland network has 35 and 13, respectively. Floral nectar was the resource used most intensely by the ants in both vegetation types. The ant-plant network of the induced grassland was significantly more nested and generalist than that of the oak forest; however, none of the networks were nested when considering the frequency of interaction. In both vegetation types, the ants were more specialized than the plants, and niche overlap was low. This could be related to the dominant species present in each type of vegetation: Prenolepis imparis in the oak forest and Camponotus rubrithorax in the grassland. The central core of cold climate ant species in the oak forest was replaced by a central core of subordinate Camponotini and tropical specialists in the induced grassland. These results suggest that the increase in nestedness and generalization in the grassland may be related to the loss of the cold climate specialists from the core of the oak forest network. Our findings provide evidence that land-use change increases the level of generalization in the ant-plant interaction networks of temperate forests. creator: Mariana Cuautle creator: Cecilia Díaz-Castelazo creator: Citlalli Castillo-Guevara creator: Carolina Guadalupe Torres Lagunes uri: https://doi.org/10.7717/peerj.13679 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cuautle et al. title: Oxygen uptake efficiency slope in healthy normal weight young males: an applicable framework for calculation and interpretation link: https://peerj.com/articles/13709 last-modified: 2022-07-13 description: BackgroundThe oxygen uptake efficiency slope (OUES) is considered a reliable indicator of cardiorespiratory fitness in young and clinical populations who cannot achieve maximal effort during a graded exercise test. However, OUES accuracy depends on the data points used for its calculation and it is still not clear if the submaximal OUES can accurately assess CRF in healthy young males.ObjectiveWe investigated the association between peak oxygen uptake and peak and submaximal OUES, and the agreement between submaximal OUES and peak OUES in male adolescents and young adults.MethodsIn this cross-sectional, observational study, fifty normal weight healthy participants (age 14–22 years, peak oxygen uptake 43.8 ± 7.3 mL·min−1·kg−1) performed a graded exercise test on a cycle ergometer and pulmonary gas exchange was assessed using breath-by-breath analysis. Peak oxygen uptake, and oxygen consumption at the aerobic and at the anaerobic threshold were determined as the 30-s average of the oxygen consumption values. Peak OUES (up to peak) and submaximal OUES (up to the aerobic and anaerobic thresholds) were calculated from the logarithmic relation between oxygen consumption and pulmonary ventilation.ResultsVery strong correlations were observed between peak oxygen uptake and peak OUES (r = 0.80–0.88) while fair-to-very strong correlations were observed between the peak oxygen uptake and the two submaximal OUES (r = 0.32–0.81). The level of agreement between peak OUES and OUES up to the anaerobic threshold (r = 0.89–0.93; Typical percentage error 6%; Intraclass correlation coefficient = 0.89–0.93) was greater than the one between the peak oxygen uptake with OUES up to the aerobic threshold (r = 0.39–0.56; Typical percentage error 15%; Intraclass correlation coefficient = 0.38–0.56).Conclusions. The peak OUES is a better indicator of aerobic fitness than the OUES up to the anaerobic threshold in healthy, young males. The OUES up to the anaerobic threshold is a valid alternative to peak OUES. creator: Lavinia Falcioni creator: Laura Guidetti creator: Carlo Baldari creator: Maria Chiara Gallotta creator: Marco Meucci uri: https://doi.org/10.7717/peerj.13709 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Falcioni et al. title: Are aerosol control devices effective in preventing the spread of dental aerosol? link: https://peerj.com/articles/13714 last-modified: 2022-07-13 description: BackgroundIn dental clinics, aerosols produced from dental instruments have become a matter of concern following breakout of coronavirus disease 19 (COVID-19) evolving into a pandemic. This study compared aerosol reduction systems and in terms of their ability to reduce Enterococcus faecalis (E. faecalis) contaminated aerosol in a simulated dental office set-up.MethodsClosed clinic model with manikin and mandibular molar typodont was simulated. For 10 min, the air and water dispersed by the rotating bur mounted on an aerator was contaminated by pouring the suspension containing 1–3 × 108 CFU/mL E. faecalis directly on the bur. During and after the procedures, the air within the cabin was also sampled. CFU count was recorded and scored. The mean CFU scores obtained from agar plate count and air sampling device was compared using Kruskal–Wallis H test among groups with 5% significance threshold.ResultsThe use of WS Aerosol Defender device led to greater CFU scores on the agars levelled to patient’s chest compared to other directions (p = 0.001). Combined use of VacStation and WS Aerosol Defender resulted in significantly decreased CFU score in the air samples compared to experimental and positive control groups (p = 0 < 0.05).ConclusionsAlthough the devices prevented the spread of aerosol around the patient to some extent, they could not completely eliminate the contaminated aerosol load in the cabin environment. creator: Elif Seher Böke creator: Ali Keleş creator: Cangül Keskin creator: Yeliz Tanrıverdi Çaycı creator: Tugba Turk uri: https://doi.org/10.7717/peerj.13714 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Böke et al. title: Insights into mobile genetic elements and the role of conjugative plasmid in transferring aminoglycoside resistance in extensively drug-resistant Acinetobacter baumannii AB329 link: https://peerj.com/articles/13718 last-modified: 2022-07-13 description: Acinetobacter baumannii is a major cause of nosocomial infection, and the incidence of extensively drug-resistant A. baumannii (XDRAB) infections has dramatically increased worldwide. In this study, we aimed to explore the complete genome sequence of XDRAB 329, ST1166/98 (Oxford/Pasteur), which is an outbreak clone from a hospital in Thailand. Whole-genome sequencing (WGS) was performed using short-read Illumina and long-read PacBio sequencing, and a conjugation assay of its plasmid was performed. The complete genome sequence of A. baumannii AB329 revealed a circular chromosome 3,948,038 bp in length with 39% GC content. Antibiotic resistance genes (ARGs), including beta-lactam resistance (blaOXA-51, blaADC-25, blaOXA-23, blaTEM-1D), aminoglycoside resistance (aph(3′)-Ia, aph(3″)-Ib, aph(6)-Id, armA), tetracycline resistance (tet(B), tet (R)), macrolide resistance (mph(E), msr(E)), and efflux pumps, were found. Mobile genetic elements (MGEs) analysis of A. baumannii AB329 revealed two plasmids (pAB329a and pAB329b), three prophages, 19 genomic islands (GIs), and 33 insertion sequences (ISs). pAB329a is a small circular plasmid of 8,731 bp, and pAB329b is a megaplasmid of 82,120 bp. aph(3′)-VIa was detected in pAB329b, and a major facilitator superfamily (MFS) transporter was detected in the prophage. Acinetobacter baumannii resistance island 4 (AbaR4) harboring tetracycline and aminoglycoside resistance was detected in the genome of A. baumannii AB329. pAB329b, which belongs to Rep-type GR6 (plasmid lineage LN_1), is a conjugative plasmid with the ability to transfer an aminoglycoside resistance gene to sodium azide-resistant A. baumannii. This study provides insights into the features of the MGEs of XDRAB, which are the main reservoir and source of dissemination of ARGs. creator: Supat Khongfak creator: Rapee Thummeepak creator: Udomluk Leungtongkam creator: Kannipa Tasanapak creator: Aunchalee Thanwisai creator: Sutthirat Sitthisak uri: https://doi.org/10.7717/peerj.13718 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Khongfak et al. title: JMJD3 suppresses tumor progression in oral tongue squamous cell carcinoma patients receiving surgical resection link: https://peerj.com/articles/13759 last-modified: 2022-07-13 description: BackgroundJumonji domain-containing-3 (JMJD3) is reported to be a histone H3 lysine 27 (H3K27) demethylase and a tumor suppressor gene. The present study designed to investigate the crucial role of JMJD3 in oral tongue squamous cell carcinoma (OTSCC) patients who received surgical resection.MethodsWe enrolled a total of 156 OTSCC patients receiving surgical resection, including 73 patients (47%) with high expression of JMJD3 and 83 patients (53%) harboring low expression of JMJD3. Two OTSCC cell lines, SAS and Cal 27, were used to explore the modulation of cancer. GSK-J4, a potent inhibitor of JMJD3, was used to treat the two OTSCC cell lines. The Chi-square test was performed to examine between-group differences in categorical variables; the Kaplan–Meier method was used to investigate survival outcome in univariate analysis, and the Cox regression model was used for multivariate analysis.ResultsThe median follow-up period was 59.2 months and he five-year disease-free survival (DFS) and overall survival (OS) rates were 46.2% and 50.0%, respectively. Better five-year DFS (59% versus 35%) and five-year OS (63% versus 39%) were mentioned in patients with high expression of JMJD3 compared to those with low expression of JMJD3. High expression of JMJD3 was significantly associated with superior DFS and OS in the univariate and multivariate analyses. Following successful inhibition of JMJD3 by GSK-J4, western blotting analysis showed the decreased expression of Rb and p21.ConclusionOur study showed that high expression of JMJD3 is a good prognostic factor in OTSCC patients who underwent surgical resection. creator: Yen-Hao Chen creator: Chang-Han Chen creator: Chih-Yen Chien creator: Yan-Ye Su creator: Sheng-Dean Luo creator: Shau-Hsuan Li uri: https://doi.org/10.7717/peerj.13759 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: Short physical performance battery as a predictor of mortality in community-dwelling older adults: a longitudinal study in the Brazilian Amazon region link: https://peerj.com/articles/13630 last-modified: 2022-07-12 description: BackgroundThe Short Physical Performance Battery (SPPB) is an instrument for assessing physical performance widely used in research among the elderly in multiple settings. We did not find Brazilian longitudinal studies that aimed to analyze the predictive capacity and accuracy of the SPPB among community-dwelling older adults and no systematic reviews were found on the accuracy of the SPPB in predicting mortality in community- dwelling older adults. This study aimed to analyze the capacity and accuracy of the SPPB for predicting mortality in community-dwelling older adults, as well as to determine cut-off points for men and women.MethodLongitudinal observational study conducted with 411 (70.1 ± 7.25 years) community-dwelling older adults, between 2017 and 2020 (37.7 ± 6.24 months). Physical performance was evaluated using the SPPB and information on the all-cause mortality rate was also recorded. Multivariate Cox regression analyses and curves were performed using the Kaplan–Meier method. Receiver Operating Characteristic (ROC) curves were constructed, with the parameters of area under the ROC curve (AUC) to determine cutoff points for discriminating mortality, considering a significance level of 5% (p < 0.05) and 95% confidence interval (CI) 95%.ResultsOlder adults with very low and low physical performance in the SPPB, showed higher risks of mortality (HR = 9.67; 95% CI [1.20–77.65]; HR = 4.06; 95% CI [1.09–15.01]), respectively. In the subtest’s analysis, older adults with low performance in the balance (HR = 0.54; 95% CI [0.36–0.81]) and gait speed tests (HR = 0.50; 95% CI [0.33–0.76]) showed greater risks of dying. The same was reproduced for categories in each test (participants that scored 2 points in the balance test had an HR = 5.86; 95% CI [1.84–18.61] and 2 points in the gait speed test, HR = 5.07; 95% CI [1.76–14.58]. The cutoff point ≤ 9 in the SPPB set the discriminator criterion for mortality in older people of both sexes.ConclusionsThe SPPB, as well as the balance and gait speed subtests were predictors of mortality, and the SPPB is accurate in predicting mortality among community-dwelling older adults. creator: Caroline de Fátima Ribeiro Silva creator: Daniela Gonçalves Ohara creator: Areolino Pena Matos creator: Ana Carolina Pereira Nunes Pinto creator: Maycon Sousa Pegorari uri: https://doi.org/10.7717/peerj.13630 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Silva et al. title: CD14 and CD26 from serum exosomes are associated with type 2 diabetes, exosomal Cystatin C and CD14 are associated with metabolic syndrome and atherogenic index of plasma link: https://peerj.com/articles/13656 last-modified: 2022-07-12 description: BackgroundExosomes are microvesicles that actively participate in signaling mechanisms and depending on their content can contribute to the development of different pathologies, such as diabetes and cardiovascular disease.ObjectiveThe aim of this study was to evaluate the association of cystatin C, CD26, and CD14 proteins in serum exosomes from patients with Type 2 Diabetes (T2D), metabolic syndrome (MetS), and atherogenic index of plasma (AIP).MethodsSerum exosomes were isolated by ultracentrifugation from 147 individuals with and without diabetes. Both anthropometric and metabolic parameters were registered from everyone. The levels of exosomal proteins cystatin C, CD26, and CD14 were quantified by ELISA. The association between protein levels and T2D or atherogenic risk factors was analyzed by linear regression and generalized regression models.ResultsWe observed a significant correlation of increased glucose with elevated levels of Cystatin C, and an effect of T2D on the levels of CD26 (β = 45.8 pg/µg; p = 0.001) and CD14 (β = 168 pg/µg; p < 0.001) compared to subjects without T2D. CD14 was significantly related to T2D, metabolic syndrome, glucose, and the Atherogenic Index of Plasma (AIP). Additionally, we observed a significant effect of metabolic syndrome MetS on the increase of exosomal Cystatin C and CD14.ConclusionsT2D may contribute to the increase of CD14 protein contained in exosomes, as well as to the predisposition of atherogenic events development due to its relationship with the increase in serum triglyceride concentrations and the AIP score. Finally, the increased levels of CD14 and Cystatin C in exosomes are related to MetS. The analysis of exosome contents of diabetic patients remains an incipient field, so extensive characterization is crucial for their use as biomarkers or to analyze their possible contribution to diabetic complications. creator: Claudia Paola Pérez-Macedonio creator: Eugenia Flores-Alfaro creator: Luz del C. Alarcón-Romero creator: Amalia Vences-Velázquez creator: Natividad Castro-Alarcón creator: Eduardo Martínez-Martínez creator: Monica Ramirez uri: https://doi.org/10.7717/peerj.13656 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Pérez-Macedonio et al. title: Prevalence of HPV genotypes and assessment of their clinical relevance in laryngeal squamous cell carcinoma in a northeastern state of Brazil—a retrospective study link: https://peerj.com/articles/13684 last-modified: 2022-07-12 description: BackgroundA high prevalence and incidence of head and neck tumors make Brazil the country with the third-highest number of cases of these malignant neoplasms. The main risk factors are smoking and alcohol consumption; however, cases related to the human papillomavirus (HPV) have tripled in number, demonstrating a changing disease profile. Studies have reported the prevalence of HPV in laryngeal squamous cell carcinoma (LSCC) to vary between 8% and 83%. The role of HPV as an important causative factor in LSCC remains unclear.MethodsThis retrospective study included 82 patients with LSCC diagnosed between 2014 and 2019 at two oncology hospitals in São Luís, Brazil. Sociodemographic and clinical data, and the histopathologic characteristics of the tumors, were collected directly from medical records. Genetic material was extracted from paraffin-embedded samples using nested polymerase chain reaction (PCR) and automated sequencing for HPV detection and genotyping. The results by social and clinicopathologic variables were then compared using the chi-squared test and multivariate analysis.ResultsSociodemographic analysesdemonstrated that most patients were men (87.8%), brown-skinned (75.6%), and resident in the state capital (53.7%). They generally had a poor education status (53.7%), having only an elementary school education (completed/incomplete), and 51.2% were self-employed in occupations such as farming or fishing. Smoking and alcohol consumption habits were observed in approximately half the patients. With respect to clinical characteristics, 39% of patients exhibited T1/T2 staging, 51.2% had no distant metastasis, and 30.5% had lymph node invasion. HPV DNA was detected in half the samples (50%), with the high oncogenic type 16 being the most prevalent. There was no significant relationship observed between the economic, educational, occupational with the HPV LSCC in the presented data, although multivariate analysis demonstrated that HPV DNA was more likely to be present in T3–T4 tumors (p = 0.002). creator: Charlles Brito creator: Rachel D. Cossetti creator: Diego Agra de Souza creator: Marcos Catanha creator: Pablo de Matos Monteiro creator: Flavia Castello Branco Vidal uri: https://doi.org/10.7717/peerj.13684 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Brito et al. title: Comparative full-length transcriptome analysis by Oxford Nanopore Technologies reveals genes involved in anthocyanin accumulation in storage roots of sweet potatoes (Ipomoea batatas L.) link: https://peerj.com/articles/13688 last-modified: 2022-07-12 description: BackgroundStorage roots of sweet potatoes (Ipomoea batatas L.) with different colors vary in anthocyanin content, indicating different economically agronomic trait. As the newest DNA/RNA sequencing technology, Oxford Nanopore Technologies (ONT) have been applied in rapid transcriptome sequencing for investigation of genes related to nutrient metabolism. At present, few reports concern full-length transcriptome analysis based on ONT for study on the molecular mechanism of anthocyanin accumulation leading to color change of tuberous roots of sweet potato cultivars.ResultsThe storage roots of purple-fleshed sweet potato (PFSP) and white-fleshed sweet potato (WFSP) at different developmental stages were subjected to anthocyanin content comparison by UV-visible spectroscopy as well as transcriptome analysis at ONT MinION platform. UV-visible spectrophotometric measurements demonstrated the anthocyanin content of PFSP was much higher than that of WFSP. ONT RNA-Seq results showed each sample generated average 2.75 GB clean data with Full-Length Percentage (FL%) over 70% and the length of N50 ranged from 1,192 to 1,395 bp, indicating reliable data for transcriptome analysis. Subsequent analysis illustrated intron retention was the most prominent splicing event present in the resulting transcripts. As compared PFSP with WFSP at the relative developmental stages with the highest (PH vs. WH) and the lowest (PL vs. WL) anthocyanin content, 282 and 216 genes were up-regulated and two and 11 genes were down-regulated respectively. The differential expression genes involved in flavonoid biosynthesis pathway include CCoAOMT, PpLDOX, DFR, Cytochrome P450, CHI, and CHS. The genes encoding oxygenase superfamily were significantly up-regulated when compared PFSP with WFSP at the relative developmental stages.ConclusionsComparative full-length transcriptome analysis based on ONT serves as an effective approach to detect the differences in anthocyanin accumulation in the storage roots of different sweet potato cultivars at transcript level, with noting that some key genes can now be closely related to flavonoids biosynthesis. This study helps to improve understanding of molecular mechanism for anthocyanin accumulation in sweet potatoes and also provides a theoretical basis for high-quality sweet potato breeding. creator: Jun Xiong creator: Xiuhua Tang creator: Minzheng Wei creator: Wenjin Yu uri: https://doi.org/10.7717/peerj.13688 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xiong et al. title: Characterization of human tear proteome reveals differentially abundance proteins in thyroid-associated ophthalmopathy link: https://peerj.com/articles/13701 last-modified: 2022-07-12 description: BackgroundThyroid-associated ophthalmopathy (TAO) is a common orbital inflammatory disease, but the abnormal expression of proteins in tears of TAO patients has not been systematically studied. The purpose of this study is to compare and analyze the total tear protein profile of TAO patients and to provide protein cues for TAO pathogenesis.MethodsTear samples were isolated from 30 TAO patients with obvious ocular surface damage and 30 healthy control subjects. Tear samples from 30 individuals were mixed and divided into three sample pools. Easy nano-scale LC-MS/MS based on labeling-free quantitative technology was utilized to profile tear proteome.ResultsHere, electrospray ionization mass spectra and SDS-PAGE results confirmed the good parallelisms among samples. A total of 313 proteins were obtained from six tear pools, among them, 103 differential abundance proteins (DAPs) were identified, including 99 up-regulated DAPs (including APOA1, HV103, IGH, and Transferrin variant) and four down-regulated DAPs (including FABA, VCC1, NUCB2, and E-cadherin) in the TAO group compared with the control group. GO analysis showed that up-regulated DAPs were mainly enriched in lipid metabolism and platelet molecular function, and down-regulated DAPs were involved in binding, cell junction, and cellular process. KEGG results indicated that DAPs were involved in 117 kinds of signal transduction pathways, among which the immune-related pathway of complement and coagulation cascades had the greatest relevance.ConclusionIn conclusion, label-free LC-MS/MS is an effective strategy for profiling tear proteins component. Our study provides proteins and pathways altered in TAO and provides protein cues for further study on the precise mechanism of TAO pathogenesis. creator: Xiaoqing Zhou creator: Ruili Wei creator: Rui Wang uri: https://doi.org/10.7717/peerj.13701 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhou et al. title: Downregulation of the enhancer of zeste homolog 1 transcriptional factor predicts poor prognosis of triple-negative breast cancer patients link: https://peerj.com/articles/13708 last-modified: 2022-07-12 description: BackgroundTriple-negative breast cancer (TNBC) is the most malignant subtype of breast cancer and lacks effective biomarkers. This study seeks to unravel the expression status and the prospective transcriptional mechanisms of EZH1/EZH2 in TNBC tissue samples. Moreover, another objective of this study is to reveal the prognostic molecular signatures for risk stratification in TNBC patients.MethodsTo determine the expression status of EZH1/EZH2 in TNBC tissue samples, microarray analysis and immunohistochemistry were performed on in house breast cancer tissue samples. External mRNA expression matrices were used to verify its expression patterns. Furthermore, the prospective transcriptional mechanisms of EZH1/EZH2 in TNBC were explored by performing differential expression analysis, co-expression analysis, and chromatin immunoprecipitation sequencing analysis. Kaplan–Meier survival analysis and univariate Cox regression analysis were utilized to detect the prognostic molecular signatures in TNBC patients. Nomogram and time-dependent receiver operating characteristic curves were plotted to predict the risk stratification ability of the prognostic-signatures-based Cox model.ResultsIn-house TMAs (66 TNBC vs. 106 non-TNBC) and external gene microarrays, as well as RNA-seq datasets (1,135 TNBC vs. 6,198 non-TNBC) results, confirmed the downregulation of EZH1 at both the protein and mRNA levels (SMD = −0.59 [−0.80, −0.37]), as is opposite to that of EZH2 (SMD = 0.74 [0.40, 1.08]). The upregulated transcriptional target genes of EZH1 were significantly aggregated in the cell cycle pathway, where CCNA2, CCNB1, MAD2L1, and PKMYT1 were determined as key transcriptional targets. Additionally, the downregulated transcriptional targets of EZH2 were enriched in response to the hormone, where ESR1 was identified as the hub gene. The six-signature-based prognostic model produced an impressive performance in this study, with a training AUC of 0.753, 0.981, and 0.977 at 3-, 5-, and 10-year survival probability, respectively.ConclusionEZH1 downregulation may be a key modulator in the progression of TNBC through negative transcriptional regulation by targeting CCNA2, CCNB1, MAD2L1, and PKMYT1. creator: Wei Peng creator: Wei Tang creator: Jian-Di Li creator: Rong-Quan He creator: Jia-Yuan Luo creator: Zu-Xuan Chen creator: Jiang-Hui Zeng creator: Xiao-Hua Hu creator: Jin-Cai Zhong creator: Yang Li creator: Fu-Chao Ma creator: Tian-Yi Xie creator: Su-Ning Huang creator: Lian-Ying Ge uri: https://doi.org/10.7717/peerj.13708 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Peng et al. title: Cyclocytidine hydrochloride inhibits the synthesis of relaxed circular DNA of hepatitis B virus link: https://peerj.com/articles/13719 last-modified: 2022-07-12 description: BackgroundCyclocytidine hydrochloride (HCl) has been reported to inhibit DNA synthesis by affecting DNA polymerase. Here, we tested the antiviral effect of cyclocytidine on hepatitis B virus (HBV) DNA synthesis, which is reliant on DNA polymerase activity.Materials and MethodsCyclocytidine HCl was treated to HBV-producing HepAD38 cells or added to an endogenous polymerase reaction, and HBV DNA was detected by Southern blot.ResultsTreatment of 20 µM cyclocytidine HCl significantly decreased the production of relaxed circular (rc) DNA in HepAD38 cells and block rcDNA synthesis in endogenous polymerase reaction (EPR), a cell free assay, possibly by inhibiting the HBV DNA polymerase activity.ConclusionCyclocytidine HCl could inhibit the synthesis of HBV rcDNA, the precursor of covalently closed circular DNA, and this result provides a case for the usage of “old” drugs for “new” applications. creator: Xue Wang creator: Yihan Xiao creator: Zhigang Cui creator: Zongxin Li creator: Lihua Li creator: Lixian Wu creator: Feifei Yin creator: Xiuji Cui uri: https://doi.org/10.7717/peerj.13719 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Estimating bite force in extinct dinosaurs using phylogenetically predicted physiological cross-sectional areas of jaw adductor muscles link: https://peerj.com/articles/13731 last-modified: 2022-07-12 description: I present a Bayesian phylogenetic predictive modelling (PPM) framework that allows the prediction of muscle parameters (physiological cross-sectional area, APhys) in extinct archosaurs from skull width (WSk) and phylogeny. This approach is robust to phylogenetic uncertainty and highly versatile given its ability to base predictions on simple, readily available predictor variables. The PPM presented here has high prediction accuracy (up to 95%), with downstream biomechanical modelling yielding bite force estimates that are in line with previous estimates based on muscle parameters from reconstructed muscles. This approach does not replace muscle reconstructions but one that provides a powerful means to predict APhys from skull geometry and phylogeny to the same level of accuracy as that measured from reconstructed muscles in species for which soft tissue data are unavailable or difficult to obtain. creator: Manabu Sakamoto uri: https://doi.org/10.7717/peerj.13731 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sakamoto title: Automated detection and removal of flat line segments and large amplitude fluctuations in neonatal electroencephalography link: https://peerj.com/articles/13734 last-modified: 2022-07-12 description: BackgroundArtefact removal in neonatal electroencephalography (EEG) by visual inspection generally depends on the expertise of the operator, is time consuming and is not a consistent pre-processing step to the pipeline for the automated EEG analysis. Therefore, there is the need for the automated detection and removal of artefacts in neonatal EEG, especially of distinct and predominant artefacts such as flat line segments (mainly caused by instrumental error where contact between electrodes and head box is lost) and large amplitude fluctuations (related to neonatal movements).MethodA threshold-based algorithm for the automated detection and removal of flat line segments and large amplitude fluctuations in neonatal EEG of infants at term-equivalent age is developed. The algorithm applies thresholds to the absolute second difference, absolute amplitude, absolute first difference and the ratio between the frequency content above 50 Hz and the frequency content across all frequencies.ResultsThe algorithm reaches a median accuracy of 0.91, a median hit rate of 0.91 and a median false discovery rate of 0.37. Also, a significant improvement (≈10%) in the performance of a four-stage sleep classifier is observed after artefact removal with the proposed algorithm as compared to before its application.SignificanceAn automated artefact removal method contributes to the pipeline of automated EEG analysis. The proposed algorithm has shown to have good performance and to be effective in neonatal EEG applications. creator: Gabriella Tamburro creator: Katrien Jansen creator: Katrien Lemmens creator: Anneleen Dereymaeker creator: Gunnar Naulaers creator: Maarten De Vos creator: Silvia Comani uri: https://doi.org/10.7717/peerj.13734 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tamburro et al. title: GABRP promotes CD44s-mediated gemcitabine resistance in pancreatic cancer link: https://peerj.com/articles/12728 last-modified: 2022-07-11 description: BackgroundPancreatic ductal adenocarcinoma (PDAC) has the worst five-year overall survival rate among all cancer types. Acquired chemoresistance is considered one of the main reasons for this dismal prognosis, and the mechanism of chemoresistance is unknown.MethodsWe previously identified a subpopulation of chemoresistant CD44high-expressing PDAC cells. Subsequently, we selected the candidate gene, gamma-aminobutyric acid receptor subunit Pi (GABRP), from three Gene Expression Omnibus datasets as the potential CD44 downstream target mediating the gemcitabine resistance. Loss and gain of function such as stable knockdown of CD44 by small hairpin (sh) RNA-mediated silencing technique and overexpression (O/E) of CD44s had been studied for comparing the gemcitabine resistance among CD44high-expressing cells, shCD44 cells, CD44low-expressing cells and O/E CD44s expressing cells. Functional assays including cell viability, colony formation, invasion, quantitative PCR and western blotting techniques were performed to validate the roles of CD44 and GABRP playing in mediating the gemcitabine resistance in pancreatic cancer cells.ResultsCD44s depletion significantly reduced gemcitabine resistance in shCD44 single clone cells compared to CD44high-expressing cells. Knockdown of CD44 cells formed less colonies, became less invasive and remarkably decreased the mRNA level of GABRP. While overexpression of CD44s had the opposite effect on gemcitabine resistance, colony formation and invasive property. Of note, long term gemcitabine resistant pancreatic cancer cells detected increased expression of CD44 and GABRP. Clinically, GABRP expression was significantly upregulated in the tissues of patients with pancreatic cancer compared to the normal samples, and the overall survival rate of patients with low GABRP expression was longer. CD44 and GABRP co-expression was positively correlated in 178 pancreatic cancer patients.ConclusionOur findings suggest that GABRP may serve as a CD44s downstream target to diminish gemcitabine resistance in pancreatic cancer, and both CD44s and GABRP molecules have the potential to become prognostic biomarkers for PDAC patients with gemcitabine resistance. creator: Chen Chen creator: Binfeng Wu creator: Mingge Wang creator: Jinghua Chen creator: Zhaohui Huang creator: Jin-Song Shi uri: https://doi.org/10.7717/peerj.12728 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: Tucuxi-BLAST: Enabling fast and accurate record linkage of large-scale health-related administrative databases through a DNA-encoded approach link: https://peerj.com/articles/13507 last-modified: 2022-07-11 description: BackgroundPublic health research frequently requires the integration of information from different data sources. However, errors in the records and the high computational costs involved make linking large administrative databases using record linkage (RL) methodologies a major challenge.MethodsWe present Tucuxi-BLAST, a versatile tool for probabilistic RL that utilizes a DNA-encoded approach to encrypt, analyze and link massive administrative databases. Tucuxi-BLAST encodes the identification records into DNA. BLASTn algorithm is then used to align the sequences between databases. We tested and benchmarked on a simulated database containing records for 300 million individuals and also on four large administrative databases containing real data on Brazilian patients.ResultsOur method was able to overcome misspellings and typographical errors in administrative databases. In processing the RL of the largest simulated dataset (200k records), the state-of-the-art method took 5 days and 7 h to perform the RL, while Tucuxi-BLAST only took 23 h. When compared with five existing RL tools applied to a gold-standard dataset from real health-related databases, Tucuxi-BLAST had the highest accuracy and speed. By repurposing genomic tools, Tucuxi-BLAST can improve data-driven medical research and provide a fast and accurate way to link individual information across several administrative databases. creator: José Deney Araujo creator: Juan Carlo Santos-e-Silva creator: André Guilherme Costa-Martins creator: Vanderson Sampaio creator: Daniel Barros de Castro creator: Robson F. de Souza creator: Jeevan Giddaluru creator: Pablo Ivan P. Ramos creator: Robespierre Pita creator: Mauricio L. Barreto creator: Manoel Barral-Netto creator: Helder I. Nakaya uri: https://doi.org/10.7717/peerj.13507 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Araujo et al. title: Effects of aerobic exercise on event-related potentials related to cognitive performance: a systematic review link: https://peerj.com/articles/13604 last-modified: 2022-07-11 description: IntroductionAerobic exercise interventions may affect different cognitive domains such as attention, working memory, inhibition, etc. However, the neural mechanisms underlying this relationship, remains uncertain.ObjectiveTo perform a systematic review on exercise intervention studies that use event-related potentials (ERPs) as outcome for cognitive performance.MethodsWe identified studies through searches in four databases reporting the effects of either an acute bout or chronic exercise on any ERP associated with cognitive performance. Study population included participants >17 years of age with or without a diagnosis.ResultsA total of 5,797 records were initially identified through database searching of which 52 were eligible for inclusion. Most studies were of acute aerobic exercise with moderate intensity. Results were heterogenious across studies, but there was a trend that ERP amplitude increased and (to a lesser extent) latencies decreased post-exercise. The P3 ERP was the most often reported ERP.ConclusionHeterogeneity across studies regarding methodology limited the possibility to draw definitive conclusions but the most consistent findings were that acute aerobic exercise was associated with higher amplitudes, and to a lesser extent shorter latencies, of ERPs. creator: Julia Gusatovic creator: Mathias Holsey Gramkow creator: Steen Gregers Hasselbalch creator: Kristian Steen Frederiksen uri: https://doi.org/10.7717/peerj.13604 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Gusatovic et al. title: Food taboos during pregnancy: meta-analysis on cross cultural differences suggests specific, diet-related pressures on childbirth among agriculturalists link: https://peerj.com/articles/13633 last-modified: 2022-07-11 description: Pregnancy is the most delicate stage of human life history as well as a common target of food taboos across cultures. Despite puzzling evidence that many pregnant women across the world reduce their intake of nutritious foods to accomplish cultural norms, no study has provided statistical analysis of cross-cultural variation in food taboos during pregnancy. Moreover, antenatal practices among forager and agriculturalists have never been compared, despite subsistence mode being known to affect staple foods and lifestyle directly. This gap hinders to us from understanding the overall threats attributed to pregnancy, and their perceived nutritional causes around the world. The present study constitutes the first cross-cultural meta-analysis on food taboos during pregnancy. We examined thirty-two articles on dietary antenatal restrictions among agricultural and non-agricultural societies, in order to: (i) identify cross-culturally targeted animal, plant and miscellaneous foods; (ii) define major clusters of taboo focus; (iii) test the hypothesis that food types and clusters of focus distribute differently between agricultural and non-agricultural taboos; and (iv) test the hypothesis that food types distribute differently across the clusters of taboo focus. All data were analysed in SPSS and RStudio using chi-squared tests and Fisher’s exact tests. We detected a gradient in taboo focus that ranged from no direct physiological interest to the fear of varied physiological complications to a very specific concern over increased birth weight and difficult delivery. Non-agricultural taboos were more likely to target non-domesticated animal foods and to be justified by concerns not directly linked to the physiological sphere, whereas agricultural taboos tended to targed more cultivated and processed products and showed a stronger association with concerns over increased birth weight. Despite some methodological discrepancies in the existing literature on food taboos during pregnancy, our results illustrate that such cultural traits are useful for detecting perception of biological pressures on reproduction across cultures. Indeed, the widespread concern over birth weight and carbohydrate rich foods overlaps with clinical evidence that obstructed labor is a major threat to maternal life in Africa, Asia and Eurasia. Furthermore, asymmetry in the frequency of such concern across subsistence modes aligns with the evolutionary perspective that agriculture may have exacerbated delivery complications. This study highlights the need for the improved understanding of dietary behaviors during pregnancy across the world, addressing the role of obstructed labor as a key point of convergence between clinical, evolutionary and cultural issues in human behavior. creator: Ornella Maggiulli creator: Fabrizio Rufo creator: Sarah E. Johns creator: Jonathan C.K. Wells uri: https://doi.org/10.7717/peerj.13633 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Maggiulli et al. title: An impact assessment of insecticides application on the non-targeted mosquito Aedes albopictus (Skuse) in Punjab rice fields, Pakistan link: https://peerj.com/articles/13697 last-modified: 2022-07-11 description: Insecticidal control of insect pests of rice crop may influence the environment and nontarget species in rice fields. Aedes albopictus, one of the most common nontarget species present in rice fields, received lethal and sublethal exposures to insecticides used in rice cultivated fields. The present work explores the effects of insecticides in six non-targeted Ae. albopictus strains collected from rice fields with a history of insecticidal usage in comparison with a laboratory susceptible reference strain (REF) and a strain (LHR) collected from a rice field with no, or minimal, history of insecticidal usage. Two types of effects, the resistance development and performance of biological traits, were studied by selecting seven commonly used insecticides in rice fields in Punjab, Pakistan. The results revealed that the strains collected from the rice fields with histories of insecticidal usage exhibited significant levels of resistance to flonicamid, chlorantraniliprole, gamma-cyhalothrin, fipronil, monomehypo, triazophos, and carbofuran, when compared with REF and LHR strains. In addition, Ae. albopictus strains revealed a significantly weaker performance of biological traits (rate of pupae formation, survival of male and female adults (except females of OKR and MTN strains), and ovipositing females) than those of the REF and LHR strains. However, the fecundity of all field strains was only significantly different with that of the REF strain. In conclusion, the results highlight the problem of the negative effects of insecticidal usage in rice fields on nontarget species present in the same environment, and emphasize the need to adopt pest management activities that are safe for the environment. creator: Hafiz Azhar Ali Khan uri: https://doi.org/10.7717/peerj.13697 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Khan title: Niche diversification of Mediterranean and southwestern Asian tortoises link: https://peerj.com/articles/13702 last-modified: 2022-07-11 description: BackgroundTortoises of the genus Testudo are widely distributed throughout the Mediterranean region and southwestern Asia. However, the evolutionary mechanisms of diversification in this genus are still poorly understood.MethodsIn this study, we assessed the evolutionary patterns in the climate niches of five species and 11 subspecies of the genus Testudo using ecological niche models and evaluated the niche overlap based on species phylogenetic distances.ResultsThe ecological models indicated that most species differ in their climate niches, but show overlap, with gradual transitions at range boundaries. As expected, the ecological divergence among subspecies was lower than that among species. Evaluation of the phylogenetic signal indicated that climate niches have been weakly conserved, but sister species also show high evolutionary divergence. creator: Daniel Escoriza creator: Jihene Ben Hassine uri: https://doi.org/10.7717/peerj.13702 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Escoriza and Ben Hassine title: TBX3 regulates the transcription of VEGFA to promote osteoblasts proliferation and microvascular regeneration link: https://peerj.com/articles/13722 last-modified: 2022-07-11 description: ObjectiveOsteochondral decellularization can promote local vascular regeneration, but the exact mechanism is unknown. The aim of this study is to study osteogenic microvascular regeneration in single cells.MethodsThe scRNA-seq dataset of human periosteal-derived cells (hPDCs) were analyzed by pySCENIC. To examine the role of TBX3 in osteogenesis and vascularization, cell transfection, qRT-PCR, western blot, and CCK-8 cell proliferation assays were performed.ResultsTCF7L2, TBX3, FLI1, NFKB2, and EZH2 were found to be transcription factors (TFs) most closely associated with corresponding cells. The regulatory network of these TFs was then visualized. Our study knocked down the expression of TBX3 in human osteoblast cell lines. In the TBX3 knockdown group, we observed decreased expression of VEGFA, VEGFB, and VEGFC. Moreover, Western blot analysis showed that downregulating TBX3 resulted in a reduction of VEGFA expression. And TBX3 stimulated osteoblast proliferation in CCK-8 assays.ConclusionTBX3 regulates VEGFA expression and promotes osteoblast proliferation in skeletal microvasculature formation. The findings provide a theoretical basis for investigating the role of TBX3 in promoting local vascular regeneration. creator: Lichuang Wu creator: Chenxian Su creator: Chuanhua Yang creator: Jinxing Liu creator: Yiheng Ye uri: https://doi.org/10.7717/peerj.13722 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wu et al. title: Wide space sowing achieved high productivity and effective nitrogen use of irrigated wheat in South Shanxi, China link: https://peerj.com/articles/13727 last-modified: 2022-07-11 description: Wheat (Triticum aestivum L.) is a staple crop worldwide, and its yield has improved since the green revolution, which was attributed to chemical nitrogen (N) fertilizer application. However, regular N application decreases N use efficiency (NUE, the ratio of grain dry matter yield to N supply from soil and fertilizer). Various practices have been implemented to maintain high crop yield and improve NUE. Nowadays, the enhanced sowing method, i.e., wide space sowing (WS), has improved the productivity of wheat crops. However, how the sowing method and N application rate affect N use and yield productivity has not been fully elucidated. Field experiments with treatments using two sowing methods (WS, and drill sowing, DS) and four N application rates (0, 180, 240, and 300 kg ha−1, represented as N0, N180, N240, and N300, respectively) were conducted from 2017 to 2019. The results showed that grain yield under WS was 13.57–16.38% higher than that under DS. The yield advantage under WS was attributed to an increased ear number. Both the higher stem and productive stem percentage accounted for the increased ear number under WS. Higher total N quantity and larger leaf area index at anthesis under WS contributed to higher dry matter production, resulting in higher grain yield. Higher dry matter production was due to pre-anthesis dry weight and post-anthesis dry weight. The wheat crop under WS had a 12.44–15.00% higher NUE than that under DS. The increased NUE under WS was attributed to higher N uptake efficiency (the ratio of total N quantity at maturity to N supply from soil and fertilizer), which was the result of greater total N quantity. The higher total N quantity under WS was due to both higher pre-anthesis N uptake and post-anthesis N uptake. Remarkably, compared to DS with 240 kg N ha−1, WS with 180 kg N ha−1 had almost equal grain yield, dry matter, and total N quantity. Therefore, wheat crops under WS could achieve both high NUE and grain yield simultaneously with only moderate N fertilizer in South Shanxi, China. creator: Qiang Wang creator: Hafeez Noor creator: Min Sun creator: Aixia Ren creator: Yu Feng creator: Peng Qiao creator: Jingjing Zhang creator: Zhiqiang Gao uri: https://doi.org/10.7717/peerj.13727 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México link: https://peerj.com/articles/13235 last-modified: 2022-07-08 description: BackgroundThe gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities.MethodsWe employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses.ResultsAs hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6–V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6–V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features. creator: David Ramirez-Delgado creator: Francesco Cicala creator: Ricardo A. Gonzalez-Sanchez creator: Rosalia Avalos-Tellez creator: Elena Solana-Arellano creator: Alexei Licea-Navarro uri: https://doi.org/10.7717/peerj.13235 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ramirez-Delgado et al. title: Identification and subcellular localization analysis of membrane protein Ycf 1 in the microsporidian Nosema bombycis link: https://peerj.com/articles/13530 last-modified: 2022-07-08 description: Microsporidia are obligate intracellular parasites that can infect a wide range of vertebrates and invertebrates including humans and insects, such as silkworm and bees. The microsporidium Nosema bombycis can cause pebrine in Bombyx mori, which is the most destructive disease in the sericulture industry. Although membrane proteins are involved in a wide range of cellular functions and part of many important metabolic pathways, there are rare reports about the membrane proteins of microsporidia up to now. We screened a putative membrane protein Ycf 1 from the midgut transcriptome of the N. bombycis-infected silkworm. Gene cloning and bioinformatics analysis showed that the Ycf 1 gene contains a complete open reading frame (ORF) of 969 bp in length encoding a 322 amino acid polypeptide that has one signal peptide and one transmembrane domain. Indirect immunofluorescence results showed that Ycf 1 protein is distributed on the plasma membrane. Expression pattern analysis showed that the Ycf 1 gene expressed in all developmental stages of N. bombycis. Knockdown of the Ycf 1 gene by RNAi effectively inhibited the proliferation of N. bombycis. These results indicated that Ycf 1 is a membrane protein and plays an important role in the life cycle of N. bombycis. creator: Yong Chen creator: Erjun Wei creator: Ying Chen creator: Ping He creator: Runpeng Wang creator: Qiang Wang creator: Xudong Tang creator: Yiling Zhang creator: Feng Zhu creator: Zhongyuan Shen uri: https://doi.org/10.7717/peerj.13530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: Ecological restoration stimulates environmental outcomes but exacerbates water shortage in the Loess Plateau link: https://peerj.com/articles/13658 last-modified: 2022-07-08 description: Restoration is the natural and intervention-assisted set of processes designed to promote and facilitate the recovery of an ecosystem that has been degraded, damaged, or destroyed. However, it can also have an adverse effect on the environment. Thus, assessing an ecological restoration project’s impact is crucial to determining its success and optimum management strategies. We performed a meta-analysis concerning the environmental outcomes during the years 2000–2015 resulting from the “Grain for Green” Project (GFGP) implementation in the Loess Plateau (LP). Data were gathered from 40 peer-reviewed English-language articles chosen from a pool of 332 articles. The results showed that, on average, GFGP increased forest coverage by 35.7% (95% CI [24.15–47.52%]), and grassland by 1.05% (95% CI [0.8–1.28%]). At the same time, GFGP has a positive impact on soil carbon (C) sequestration, net ecosystem production (NEP), and net primary production (NPP), from the years 2000 to 2015 by an average of 36% (95% CI [28.96–43.18%]), 22.7% (95% CI [9.10–36.79%]), and 13.5% (95% CI [9.44–17.354%]), respectively. Soil erosion, sediment load, runoff coefficient, and water yield were reduced by 13.3% (95% CI [0.27–25.76%]), 21.5% (95% CI [1.50–39.99%]), 22.4% (95% CI [5.28–40.45%]) and 43.3% (95% CI [27.03–82.86%]), respectively, from the years 2000 to 2015. Our results indicate that water supply decreased with the increase of vegetation coverage. Therefore, to balance the needs for green space, GFGP policies and strategies should recover, enhance, and sustain more resilient ecosystems. creator: Mbezele Junior Yannick Ngaba creator: Yves Uwiragiye creator: Hongzhi Miao creator: Zhiqin Li creator: Paulo Pereira creator: Jianbin Zhou uri: https://doi.org/10.7717/peerj.13658 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ngaba et al. title: Evaluating pharmacists’ knowledge, attitude, and practices toward amiodarone cross-reactivity with iodine: a cross-sectional pilot study link: https://peerj.com/articles/13665 last-modified: 2022-07-08 description: IntroductionIodine is a vital mineral of the human body that acts by maintaining the health of the thyroid gland. Research has shown that iodine-rich food allergy (i.e., seafood allergy) is not caused by iodine itself; instead, it is caused by other proteins including tropomyosin and parvalbumin in shellfish and fish, respectively. Amiodarone is a commonly used antiarrhythmic agent containing a significant amount of iodine.ObjectiveThis study’s objective was to assess pharmacists’ knowledge, attitude, and practices toward the misconception of iodine allergy and the cross-reactivity with amiodarone.MethodsIn February 2020, a cross-sectional study was conducted by sending out an online survey to three pharmaceutical organizations (Saudi Pharmaceutical Society, Kuwait Pharmaceutical Association, and Oman Pharmaceutical Society). Additionally, an electronic questionnaire was administered to pharmacists attending the Dubai International Pharmaceuticals and Technologies Conference and Exhibition 2020 (DUPHAT). Chi-square or Fisher’s exact test, when appropriate, were used to compare categorical variables. The statistical analyses were carried out using SPSS software.ResultsData were collected from 66 respondents. However, only 61 (92.4%) were included in the final analysis following the exclusion of incomplete responses. The mean age of participants was 35 ± 8.48 years. The majority of participants did not have the Board of Pharmacy Specialties Certification (54.1%). Moreover, (41%) of participants licensed as pharmacists with more than 10 years of initial pharmacy licensure. Forty-three (70.5%) of participants had the misconception that iodine allergy should be considered before amiodarone administration, 20/32 (62.5%) of whom considered iodine allergy alone thought that premedication with corticosteroids and/or antihistamines is necessary. Concerning iodine allergy and amiodarone use, there was no significant difference in knowledge between the pharmacists who have board certification and those who did not.ConclusionPharmacists’ misconception concerning iodine allergy and cross-reactivity with amiodarone was evident. Implementation of educational programs targeting pharmacists is necessary to correct these misconceptions. creator: Nura Abdullah Alshehab creator: Munirah Abdullah Alhumaid creator: Mohammed Abdulrazaq Alabdulwahed creator: Abdulaziz Saleh Almulhim uri: https://doi.org/10.7717/peerj.13665 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Alshehab et al. title: Optimizing human coronavirus OC43 growth and titration link: https://peerj.com/articles/13721 last-modified: 2022-07-08 description: Coronaviruses have been at the forefront of the news for the last 2 years. Unfortunately, SARS-CoV-2, the etiologic agent for the COVID-19 pandemic, must be manipulated in biosecurity level 3 settings, which significantly limits research. Meanwhile, several less pathogenic human coronaviruses (HCoV) exist and can be studied in much more common biosafety level 2 laboratories. Among them, HCoV-OC43 is a good surrogate candidate for SARS-CoV-2 since both are phylogenetically related human Betacoronaviruses. However, one issue has been the lack of standardized means among laboratories to propagate and titer this less virulent coronavirus. The present study probes the optimal parameters to propagate HCoV-OC43. First, testing of five different cell lines (MRC-5, Huh7.5, Vero, HCT-8, HRT-18) indicated that the physiologically relevant MRC-5 human lung cell line produced among the highest viral titers. HRT-18 may however be an interesting alternative as they are quick growing cells that also led to higher viral titers and a better tropism for various HCoV-OC43 variants. We also probed the impact of serum and temperature during viral expansion and confirmed that the normal temperature of the upper respiratory track (33 °C) improves viral yields over the typical 37 °C used to grow many other viruses. Meanwhile, we did not notice any evidence that serum concentrations significantly affected the virus but interestingly noted that the virus grew quite efficiently in a serum-free media formulation. Meanwhile sonication of viral stocks somewhat improved viral titers. Four titration methods (plaque assays, TCID50-CPE, TCID50-IFA and TCID50–IPA) were also probed using two cell lines (VeroE6 and HRT-18). In our hands, plaque assays proved unreliable and quantification of the virus by scoring CPE positive wells was significantly less sensitive than antibody-based assays (IFA and IPA). While the latter methods were equally sensitive, we favor the TCID50-IPA method since simpler, faster and cheaper than the IFA protocol. Moreover, the HRT-18 cells appeared more sensitive to quantify the virus. Perhaps most importantly, these optimized protocols routinely led to high titer viral stocks in the order of 108 TCID50/ml magnitude, which should fulfill the requirements of most experimental settings. creator: Christopher Savoie creator: Roger Lippé uri: https://doi.org/10.7717/peerj.13721 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Savoie and Lippé title: Effects of school-based neuromuscular training on fundamental movement skills and physical fitness in children: a systematic review link: https://peerj.com/articles/13726 last-modified: 2022-07-08 description: ObjectivesThe primary purpose of this review was to clarify the effects of school-based integrated neuromuscular training (INT) on fundamental movement skills and physical fitness in children. The secondary purpose was to examine whether school-based INT intervention is superior to physical education (PE) intervention in enhancing motor skills and fitness.MethodsA systematic literature search was performed in four electronic databases: PubMed, Web of Science, MEDLINE (EBSCOhost), and Cochrane Central Register of Controlled Trials. The last search was performed on December 21, 2021, and was limited to the English language, human species, and peer reviewed journals. Randomized controlled trials and cluster randomized controlled trials that examine the effects of school-based INT on motor skills and/or fitness in healthy children who were aged up to 14 years old were included. Moreover, studies included in this study should compare school-based INT-induced adaptions with those generated by PE interventions. Studies that involve athletic children and additional exercise training were excluded. The Physiotherapy Evidence Database (PEDro) scale was used to assess the quality of the study.ResultsOf 1,026 studies identified, seven original trials that meet the inclusion criteria were included in this review. Based on the PEDro scale, the PEDro score of seven studies was between six and eight points with a mean score of 5.29. Among the seven studies included in this study, four studies assessed physical fitness including muscular fitness (n = 4), speed (n = 3), endurance (n = 2), and flexibility (n = 2). Three studies examined the effects of INT on postural control and three studies explored its effects on motor skills. Concerning movement competence, significant and greater improvements in postural control and fundamental motor skills were observed following school-based INT interventions compared to PE intervention in two and three studies, respectively. Regarding physical fitness, neuromuscular training significantly increased muscular fitness, speed, endurance, flexibility in three, two, one, and one studies, respectively. However, only greater improvements in muscle fitness were observed in school-based INT group compared to PE group. The main limitations of this review were the lack of descriptions of training intensity and volume and the low methodological quality of the included studies.ConclusionThis review provides evidence that school-based neuromuscular training programs are superior to PE lessons in improving postural control, fundamental motor skills and muscular strength. Therefore, INT could be incorporated into traditional physical education classes in school. Trial registration number: CRD42022297349. creator: Junlei Lin creator: Ruofei Zhang creator: Jie Shen creator: Aiguo Zhou uri: https://doi.org/10.7717/peerj.13726 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lin et al. title: The osteology and affinities of Eotyrannus lengi, a tyrannosauroid theropod from the Wealden Supergroup of southern England link: https://peerj.com/articles/12727 last-modified: 2022-07-07 description: Eotyrannus lengiHutt et al., 2001 from the Lower Cretaceous Wessex Formation (part of the Wealden Supergroup) of the Isle of Wight, southern England, is described in detail, compared with other theropods, and evaluated in a new phylogenetic analysis. Eotyrannus is represented by a single individual that would have been c. 4.5 m long; it preserves the anterior part of the skull, a partial forelimb and pectoral girdle, various cervical, dorsal and caudal vertebrae, rib fragments, part of the ilium, and hindlimb elements excluding the femur. Lack of fusion with regard to both neurocentral and sacral sutures indicates subadult status. Eotyrannus possesses thickened, fused, pneumatic nasals with deep lateral recesses, elongate, tridactyl forelimbs and a tyrannosaurid-like scapulocoracoid. The short preantorbital ramus of the maxilla and nasals that are approximately seven times longer than they are wide show that Eotyrannus was not longirostrine. A posterodorsally inclined ridge on the ilium’s lateral surface fails to reach the dorsal margin: a configuration seen elsewhere in Juratyrant. Eotyrannus is not arctometatarsalian. Autapomorphies include the presence of curving furrows on the dentary, a block-like humeral entepicondyle, and a distoproximally aligned channel close to the distolateral border of the tibia. Within Tyrannosauroidea, E. lengi is phylogenetically intermediate between Proceratosauridae and Yutyrannus and the clade that includes Xiongguanlong, Megaraptora, Dryptosaurus and Tyrannosauridae. We do not find support for a close affinity between Eotyrannus and Juratyrant. Our analysis supports the inclusion of Megaraptora within Tyrannosauroidea and thus increases Cretaceous tyrannosauroid diversity and disparity. A proposal that Eotyrannus might belong within Megaraptora, however, is based on character states not present in the taxon. Several theropods from the Wessex Formation are based on material that overlaps with the E. lengi holotype but none can be shown to be synonymous with it. creator: Darren Naish creator: Andrea Cau uri: https://doi.org/10.7717/peerj.12727 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Naish and Cau title: The expanding roles of neuronal nitric oxide synthase (NOS1) link: https://peerj.com/articles/13651 last-modified: 2022-07-07 description: The nitric oxide synthases (NOS; EC 1.14.13.39) use L-arginine as a substrate to produce nitric oxide (NO) as a by-product in the tissue microenvironment. NOS1 represents the predominant NO-producing enzyme highly enriched in the brain and known to mediate multiple functions, ranging from learning and memory development to maintaining synaptic plasticity and neuronal development, Alzheimer’s disease (AD), psychiatric disorders and behavioral deficits. However, accumulating evidence indicate both canonical and non-canonical roles of NOS1-derived NO in several other tissues and chronic diseases. A better understanding of NOS1-derived NO signaling, and identification and characterization of NO-metabolites in non-neuronal tissues could become useful in diagnosis and prognosis of diseases associated with NOS1 expression. Continued investigation on the roles of NOS1, therefore, will synthesize new knowledge and aid in the discovery of small molecules which could be used to titrate the activities of NOS1-derived NO signaling and NO-metabolites. Here, we address the significance of NOS1 and its byproduct NO in modifying pathophysiological events, which could be beneficial in understanding both the disease mechanisms and therapeutics. creator: Kundan Solanki creator: Sajjan Rajpoot creator: Evgeny E. Bezsonov creator: Alexander N. Orekhov creator: Rohit Saluja creator: Anita Wary creator: Cassondra Axen creator: Kishore Wary creator: Mirza S. Baig uri: https://doi.org/10.7717/peerj.13651 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Solanki et al. title: Quantification of water requirement of some major crops under semi-arid climate in Turkey link: https://peerj.com/articles/13696 last-modified: 2022-07-07 description: The Southeastern Anatolian Region of Turkey is located in semi arid climate zone and therefore requires an efficient water use. Well-planned irrigation with optimum water required by the crops is essential for the limited water resources of the region. The numerical tool CROPWAT of the Food and Agriculture Organization (FAO) was used for modelling efficient irrigation of local crops pistachio, olive, almond and grape without reducing the yield. Local climatic, soil, plant and rainfall information were used as inputs to CROPWAT model to predict the reference evapotranspiration (ETo) values. The crop water requirement (CWR) for pistachio, olive, almond, and grape was calculated as 1,294.0 mm, 659.4 mm, 790.2 mm, and 752.0 mm, respectively, The number of irrigation needed during growth stages was determined as eight for pistachio, three for olive, six for almond and five for grape. creator: Yusuf Aydın uri: https://doi.org/10.7717/peerj.13696 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Aydın title: Wikidata and the bibliography of life link: https://peerj.com/articles/13712 last-modified: 2022-07-07 description: Biological taxonomy rests on a long tail of publications spanning nearly three centuries. Not only is this literature vital to resolving disputes about taxonomy and nomenclature, for many species it represents a key source—indeed sometimes the only source—of information about that species. Unlike other disciplines such as biomedicine, the taxonomic community lacks a centralised, curated literature database (the “bibliography of life”). This article argues that Wikidata can be that database as it has flexible and sophisticated models of bibliographic information, and an active community of people and programs (“bots”) adding, editing, and curating that information. creator: Roderic D. M. Page uri: https://doi.org/10.7717/peerj.13712 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Page title: Characterization of phenylalanine ammonia-lyase genes facilitating flavonoid biosynthesis from two species of medicinal plant Anoectochilus link: https://peerj.com/articles/13614 last-modified: 2022-07-06 description: BackgroundAnoectochilus roxburghii and Anoectochilus formosanus, belong to the Anoectochilus genus, have been used for Chinese herbal drugs as well as health food. Phenylalanine ammonia-lyase (PAL), the key enzyme in primary metabolism and phenylpropanoid metabolism, produces secondary metabolites (flavonoids) in plants, which are beneficial for the biosynthesis of phenylpropanoid metabolites.MethodsThe PAL genes were cloned from A. formosanus and A. roxburghii according to our previous transcriptomic analysis. The PALs were introduced into pCAMBIA2300-35S-PAL-eGFP to generate 35S-PAL-eGFP. The constructs were further used for subcellular localization and transgenic Arabidopsis. The expression of AfPAL and ArPAL under precursor substance (L-Phe), NaCl, UV, and red-light were analyzed by real-time quantitative PCR (RT-qPCR).ResultsAfPAL and ArPAL , encoding 2,148 base pairs, were cloned from A. formosanus and A. roxburghii. The subcellular localization showed that the ArPAL and AfPAL were both localized in the nucleus with GPF. Quantitative RT-PCR analysis indicated that the ArPAL and AfPAL genes function in the phenylalanine pathway as well as response to induced conditions. Overexpression of the AfPAL and ArPAL could increase flavonoids and anthocyanin content in the transgenic Arabidopsis.DiscussionThe results suggest that AfPAL and ArPAL play a crucial role in the flavonoid biosynthesis in Anoectochilus. Also, our study provides new insights into the enrichment of secondary metabolites of traditional Chinese medicines A. formosanus and A. roxburghii, which can improve their medicinal active ingredients and be used for drug discovery in plants. creator: Lin Yang creator: Wan-Chen Li creator: Feng-ling Fu creator: Jingtao Qu creator: Fuai Sun creator: Haoqiang Yu creator: Juncheng Zhang uri: https://doi.org/10.7717/peerj.13614 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: Marker-assisted pyramiding of γ-tocopherol methyltransferase and glutamate formiminotransferase genes for development of biofortified sweet corn hybrids link: https://peerj.com/articles/13629 last-modified: 2022-07-06 description: Micronutrients, including vitamins, minerals, and other bioactive compounds, have tremendous impacts on human health. Much progress has been made in improving the micronutrient content of inbred lines in various crops through biofortified breeding. However, biofortified breeding still falls short for the rapid generation of high-yielding hybrids rich in multiple micronutrients. Here, we bred multi-biofortified sweet corn hybrids efficiently through marker-assisted selection. Screening by molecular markers for vitamin E and folic acid, we obtained 15 inbred lines carrying favorable alleles (six for vitamin E, nine for folic acid, and three for both). Multiple biofortified corn hybrids were developed through crossing and genetic diversity analysis. creator: Guihua Lv creator: Xiaolong Chen creator: Duo Ying creator: Jiansheng Li creator: Yinghu Fan creator: Bin Wang creator: Ruiqiu Fang uri: https://doi.org/10.7717/peerj.13629 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lv et al. title: Evaluation of potential anti-metastatic and antioxidative abilities of natural peptides derived from Tecoma stans (L.) Juss. ex Kunth in A549 cells link: https://peerj.com/articles/13693 last-modified: 2022-07-06 description: BackgroundTecoma stans (L.) Juss. ex Kunth is a well-known medicinal plant found in tropical and subtropical regions. It contains a broad range of bioactive compounds that exhibit many biological effects, including antidiabetic, antibacterial, and antioxidative activities. However, the effect of natural peptides from T. stans against cancer progression and free radical production is unknown. This study aims to evaluate the cytotoxic, anti-metastatic, and antioxidative activities of natural peptides from T. stans on A549 cells.MethodsThe natural peptides were extracted from the flower of T. stans using the pressurized hot water extraction (PHWE) method, followed by size exclusion chromatography and solid-phase extraction-C18. The cytotoxic and anti-metastatic effects of natural peptides were evaluated using MTT and transwell chamber assays, respectively. The free radical scavenging activity of natural peptides was determined using ABTS, DPPH, and FRAP assays. The cells were pretreated with the IC50 dosage of natural peptides and stimulated with LPS before analyzing intracellular reactive oxygen species (ROS) and proteomics.ResultsNatural peptides induced cell toxicity at a concentration of less than 1 ng/ml and markedly reduced cell motility of A549 cells. The cells had a migration rate of less than 10% and lost their invasion ability in the treatment condition. In addition, natural peptides showed free radical scavenging activity similar to standard antioxidants and significantly decreased intracellular ROS in the LPS-induced cells. Proteomic analysis revealed 1,604 differentially expressed proteins. The self-organizing tree algorithm (SOTA) clustered the protein abundances into eleven groups. The volcano plot revealed that the cancer-promoting proteins (NCBP2, AMD, MER34, ENC1, and COA4) were down-regulated, while the secretory glycoprotein (A1BG) and ROS-reducing protein (ASB6) were up-regulated in the treatment group.ConclusionThe anti-proliferative and anti-metastatic activities of natural peptides may be attributed to the suppression of several cancer-promoting proteins. In contrast, their antioxidative activity may result from the up-regulation of ROS-reducing protein. This finding suggests that natural peptides from T. stans are viable for being the new potential anti-cancer and antioxidative agents. creator: Sucheewin Krobthong creator: Yodying Yingchutrakul creator: Wattanapong Sittisaree creator: Tatpong Tulyananda creator: Pawitrabhorn Samutrtai creator: Kiattawee Choowongkomon creator: Udom Lao-On uri: https://doi.org/10.7717/peerj.13693 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Krobthong et al. title: Ferroptotic cardiomyocyte-derived exosomes promote cardiac macrophage M1 polarization during myocardial infarction link: https://peerj.com/articles/13717 last-modified: 2022-07-06 description: Ferroptosis is a mode of cell death that occurs in myocardial infarction (MI). Signals emanating from apoptotic cells are able to induce macrophage polarization through exosome-loading cargos, which plays a vital role in the process of disease. However, whether ferroptotic cardiomyocytes derived exosome (MI-Exo) during MI act on macrophage polarization and its mechanism remain unclear. In this study, a MI mouse model was established, and cardiac function evaluation and pathological staining were performed. The effect of MI-Exo on polarization of RAW264.7 cells was assessed by the expression of IL-10 and NOS2. Ferroptosis inhibitor of ferrostatin-1 was used to verify whether MI-Exo function was dependents on ferroptosis. Cardiac function and myocardial histomorphology were markedly impaired and massive immune cell infiltration in MI mice, compared with the sham group. The significantly increased MDA content and Fe2+ accumulation in the heart tissue of MI mice suggested cardiomyocyte ferroptosis. Compared with the sham group, the expression of M1 marker NOS2 was significantly up-regulated and M2 marker IL-10 was significantly down-regulated in the heart tissue of MI mice. Exosome-derived from MI HL-1 cell-treated with ferrostatin-1 (Fer-1-Exo) and MI-Exo were internalized by RAW 264.7 cells. Compared with culture alone, co-cultured with MI-Exo significantly promoted NOS2 expression and suppressed IL-10 expression, and decreased proportion of Arginase-1-labeled M2 macrophages, also inhibited phagocytosis of RAW 264.7 cells. Wnt1 and β-cantenin expression also elevated after treated with MI-Exo. However, co-cultured with Fer-1-Exo significantly reversed the above changes on RAW 264.7 cells induced by MI-Exo. In conclusion, ferroptotic cardiomyocytes-derived exosome crosstalk macrophage to induce M1 polarization via Wnt/β-cantenin pathway, resulting in pathological progress in MI. This understanding provides novel therapeutic target for MI. creator: Shengjia Sun creator: Yurong Wu creator: Alimujiang Maimaitijiang creator: Qingyu Huang creator: Qiying Chen uri: https://doi.org/10.7717/peerj.13717 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sun et al. title: Gene ssa-miR-301a-3p improves rainbow trout (Oncorhynchus mykiss) resistance to heat stress by targeting hsp90b2 link: https://peerj.com/articles/13476 last-modified: 2022-07-05 description: Rainbow trout (Oncorhynchus mykiss) is a cold-water fish that is commonly harmed by high temperatures. MicroRNAs (miRNAs) are being investigated intensively because they act as essential metabolic regulators and have a role in the heat stress response. Although there have been numerous studies on rainbow trout heat stress, research on miRNA implicated in rainbow trout heat stress is quite restricted. Rainbow trout were sampled at 18 and 24 °C, respectively, to examine the mechanism of miRNA under heat stress, and we identified a heat stress-induced miRNA, ssa-miR-301a-3p, for further investigation based on our bioinformatics analysis of rainbow trout small RNA sequencing data. Bioinformatics research suggested that hsp90b2 is a probable target gene for ssa-miR-301a-3p. QRT-PCR was used to confirm the expression levels of ssa-miR-301a-3p and hsp90b2. Meanwhile, the dual-luciferase reporter assay was employed to validate the ssa-miR-301a-3p-hsp90b2 targeted connection. The results indicated that at 24 °C, the relative expression of ssa-miR-301a-3p was considerably lower than at 18 °C. On the other hand, hsp90b2 expression, followed the opposite pattern. The binding of ssa-miR-301a-3p to the 3′-UTR of hsp90b2 resulted in a substantial decrease in luciferase activity. The findings showed that ssa-miR-301a-3p was implicated in heat stress, and our findings provide fresh insights into the processes of miRNA in response to heat stress in rainbow trout. creator: Zhe Liu creator: Fang Ma creator: Yujun Kang creator: Xiaoxia Liu uri: https://doi.org/10.7717/peerj.13476 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al. title: G6PD and HBB polymorphisms in the Senegalese population: prevalence, correlation with clinical malaria link: https://peerj.com/articles/13487 last-modified: 2022-07-05 description: BackgroundHost genetic factors contribute to the variability of malaria phenotypes and can allow a better understanding of mechanisms involved in susceptibility and/or resistance to Plasmodium falciparum infection outcomes. Several genetic polymorphisms were reported to be prevalent among populations living in tropical malaria-endemic regions and induce protection against malaria. The present study aims to investigate the prevalence of HBB (chr11) and G6PD (chrX) deficiencies polymorphisms among Senegalese populations and their associations with the risk for severe Plasmodium falciparum malaria occurrence.MethodsWe performed a retrospective study with 437 samples, 323 patients recruited in hospitals located in three different endemic areas where malaria episodes were confirmed and 114 free malaria controls. The patients enrolled were classified into two groups: severe malaria (SM) (153 patients) and uncomplicated malaria (UM) (170 patients). PCR and DNA sequencing assessed host genetic polymorphisms in HBB and G6PD. Using a multivariate regression and additive model, estimates of the impact of human HBB and G6PD polymorphisms on malaria incidence were performed.ResultsSix frequent SNPs with minor allele frequencies (MAF) > 3% were detected in the HBB gene (rs7946748, rs7480526, rs10768683, rs35209591, HbS (rs334) and rs713040) and two in the G6PD gene (rs762515 and rs1050828 (G6PD-202 G > A). Analysis of selected HbS polymorphism showed significant association with protective effect against severe malaria with a significant p-value = 0.033 (OR 0.38, 95% CI [0.16–0.91]) for SM vs. UM comparison. Surprisingly, our study did not identify the protective effect of variant HbC polymorphism against severe malaria. Finally, we found some of the polymorphisms, like HbS (rs334), are associated with age and biological parameters like eosinophils, basophils, lymphocytes etc.ConclusionOur data report HBB and G6PD polymorphisms in the Senegalese population and their correlation with severe/mild malaria and outcome. The G6PD and HBB deficiencies are widespread in West Africa endemic malaria regions such as The Gambia, Mali, and Burkina Faso. The study shows the critical role of genetic factors in malaria outcomes. Indeed, genetic markers could be good tools for malaria endemicity prognosis. creator: Fatou Thiam creator: Gora Diop creator: Cedric Coulonges creator: Céline Derbois creator: Babacar Mbengue creator: Alassane Thiam creator: Cheikh Momar Nguer creator: Jean Francois Zagury creator: Jean-Francois Deleuze creator: Alioune Dieye uri: https://doi.org/10.7717/peerj.13487 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Thiam et al. title: Characteristics and risk factors of infections in patients with HBV-related acute-on-chronic liver failure: a retrospective study link: https://peerj.com/articles/13519 last-modified: 2022-07-05 description: BackgroundAcute-on-chronic liver failure (ACLF) is a syndrome characterized by acute decompensation, organ failures, and high short-term mortality whose main cause in China is the Hepatitis B virus (HBV). Moreover, one of the most important causes of morbidity and mortality in HBV-ACLF patients is bacterial infection. Therefore, we investigate the clinical features, risk factors, prophylaxis and management of infections in patients with HBV-ACLF.MethodsWe conducted a retrospective analysis of 539 patients with HBV-ACLF in Wuhan Tongji Hospital from October 2015 to May 2018. Differences among groups were compared with Student’s t test, Mann–Whitney U test, χ2 test, or Fisher exact test as appropriate. Univariate and Multivariate logistic regression analysis was used for modeling the relationship between infection and clinical characteristics of HBV-ACLF.ResultsIn total 58.81% (317/539) of patients with HBV-ACLF became complicated with infections, and the most common types were spontaneous bacterial peritonitis, urinary tract infection and pulmonary infection. Additionally, 32.18% (102/317) of patients suffered multi-organ infections, and 95.73% (516/539) of patients received anti-infective therapy. We detected a total of 202 isolates in all infected patients, and Escherichia coli (36.14%, 73/202) was the most common causative organism. Moreover, antibiotic susceptibility test patterns showed that 52.97% (107/202) of pathogens were MDR bacteria and 4.95% (10/202) were XDR bacteria. Univariate analysis indicated that patients with infection had a higher proportion of females, taking alcohol, diuretics, hepatic encephalopathy (HE), hepatorenal syndrome (HS), cirrhosis, a long-time in bed and mechanical ventilation, lower prothrombin activity (PTA), alanine aminotransferase (ALT), albumin, total cholesterol (TC), estimated glomerular filtration rate (eGFR), hemoglobin (Hb) and platelet (PLT) and higher age, model for end-stage liver disease (MELD) scores and ACLF grade than patients without infection. Multivariate logistic regression analysis showed that taking alcohol, HE, HS, cirrhosis, albumin and eGFR were risk factors for the development of infection.ConclusionsBacterial infections were very common in patients with HBV-ACLF. Taking alcohol, the occurrence of complications (HE, HS and cirrhosis), hypoalbuminemia and poor renal function often predict the higher prevalence of infections in patients with HBV-ACLF. It is important to focus on exploring the early recognition of infection and early intervention of those risk factors in patients with HBV-ACLF. creator: Qian Zhang creator: Baoxian Shi creator: Liang Wu uri: https://doi.org/10.7717/peerj.13519 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Soil mineralized carbon drives more carbon stock in coniferous-broadleaf mixed plantations compared to pure plantations link: https://peerj.com/articles/13542 last-modified: 2022-07-05 description: Forest soil carbon (C) sequestration has an important effect on global C dynamics and is regulated by various environmental factors. Mixed and pure plantations are common afforestation choices in north China, but how forest type and environmental factors interact to affect soil C stock remains unclear. We hypothesize that forest type changes soil physicochemical properties and surface biological factors, and further contributes to soil active C components, which together affect soil C sequestration capacity and C dynamic processes. Three 46-year-old 25 m × 25 m pure Pinus tabulaeformis forests (PF) and three 47-year-old 25 m × 25 m mixed coniferous-broadleaf (Pinus tabulaeformis-Quercus liaotungensis) forests (MF) were selected as the two treatments and sampled in August 2016. In 2017, soil temperature (ST) at 10 cm were measured every 30 min for the entire vegetation season. Across 0–50 cm (five soil layers, 10 cm per layer), we also measured C components and environmental factors which may affect soil C sequestration, including soil organic carbon (SOC), soil total nitrogen (STN), dissolved organic carbon (DOC), microbial biomass carbon (MBC), soil moisture (SM) and soil pH. We then incubated samples for 56 days at 25 °C to monitor the C loss through CO2 release, characterized as cumulative mineralization carbon (CMC) and mineralized carbon (MC). Our results indicate that ST, pH, SM and litter thickness were affected by forest type. Average SOC stock in MF was 20% higher than in PF (MF: 11.29 kg m−2; PF: 13.52 kg m−2). Higher CMC under PF caused more soil C lost, and CMC increased 14.5% in PF (4.67 g kg−1 soil) compared to MF (4.04 g kg−1 soil) plots over the two-month incubation period. SOC stock was significantly positively correlated with SM (p < 0.001, R2 = 0.43), DOC (p < 0.001, R2 = 0.47) and CMC (p < 0.001, R2 = 0.33), and significantly negatively correlated with pH (p < 0.001, R2 = −0.37) and MC (p < 0.001, R2 = −0.32). SOC stock and litter thickness may have contributed to more DOC leaching in MF, which may also provide more C source for microbial decomposition. Conversely, lower SM and pH in MF may inhibit microbial activity, which ultimately makes higher MC and lower CMC under MF and promotes C accumulation. Soil mineralized C drives more C stock in coniferous-broadleaf mixed plantations compared to pure plantations, and CMC and MC should be considered when soil C balance is assessed. creator: Zhenzhen Hao creator: Zhanjun Quan creator: Yu Han creator: Chen Lv creator: Xiang Zhao creator: Wenjie Jing creator: Linghui Zhu creator: Junyong Ma uri: https://doi.org/10.7717/peerj.13542 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hao et al. title: A comprehensive drought monitoring method integrating multi-source data link: https://peerj.com/articles/13560 last-modified: 2022-07-05 description: Droughts are the most expensive natural disasters on the planet. As a result of climate change and human activities, the incidence and impact of drought have grown in China. Timely and effective monitoring of drought is crucial for water resource management, drought mitigation, and national food security. In this study, we constructed a comprehensive drought index (YCDI) suitable for the Yellow River Basin using principal component analysis and the entropy weight-AHP method, which integrated a standardized precipitation evapotranspiration index (SPEI), self-calibrating Palmer drought severity index (scPDSI), vegetation condition index (VCI), and standardized water storage index (SWSI). SWSI is calculated by the terrestrial water storage anomaly (TWSA), which can more comprehensively reflect the impact of surface water resources on drought (as compared with soil moisture-based indexes). The study results showed that: (1) compared with single drought index, YCDI has stronger ability to monitor drought process. In terms of time scale and drought degree, the monitoring results based on YCDI were similar with data presented in the China Flood and Drought Bulletin and Meteorological Drought Yearbook, reaching ~87% and ~69%, respectively. The correlation between drought intensity and crop harvest area was 0.56. (2) By the combined analysis of the Mann-Kendall test and Moving T test, it was found that the abrupt change of YCDI index at the time of 2009, mainly due to the precipitation in 2009 reached the lowest value in the past 30 years in northern China and extreme high temperature weather. (3) The YCDI of Henan and Shandong provinces in the middle and lower reaches of the basin decreased more significantly, with the maximum value reaching 0.097/yr, while the index in the upper reaches showed an increasing trend with the maximum rate of 0.096/yr. (4) The frequency of mild drought, moderate drought, severe drought and extreme drought in the Yellow River basin during the study period was 15.84%, 12.52%, 4.03% and 0.97%, respectively. Among them, the highest frequency of droughts occurred in Ningxia, Inner Mongolia and central Shaanxi provinces. Drought causation in the Yellow River basin is more influenced by human activities than climate change in the middle and lower reaches, while climate change is the main factor in the upper reaches. Overall, YCDI is a reliable indicator for monitoring the spatial and temporal evolution of drought in the Yellow River basin, and it can be used for monitoring soil moisture changes and vegetation dynamics, which can provide scientific guidance for regional drought governance. creator: Xiaoliang Shi creator: Hao Ding creator: Mengyue Wu creator: Mengqi Shi creator: Fei Chen creator: Yi Li creator: Yuanqi Yang uri: https://doi.org/10.7717/peerj.13560 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Shi et al. title: Telomere-to-telomere genome assembly of Phaeodactylum tricornutum link: https://peerj.com/articles/13607 last-modified: 2022-07-05 description: Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomere genome for Phaeodactylum tricornutum. We developed a graph-based approach to extract all unique telomeres, and used this information to manually correct assembly errors. In total, we found 25 nuclear chromosomes that comprise all previously assembled fragments, in addition to the chloroplast and mitochondrial genomes. We found that chromosome 19 has filtered long-read coverage and a quality estimate that suggests significantly less haplotype sequence variation than the other chromosomes. This work improves upon the previous genome assembly and provides new opportunities for genetic engineering of this species, including creating designer synthetic chromosomes. creator: Daniel J. Giguere creator: Alexander T. Bahcheli creator: Samuel S. Slattery creator: Rushali R. Patel creator: Tyler S. Browne creator: Martin Flatley creator: Bogumil J. Karas creator: David R. Edgell creator: Gregory B. Gloor uri: https://doi.org/10.7717/peerj.13607 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Giguere et al. title: Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity link: https://peerj.com/articles/13626 last-modified: 2022-07-05 description: BackgroundInterleukin-18 (IL-18) is prone to form multimers resulting in inactive aggregates, making this cytokine unstable for clinical use. Therefore, mutations have been introduced into recombinant IL-18 to overcome this issue.MethodsTo prevent the formation of disulfide bonds between the IL-18 molecules, multiple mutations targeting surface cysteines (C38, C68, C76, and C127) were introduced into our previously modified human IL-18 double mutant E6K+T63A (IL-18 DM) by direct gene synthesis. The open reading frames of IL-18 wild-type (WT), IL-18 DM, and IL-18 multiple mutant E6K+T63A+C38S+C68S+C76S+C127S (IL-18 DM1234) were inserted in the pET28a expression vector and transformed into Escherichia coli Rosetta2 (DE3) pLysS cells for protein production. The inclusion bodies of WT and mutated IL-18 were extracted by sonication and refolded by stepwise dialysis using 8 M urea as the starting concentration. The refolded IL-18 proteins were tested for aggregation using the ProteoStat protein aggregation assay. Their activity was also investigated by treating NK-92MI cells with each IL-18 at concentrations of 75, 150, and 300 ng/ml with 0.5 ng/ml of human IL-12 and interferon-gamma (IFN-γ) levels in the supernatant were evaluated using ELISA. The structure of modified IL-18 was visualized using molecular dynamics (MD) simulations.ResultsIL-18 DM1234 exhibited the lowest aggregation signal, approximately 1.79- and 1.63-fold less than that of the WT and IL-18 DM proteins. Additionally, the IFN-γ inducing activity of IL-18 DM1234 was about 10 and 2.8 times higher than that of the WT and IL-18 DM, respectively. MD simulations revealed that binding site I of IL-18 DM1234 was altered mainly due to surface cysteine replacement with serine (C-to-S substitution). This is the first report showing that C-to-S substitutions in IL-18 improved its activity and stability, suggesting the use of this modified IL-18 for medical purposes in the future. creator: Jirakrit Saetang creator: Niran Roongsawang creator: Surasak Sangkhathat creator: Supayang Piyawan Voravuthikunchai creator: Natnaree Sangkaew creator: Napat Prompat creator: Teerapol Srichana creator: Varomyalin Tipmanee uri: https://doi.org/10.7717/peerj.13626 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Saetang et al. title: Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2 link: https://peerj.com/articles/13680 last-modified: 2022-07-05 description: BackgroundThe COVID-19 pandemic is still a global public health issue. Omicron, a SARS-CoV-2 B.1.1.529 variant, has raised concerns about transmission and vaccine effectiveness. Omicron currently has the greatest number of variantions.MethodsTo gain a better understanding of the significance of these variations and the dynamics of the interaction between the Omicron spike (S) protein and its human host factor angiotensin-converting enzyme 2 (ACE2), triplicate 500 ns molecular dynamics simulations were run using the structure of the S protein’s receptor-binding domain (RBD) in complex with ACE2. The interaction and binding energy, determined using the molecular mechanics—generalized Born surface area approach, were compared to the original SARS-CoV-2 and the B.1.617 variant.ResultsThough mutations K417N and G496S in the S protein RBD disrupt interactions found in the original SARS-CoV-2 complex, mutations Q493R and N501Y introduce interactions not found in the original complex. Interaction at a key viral hotspot and hydrophobic contacts at ACE2’s N-terminus were preserved, but intermolecular hydrogen bonds and polar contacts in the S-ACE2 interface were lower than in the original SARS-CoV-2 interface. creator: Priya Antony creator: Amie Jobe creator: Ranjit Vijayan uri: https://doi.org/10.7717/peerj.13680 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Antony et al. title: The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents link: https://peerj.com/articles/13687 last-modified: 2022-07-05 description: BackgroundExtensive literature revealed the relations of depression with behavioral inhibition system (BIS) and behavioral activation system (BAS) as vulnerability and with resilience separately. Besides, the concept of resilience is still broad and ambiguous. Thus, this study aimed to reveal the mediation of two aspects of resilience: trait and process, in the relations of BIS and BAS to depression among adolescents.MethodsThe data set used in this study was a cross-sectional survey among 965 adolescents. The obtained data from the self-reported questionnaires used in this study were as below: Depression Serf-Rating Scale for Children (DSRS-C), Behavioral Inhibition and Behavioral Activation System Scale (BIS/BASS), and Bidimensional Resilience Scale (BRS). Structural equation modeling (SEM) was conducted to verify the hypothesized relations among BIS/BAS, trait and behavior resilience, and depressive symptoms.ResultsThe obtained indices of fit from SEM were good or sufficient (χ2 = 562.911, df = 96, p < 0.001; CFI = 0.925; NFI = 0.913; RMSEA = 0.073, 90% CI [0.067, 0.079]; SRMR = 0.066). And the modeling showed that both BIS/BAS directly and indirectly influenced to depression. The indirect effects of BIS/BAS were mediated only trait resilience except the indirect effect of BIS via behavioral resilience.DiscussionOur results suggested that trait resilience played a significant mediation role in the relationships between BIS/BAS and depression. Trait but not process resilience could be considered suitable as an intervention target in line with decreasing depression. creator: Akihiro Masuyama creator: Takahiro Kubo creator: Hiroki Shinkawa creator: Daichi Sugawara uri: https://doi.org/10.7717/peerj.13687 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Masuyama et al. title: Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus link: https://peerj.com/articles/13689 last-modified: 2022-07-05 description: BackgroundCyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages.MethodsA combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated.ResultsThe results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus.ConclusionsLeaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan). creator: Zhaokui Du creator: Weida Lin creator: Jinxing Zhu creator: Junmin Li uri: https://doi.org/10.7717/peerj.13689 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Du et al. title: Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area link: https://peerj.com/articles/13690 last-modified: 2022-07-05 description: We evaluated the role of gene flow and wild-crop introgression on the structure and genetic diversity of Lima bean (Phaseolus lunatus) in the Yucatan Peninsula, an important Mesoamerican diversity area for this crop, using a genotyping-by-sequencing approach (15,168 SNP markers) and two scales. At the local scale, STRUCTURE and NGSEP analyses showed predominantly crop-to-wild introgression, but also evidence of a bidirectional gene flow in the two wild-weedy-crop complexes studied (Itzinté and Dzitnup). The ABBA-BABA tests showed a higher introgression in Itzinté (the older complex) than in Dzitnup (the younger one); at the allelic level, the wild-crop introgression in Itzinté was similar in both directions, in Dzitnup it was higher from crop-to-wild; and at the chromosomal level, introgression in Itzinté was from wild-to-crop, whereas in Dzitnup it occured in the opposite direction. Also, we found HE values slightly higher in the domesticated accessions than in the wild ones, in both complexes (Itzinté: wild = 0.31, domesticated = 0.34; Dzinup: wild = 0.27, domesticated = 0.36), but %P and π estimators were higher in the wild accessions than in the domesticated ones. At a regional scale, STRUCTURE and MIGRATE showed a low gene flow, predominantly from crop-to-wild; and STRUCTURE, Neighbor-Joining and PCoA analyses indicated the existence of two wild groups and one domesticated group, with a marked genetic structure based in the existence of domesticated MI and wild MII gene pools. Also, at the regional scale, we found a higher genetic diversity in the wild accessions than in the domesticated ones, in all estimators used (e.g., HE = 0.27 and HE = 0.17, respectively). Our results indicate that gene flow and introgression are playing an important role at the local scale, but its consequences on the structure and genetic diversity of the Lima bean are not clearly reflected at the regional scale, where diversity patterns between wild and domesticated populations could be reflecting historical events. creator: Mauricio Heredia-Pech creator: Mariana Chávez-Pesqueira creator: Matilde M. Ortiz-García creator: Rubén Humberto Andueza-Noh creator: María Isabel Chacón-Sánchez creator: Jaime Martínez-Castillo uri: https://doi.org/10.7717/peerj.13690 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Heredia-Pech et al. title: Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis) link: https://peerj.com/articles/13491 last-modified: 2022-07-04 description: BackgroundWRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses.ResultsA total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT–PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways.ConclusionsWe conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding. creator: Zhenfan Yu creator: Dongdong Zhang creator: Bin Zeng creator: Xingyue Liu creator: Jiahui Yang creator: Wenwen Gao creator: Xintong Ma uri: https://doi.org/10.7717/peerj.13491 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yu et al. title: Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations link: https://peerj.com/articles/13575 last-modified: 2022-07-04 description: Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula populations differ between the northeastern Atlantic Ocean and the Mediterranean Sea based on biological features and genetic analysis. In this study, we sample more than 3,000 teeth from 56 S. canicula specimens caught incidentally off Roscoff and Banyuls-sur-Mer. We investigate population differences based on tooth shape and form by using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils. creator: Fidji Berio creator: Yann Bayle creator: Daniel Baum creator: Nicolas Goudemand creator: Mélanie Debiais-Thibaud uri: https://doi.org/10.7717/peerj.13575 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Berio et al. title: Sea urchins: an update on their pharmacological properties link: https://peerj.com/articles/13606 last-modified: 2022-07-04 description: Sea urchins are a group of benthic invertebrates characterized by having rigid globose bodies, covered in spines, and have an innate immune system that has allowed them to survive in the environment and defend against many pathogens that affect them. They are consumed for their unique flavor, but also for possessing a rich source of bioactive compounds which make them a source for a wide array of medicinal properties. Thus, these may be used to discover and develop new drugs such as anti-bacterials, anti-carcinogenics and anti-virals. Precisely for those reasons, this revision is centered on the known biological activities in various sea urchin species. Recently, the potential pharmacological benefits of nine sea urchin species [Diadema antillarum (Philippi 1845), Echinometra mathaei (de Blainville), Evechinus chloroticus (Valenciennes), Mesocentrotus nudus (Agassiz, 1863), Paracentrotus lividus (Lamarck, 1816), Scaphechinus mirabilis (Agazzis, 1863), Stomopneustes variolaris (Lamarck, 1816), Tripneustes depressus (Agassiz, 1863), and Tripneustes ventricosus (Lamarck, 1816)] have been evaluated. Our work includes a comprehensive review of the anti-fungal, anti-parasitic, anti-inflammatory, hepatoprotective, anti-viral, anti-diabetic, anti-lipidemic, gastro-protective and anti-cardiotoxic effects. Furthermore, we revised the compounds responsible of these pharmacological effects. This work was intended for a broad readership in the fields of pharmacology, drugs and devices, marine biology and aquaculture, fisheries and fish science. Our results suggest that organic extracts, as well as pure compounds obtained from several parts of sea urchin bodies are effective in vitro and in vivo pharmacological models. As such, these properties manifest the potential use of sea urchins to develop emergent active ingredients. creator: Dulce María Moreno-García creator: Monica Salas-Rojas creator: Eduardo Fernández-Martínez creator: Ma del Rocío López-Cuellar creator: Carolina G. Sosa-Gutierrez creator: Armando Peláez-Acero creator: Nallely Rivero-Perez creator: Adrian Zaragoza-Bastida creator: Deyanira Ojeda-Ramírez uri: https://doi.org/10.7717/peerj.13606 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Moreno-García et al. title: The influence of penguin activity on soil diatom assemblages on King George Island, Antarctica with the description of a new Luticola species link: https://peerj.com/articles/13624 last-modified: 2022-07-04 description: BackgroundIce-free areas in the Antarctic region are strongly limited. The presence of marine mammals and birds in those areas influence soil properties and vegetation composition. Studies on the terrestrial diatom flora in soils influenced by sea birds in the Maritime Antarctic region are scarce.MethodsSamples were collected from two transects on the western shore of the Admiralty Bay region. Light and scanning electron microscopic observations and statistical analyses were conducted to consider the impact of penguin rookeries on soil diatom assemblages.ResultsThe disturbance associated with the presence of penguin rookeries clearly influences the soil diatom diversity. Assemblages from areas with the highest nutrient input were characterized by a much lower diversity with only few species dominating the flora. One of recorded taxa could not be assigned to any of the known species. Therefore, based on the combination of morphological features analyzed using light and scanning electron microscopes and comparison with similar taxa in the Antarctic region and worldwide, the species is described hereby as new to science–Luticola kaweckae sp.nov. The new species is characteristic for soil habitats with strong penguin influence. creator: Natalia Kochman-Kędziora creator: Teresa Noga creator: Maria Olech creator: Bart Van de Vijver uri: https://doi.org/10.7717/peerj.13624 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kochman-Kędziora et al. title: Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland link: https://peerj.com/articles/13652 last-modified: 2022-07-04 description: Excrement-shaped ferruginous masses have been recovered from the Miocene of Turów mine in south-western Poland. These siderite masses have been the subject of much controversy, having been interpreted either as being coprolites, cololithes or pseudofossils created by mechanical deformation of plastic sediment. Here we present the results of mineralogical, geochemical, petrographic and microtomographical analyses. Our data indicate that these masses consist of siderite and iron oxide rather than phosphate, and rarely contain recognizable food residues, which may suggest abiotic origins of these structures. On the other hand, evidence in support of a fecal origin include: (i) the presence of two distinct morphotypes differing in size and shape, (ii) the presence of rare hair-like structures or coalified inclusions and (iii) the presence of rare fine striations on the surface. Importantly, comparative actualistic study of recent vertebrate feces shows overall resemblance of the first morphotype (sausage-shaped with rare coalified debris) to excrements of testudinoid turtles (Testudinoidea), whose shell fragment was found in the investigated locality. The second morphotype (rounded to oval-shaped with hair-like structures), in turn, is similar to the feces of some snakes (Serpentes), the remains of which were noted in the Miocene of the neighborhood areas. Other potential producers (such as lizards and crocodiles) and even abiotic origins cannot be fully excluded but are less likely. creator: Tomasz Brachaniec creator: Dorota Środek creator: Dawid Surmik creator: Robert Niedźwiedzki creator: Georgios L. Georgalis creator: Bartosz J. Płachno creator: Piotr Duda creator: Alexander Lukeneder creator: Przemysław Gorzelak creator: Mariusz A. Salamon uri: https://doi.org/10.7717/peerj.13652 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Brachaniec et al. title: Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation link: https://peerj.com/articles/13657 last-modified: 2022-07-04 description: BackgroundCurcumin is an active compound derived from turmeric, Curcuma longa, and is known for its benefits to human health. The amoebicidal activity of curcumin against Acanthamoeba triangularis was recently discovered. However, a physiological change of intracellular pathways related to A. triangularis encystation mechanism, including autophagy in the surviving amoeba after curcumin treatment, has never been reported. This study aims to investigate the effect of curcumin on the survival of A. triangularis under nutrient starvation and nutrient-rich condition, as well as to evaluate the A. triangularis encystation and a physiological change of Acanthamoeba autophagy at the mRNA level.MethodsIn this study, A. triangularis amoebas were treated with a sublethal dose of curcumin under nutrient starvation and nutrient-rich condition and the surviving amoebas was investigated. Cysts formation and vacuolization were examined by microscopy and transcriptional expression of autophagy-related genes and other encystation-related genes were evaluated by real-time PCR.ResultsA. triangularis cysts were formed under nutrient starvation. However, in the presence of the autophagy inhibitor, 3-methyladenine (3-MA), the percentage of cysts was significantly reduced. Interestingly, in the presence of curcumin, most of the parasites remained in the trophozoite stage in both the starvation and nutrient-rich condition. In vacuolization analysis, the percentage of amoebas with enlarged vacuole was increased upon starvation. However, the percentage was significantly declined in the presence of curcumin and 3-MA. Molecular analysis of A. triangularis autophagy-related (ATG) genes showed that the mRNA expression of the ATG genes, ATG3, ATG8b, ATG12, ATG16, under the starvation with curcumin was at a basal level along the treatment. The results were similar to those of the curcumin-treated amoebas under a nutrient-rich condition, except AcATG16 which increased later. On the other hand, mRNA expression of encystation-related genes, cellulose synthase and serine proteinase, remained unchanged during the first 18 h, but significantly increased at 24 h post treatment.ConclusionCurcumin inhibits cyst formation in surviving trophozoites, which may result from its effect on mRNA expression of key Acanthamoeba ATG-related genes. However, further investigation into the mechanism of curcumin in A. triangularis trophozoites arrest and its association with autophagy or other encystation-related pathways is needed to support the future use of curcumin. creator: Rachasak Boonhok creator: Suthinee Sangkanu creator: Suganya Phumjan creator: Ramita Jongboonjua creator: Nawarat Sangnopparat creator: Pattamaporn Kwankaew creator: Aman Tedasen creator: Chooi Ling Lim creator: Maria de Lourdes Pereira creator: Mohammed Rahmatullah creator: Polrat Wilairatana creator: Christophe Wiart creator: Karma G. Dolma creator: Alok K. Paul creator: Madhu Gupta creator: Veeranoot Nissapatorn uri: https://doi.org/10.7717/peerj.13657 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Boonhok et al. title: Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L. link: https://peerj.com/articles/13659 last-modified: 2022-07-04 description: Dioscorea cirrhosa is a plant that is used as a dye as well as in medicine. Many metabolites with pharmacological activity exist in the tubers of D. cirrhosa. However, little is known about the mechanism regulating biosynthesis in these metabolites. In this study, transcriptome and metabolome profiling were performed in four color tubers. A total of 531 metabolites, including 62 flavonoids, were identified. Epicatechin and proanthocyanin B2 were the key metabolites that exhibited high content levels in the four tubers. These metabolites were divided into nine classes with distinct change patterns. A total of 22,865 differentially expressed genes (DEGs) were identified by transcriptome analysis. Among these DEGs, we identified 67 candidate genes related to the flavonoid biosynthesis pathway and three genes that played pivotal roles in proanthocyanin (PA) synthesis. A weighted gene co-expression network analysis (WGCNA) revealed that the two modules, “MEblue” and “MEblack,” were two key gene sets strongly associated with phenylpropanoid and flavonoid biosynthesis. We also found that the plant hormone signal transduction biological process exhibited activity in the late stage of tuber color formation. Additionally, we identified 37 hub transcript factors related to flavonoid biosynthesis, of which 24 were found to be highly associated with flavonoid pathway genes. In addition to the MYB-bHLH-WD40 (MBW) genes, we found that the plant hormone gene families exhibited high expression levels. This study provides a reference for understanding the synthesis of D. cirrhosa tuber metabolites at the molecular level and provides a foundation for the further development of D. cirrhosa related plant pigments as well as its further use in the pharmaceutical industry. creator: Lin Yan creator: Haijun Yang creator: Qiang Ye creator: Zhihua Huang creator: Hongying Zhou creator: Dafang Cui uri: https://doi.org/10.7717/peerj.13659 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yan et al. title: What makes a house a home? Nest box use by West European hedgehogs (Erinaceus europaeus) is influenced by nest box placement, resource provisioning and site-based factors link: https://peerj.com/articles/13662 last-modified: 2022-07-04 description: Artificial refuges provided by householders and/or conservation practitioners potentially represent one mechanism for mitigating declines in the availability of natural nest sites used for resting, breeding and hibernating in urban areas. The effectiveness of such refuges for different species is, however, not always known. In this study, we conducted a questionnaire survey of UK householders to identify factors associated with the use of ground-level nest boxes for West European hedgehogs (Erinaceus europaeus), a species of conservation concern. Overall, the percentage of boxes used at least once varied with season and type of use: summer day nesting (35.5–81.3%), breeding (7.2–28.2%), winter day nesting (20.1–66.5%) and hibernation (21.7–58.6%). The length of time the box had been deployed, the availability of artificial food and front garden to back garden access significantly increased the likelihood that a nest box had been used for all four nesting types, whereas other factors related to placement within the garden (e.g., in a sheltered location, on hardstanding such as paving, distance from the house) and resource provisioning (bedding) affected only some nesting behaviours. The factors most strongly associated with nest box use were the provisioning of food and bedding. These data suggest, therefore, that householders can adopt simple practices to increase the likelihood of their nest box being used. However, one significant limitation evident within these data is that, for welfare reasons, householders do not routinely monitor whether their box has been used. Consequently, future studies need to adopt strategies which enable householders to monitor their boxes continuously. Ultimately, such studies should compare the survival rates and reproductive success of hedgehogs within artificial refuges versus more natural nest sites, and whether these are affected by, for example, the impact of nest box design and placement on predation risk and internal microclimate. creator: Abigail Gazzard creator: Philip J. Baker uri: https://doi.org/10.7717/peerj.13662 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Gazzard and Baker title: A complete season with attendance restrictions confirms the relevant contribution of spectators to home advantage and referee bias in association football link: https://peerj.com/articles/13681 last-modified: 2022-07-04 description: BackgroundDue to the unfortunate pandemic situation, the phenomena of home advantage and referee bias in sports have recently received a particular research attention, especially in association football. In this regard, several studies were conducted on the last portion of the 2019–20 season: the majority of them suggests a reduction—but not the elimination—of the two phenomena, with some exceptions in which no reduction was found or, at the other extreme, the phenomena were not observed at all.MethodsThe continuation of the pandemic made it possible to replicate the previous studies considering the complete 2020–21 season, thus with the important added value of having a fully balanced home/away schedule—and a higher number of matches—in the various leagues. In particular, the sample of the present study consisted of 3,898 matches from the first and second divisions of the UEFA top five ranked countries, that is, England, Spain, Italy, Germany, and France. For the home advantage, the following variables were examined: distribution of matches outcomes and home advantage for points (also for previous seasons from the 2014–15 one); ball possession; total shots; shots on goal; and corner kicks. Instead, for he referee bias, the following variables were examined: fouls; yellow cards; red cards; penalty kicks; and extra time. Chi-square tests were used to compare the distribution of matches outcomes, and t-tests to compare home vs. away data for the other variables in the 2020–21 season; Bayesian and equivalence analyses were also conducted.ResultsThe main results are as follows: (a) the distribution of matches outcomes in the 2020–21 season was significantly different from that of the last five complete seasons with spectators (Chi-square = 37.42, df = 2, p < 0.001), with fewer home victories and more away victories; the resulting values of the home advantage for points were 54.95% for the 2020–21 season, and 59.36% for the previous seasons; (b) for the other home advantage variables, a statistically significant overall advantage for the home team emerged; nevertheless, the strength of the differences between home and away teams was generally small (0.09 < Cohen’s d < 0.17), and the corresponding means can be considered statistically equivalent for all variables but the total shots; (c) no statistically significant differences emerged between home and away teams for any of the referee bias variables.DiscussionThese findings demonstrate that the absence of spectators significantly reduced the home advantage compared to previous seasons with spectators. A slight home advantage persisted in the 2020–21 season, probably due to other factors, namely, learning and travel, according to the model by Courneya & Carron (1992). Conversely, the referee bias was not observed, suggesting that it mainly derives from the pressure normally exerted by spectators. creator: Fabrizio Sors creator: Michele Grassi creator: Tiziano Agostini creator: Mauro Murgia uri: https://doi.org/10.7717/peerj.13681 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sors et al. title: Effect of icaritin on autophagy-related protein expression in TDP-43-transfected SH-SY5Y cells link: https://peerj.com/articles/13703 last-modified: 2022-07-04 description: ObjectiveTo study the protective effect and mechanism of icaritin (ICT) in a SH-SY5Y cells with virus-loaded TAR DNA-binding domain protein 43(TDP-43) by examining the effect of ICT on the expression of autophagy-related proteins in TDP-43-infected SH-SY5Y cells.MethodsA TDP-43-induced neuronal cell injury model was established by transfecting well-growing SH-SY5Y cells with virus loaded with the TDP-43 gene. The changes in cell viability were detected by the CCK-8 method. After successful transfection, the establishment of the model was verified by real-time quantitative PCR (qPCR) and Western blot methods. After the cells were subjected to drug intervention with ICT, the changes in the expression levels of TDP-43, cleaved Caspase-3, LC3 II/I, Beclin-1 and p62 were detected by Western blotting.ResultsAfter ICT intervention, it was found that compared with that of the TDP-43 group, the cell viability of the TDP-43+ICT group increased, the expression level of TDP-43 decreased, and the expression levels of the apoptotic protein cleaved Caspase-3, autophagy protein Beclin-1, and LC3-II/I decreased, while the expression level of the autophagy protein p62 increased.ConclusionICT has a protective effect on the SH-SY5Y cell injury model transfected with TDP-43. This protective effect may be related to reducing the protein expression of TDP-43 and inhibiting autophagy. creator: Yanjun Zhou creator: Nanqu Huang creator: Yuanyuan Li creator: Zhisheng Ba creator: Yong Luo uri: https://doi.org/10.7717/peerj.13703 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhou et al. title: Newly described nesting sites of the green sea turtle (Chelonia mydas) and the hawksbill sea turtle (Eretmochelys imbricata) in the central Red Sea link: https://peerj.com/articles/13408 last-modified: 2022-07-01 description: BackgroundThere is relatively little published information about sea turtle nesting distribution and seasonality in the Saudi Arabian Red Sea. Upcoming large-scale developments occurring along the Saudi Arabian Red Sea coast could negatively affect many sea turtle nesting beaches with potential impacts on the survival of local populations.MethodsIn 2019, two coastal beaches and three near-shore islands were surveyed for turtle nesting in the central Red Sea. We recorded all emergences, examined beach morphology, and collected sand samples to determine grain size, moisture content and colour.ResultsSea turtle nesting was found at all surveyed sites, though emergence counts were often low. The limited occurrence of nesting at several previously undocumented sites suggests that nesting activity may be widespread, but sparsely distributed, in the central Red Sea region. In addition, nesting at novel sites appeared to favour the seaward side of islands, a pattern that was not observed in previously documented areas. The substrate of most surveyed sites was composed of calcium carbonate with Ras Baridi as the only exception; it was composed of dark quartz-rich sediment. This study highlights several important sea turtle rookeries while also demonstrating that low levels of nesting occur throughout the region, although inter-annual nesting patterns still need to be determined. Future developments should be steered away from key nesting areas and the seaward bias in marginal rookeries should be taken into account where possible. creator: Kirsty Scott creator: Lyndsey K. Tanabe creator: Jeffrey D. Miller creator: Michael L. Berumen uri: https://doi.org/10.7717/peerj.13408 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Scott et al. title: Can high-intensity interval training and small-sided games be effective for improving physical fitness after detraining? A parallel study design in youth male soccer players link: https://peerj.com/articles/13514 last-modified: 2022-07-01 description: BackgroundThe aim of this study was two-fold: (i) analyze the within-group physical fitness adaptations promoted by a detraining period (4 weeks) followed by an intervention period (4 weeks) using small-sided games (SSGs) or running-based high intensity interval training (HIIT); and (ii) analyze the between-group differences aiming to identify the effectiveness of each training intervention on the physical fitness of youth male soccer players.MethodsThis study followed a randomized parallel study design. Forty male soccer players (age: 16.4 ± 0.5 years old) were assessed three times: (i) baseline; (ii) after 4 weeks of detraining; and (iii) after a retraining period of 4 weeks. After returning from detraining, players were randomized to an SSG-based training intervention (n = 20) or running-based HIIT (n = 20). Interventions lasted 4 weeks, with a training frequency of three sessions per week. At all timepoints, players were assessed by: (i) anthropometry (height, body mass, fat mass (FM)), countermovement jump (CMJ), standing broad jump (SBJ), triple hop jump (THJ), linear sprint test (5-, 10-, and 20-m), zig-zag test with (ZZwB) and without (ZZwoB) ball, three corner run test (3CRT), Y-balance test and the Yo-Yo intermittent recovery test level 1 (YYIRT). Mixed ANOVA (time * group) was conducted for testing interactions between the three timepoints of repeated measures and the two groups. Effect size (ES) for pairwise comparisons was calculated using Cohen’s.ResultsBetween-group analysis revealed significantly smaller SBJ (t = −2.424, p = 0.020, d = −0.767 small ES) and THT (t = −4.353, p < 0.001, d = −1.376 large ES) in the SSG group after the retraining period. At the same time, SSG presented significantly greater FM after retraining compared to HIIT (t = 3.736, p < 0.001, d = 1.181 large ES). Additionally, SSG had significantly smaller values than HIIT in the ZZwB (t = −3.645, p < 0.001, d = −1.153 large ES), but greater times in the ZZwoB (t = 2.679, p = 0.011, d = 0.847 large ES) and 3CRT (t = 3.126, p = 0.003, d = 0.989 large ES).ConclusionsAlthough SSG and HIIT interventions improved physical fitness outcomes after a period of detraining, they were not able to effectively restore body composition, CMJ, 20-m sprint, ZZwB, and YYIRT compared with the baseline assessments (before detraining). Only HIIT was significantly effective for restoring SBJ, short linear sprin speed, and change-of-direction compared with baseline. HIIT was also significantly better than SSG in improving SBJ and ZZwoB. Although the small sample, the non determination of maturation status and the need to be cautious regarding generalization, HIIT appears to be more beneficial than SSG after a detraining period for recovery of body composition and physical fitness qualities in this specific context of youth soccer players. creator: Filipe Manuel Clemente creator: Yusuf Soylu creator: Ersan Arslan creator: Bulent Kilit creator: Joel Garrett creator: Daniel van den Hoek creator: Georgian Badicu creator: Ana Filipa Silva uri: https://doi.org/10.7717/peerj.13514 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Clemente et al. title: Dopamine receptor activation elicits a possible stress-related coping behavior in a wild-caught songbird link: https://peerj.com/articles/13520 last-modified: 2022-07-01 description: Animals experience stress throughout their lives and exhibit both physiological and behavioral responses to cope with it. The stress response can become harmful when prolonged and increasing evidence suggests that dopamine plays a critical role in extinguishing the stress response. In particular, activation of the D2 dopamine receptor reduces glucocorticoids and increases coping behavior, i.e., behavioral responses to adverse stimuli that reduce the harmful effects of stress. However, few studies have examined the effects of dopamine on the stress responses of wild species. We therefore tested the hypothesis that activation of the D2 dopamine receptor influences coping-like behavior in a wild-caught species. We recorded behavior of house sparrows (Passer domesticus) before and after they received injections of D2 dopamine agonists, D2 dopamine antagonists, or saline. House sparrows are common in urban environments and understanding how they cope with stress may help us better understand how animals cope with urban stressors. We found that the birds significantly increased biting of inanimate objects after the agonist but there was no change following the antagonist or saline. The biting of inanimate objects may be a mechanism of behavioral coping. This change in biting behavior was not correlated with general movement. This study supports the hypothesis that D2 dopamine receptor activation is involved in the regulation of the stress response in a wild bird. creator: Melanie R. Florkowski creator: Jessica L. Yorzinski uri: https://doi.org/10.7717/peerj.13520 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Florkowski and Yorzinski title: Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae) link: https://peerj.com/articles/13570 last-modified: 2022-07-01 description: Dalbergia spp. are numerous and widely distributed in pantropical areas in Asia, Africa and America, and most of the species have important economic and ecological value as precious timber. In this study, we determined and characterized six complete chloroplast genomes of Dalbergia species (Dalbergia obtusifolia, D. hupeana, D. mimosoides, D. sissoo, D. hancei, D. balansae), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (D. hancei) to 156,419 bp (D. obtusifolia). The complete chloroplast genomes of Dalbergia include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of Dalberigia chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (rps16-accD, trnR-UCU-trnG-UCC, ndhE-ndhG, trnG-UCC-psbZ, rps8-rpl14, trnP-UGG-psaJ, ndhH-rps15, trnQ-UUG-rps16, trnS-GCU-psbI, rps12-clpP, psbA-trnK-UUU, trnK-UUU-intron), and four coding regions (rps16, ycf1, rps15 and ndhF) showed many nucleotide variations that could be used as potential molecular markers. Based on a site-specific model, we analysed the selective pressure of chloroplast genes in Dalbergia species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (ndhC, adhD, ndhF, petB, psaA, psaB, psbB, psbC, psbK and rbcL), self-replication category of genes (rpoA, rpoC2, rps3, rps12 and rps18) and others (accD, ccsA, cemA, clpP, matK, ycf1 and ycf2). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus Dalbergia. Furthermore, the comparative analysis of cp genomes of Dalbergieae species indicated that the boundary of IRs/SSC was highly variable, which resulted in the size variation of cp genomes. Finally, phylogenetic analysis showed an inferred phylogenetic tree of Papilionoideae species with high bootstrap support and suggested that Amorpheae was the sister of the clade Dalbergieae. Moreover, three genera of the Pterocarpus clade showed a nested evolutionary relationship. These complete cp genomes provided valuable information for understanding the genetic variation and phylogenetic relationship of Dalbergia species with their relatives. creator: Changhong Li creator: Yu Liu creator: Furong Lin creator: Yongqi Zheng creator: Ping Huang uri: https://doi.org/10.7717/peerj.13570 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Genome-wide identification and functional analysis of class III peroxidases in Gossypium hirsutum link: https://peerj.com/articles/13635 last-modified: 2022-07-01 description: Class III peroxidase (PRX) genes play essential roles in various processes, such as auxin catabolism, removal of H2O2, crosslinking cell wall components, and response to biotic and abiotic stresses. In this study, we identified 166, 78 and 89 PRX genes from G. hirsutum, G. arboretum and G. raimondii, respectively. These PRX genes were classified into seven subfamilies based on phylogenetic tree analysis and the classification of PRX genes in Arabidopsis. Segmental duplication and purifying selection were the major factors driving the evolution of GhPRXs. GO and KEGG enrichment analysis revealed that GhPRX genes were mainly associated with responding to oxidative stresses, peroxidase activities and phenylpropanoid biosynthesis pathways. Transcriptome data analysis showed that GhPRX genes expression were significantly different in microspore development between the sterility line-JinA and the maintainer line MB177. We confirmed the up-regulation of GhPRX107 and down-regulation of GhPRX128 in the sterile line compared to its maintainer line using qRT-PCR, suggesting their roles in pollen fertility. In addition, silencing GhPRX107 in cotton showed a significant decrease of the reactive oxygen species (ROS) levels of microsporocyte stage anthers compared to control. Overexpressing GhPRX107 in Arabidopsis significantly increased the ROS levels of anthers compared to wild type. In conclusion, we identified GhPRX107 as a determinant of ROS levels in anther. This work sets a foundation for PRX studies in pollen development. creator: Yi Chen creator: Jiajia Feng creator: Yunfang Qu creator: Jinlong Zhang creator: Li Zhang creator: Dong Liang creator: Yujie Yang creator: Jinling Huang uri: https://doi.org/10.7717/peerj.13635 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Recent advances in methods for in situ root phenotyping link: https://peerj.com/articles/13638 last-modified: 2022-07-01 description: Roots assist plants in absorbing water and nutrients from soil. Thus, they are vital to the survival of nearly all land plants, considering that plants cannot move to seek optimal environmental conditions. Crop species with optimal root system are essential for future food security and key to improving agricultural productivity and sustainability. Root systems can be improved and bred to acquire soil resources efficiently and effectively. This can also reduce adverse environmental impacts by decreasing the need for fertilization and fresh water. Therefore, there is a need to improve and breed crop cultivars with favorable root system. However, the lack of high-throughput root phenotyping tools for characterizing root traits in situ is a barrier to breeding for root system improvement. In recent years, many breakthroughs in the measurement and analysis of roots in a root system have been made. Here, we describe the major advances in root image acquisition and analysis technologies and summarize the advantages and disadvantages of each method. Furthermore, we look forward to the future development direction and trend of root phenotyping methods. This review aims to aid researchers in choosing a more appropriate method for improving the root system. creator: Anchang Li creator: Lingxiao Zhu creator: Wenjun Xu creator: Liantao Liu creator: Guifa Teng uri: https://doi.org/10.7717/peerj.13638 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Genetic diversity of enterotoxigenic Bacillus cereus strains in coriander in southwestern Mexico link: https://peerj.com/articles/13667 last-modified: 2022-07-01 description: BackgroundCoriander, like other leafy green vegetables, is available all year round and is commonly consumed raw in Mexico as in other countries in the preparation of street or homemade food. Bacillus cereus (B. cereus) is a microorganism that can reach coriander because it is usually found in the soil and in some regions the vegetables are irrigated with polluted water. Therefore, the aim of this study was to determinate the presence of B. cereus in coriander used for human consumption in southwestern Mexico and determine the toxigenic profile, biofilm production, genes associated with the production of biofilms, sporulation rates, enzymatic profile, psychotropic properties, and genetic diversity of B. cereus.MethodsFresh coriander samples were collected from several vegetable retailers in different markets, microbiological analysis was performed. Molecular identification, genes related to the production of biofilm, and toxin gene profiling of B. cereus isolates were determined by PCR. The biofilm formation was measured by performing a crystal violet assay. The genetic diversity of B. cereus strains was determined by PCR of repetitive elements using oligonucleotide (GTG) 5.ResultsWe found a frequency of B. cereus in vegetables was 20% (13/65). In this study, no strains with genes for the HBL toxin were found. In the case of genes related to biofilms, the frequency was low for sipW [5.8%, (1/17)] and tasA [11.7%, (2/17)]. B. cereus strains produce a low amount of biofilm with sporulation rates around 80%. As for genetic diversity, we observed that strains isolated from the same market, but different vegetable retailers are grouped into clusters. In the coriander marketed in southwestern Mexico, were found B. cereus strains with genes associated with the production of diarrheal toxins. Together, these results show actual information about the state of art of B. cereus strains circulating in the southwestern of Mexico. creator: Daniel Alexander Castulo-Arcos creator: Roberto Adame-Gómez creator: Natividad Castro-Alarcón creator: Aketzalli Galán-Luciano creator: María Cristina Santiago Dionisio creator: Marco A. Leyva-Vázquez creator: Jose-Humberto Perez-Olais creator: Jeiry Toribio-Jiménez creator: Arturo Ramirez-Peralta uri: https://doi.org/10.7717/peerj.13667 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Castulo-Arcos et al. title: Manipulation of light quality is an effective tool to regulate photosynthetic capacity and fruit antioxidant properties of Solanum lycopersicum L. cv. ‘Microtom’ in a controlled environment link: https://peerj.com/articles/13677 last-modified: 2022-07-01 description: Light quality plays an essential role in setting plant structural and functional traits, including antioxidant compounds. This paper aimed to assess how manipulating the light spectrum during growth may regulate the photosynthetic activity and fruit bioactive compound synthesis in Solanum lycopersicum L. cv. ‘Microtom’ to improve plant physiological performance and fruit nutritional value. Plants were cultivated under three light quality regimes: red-green-blue LEDs (RGB), red-blue LEDs (RB) and white fluorescent lamps (FL), from sowing to fruit ripening. Leaf functional traits, photosynthetic efficiency, Rubisco and D1 protein expression, and antioxidant production in fruits were analyzed. Compared to FL, RGB and RB regimes reduced height and increased leaf number and specific leaf area, enhancing plant dwarf growth. The RGB regime improved photosynthesis and stomatal conductance despite lower biomass, favoring Rubisco synthesis and carboxylation rate than RB and FL regimes. The RB light produced plants with fewer flowers and fruits with a lower ascorbic acid amount but the highest polyphenol content, antioxidant capacity and SOD and CAT activities. Our data indicate that the high percentage of the green wavelength in the RGB regime promoted photosynthesis and reduced plant reproductive capacity compared to FL and RB. Conversely, the RB regime was the best in favoring the production of health-promoting compounds in tomato berries. creator: Ermenegilda Vitale creator: Violeta Velikova creator: Tsonko Tsonev creator: Giulia Costanzo creator: Roberta Paradiso creator: Carmen Arena uri: https://doi.org/10.7717/peerj.13677 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Vitale et al.