title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=924 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Experiencing fear during the pandemic: validation of the fear of COVID-19 scale in Polish link: https://peerj.com/articles/11263 last-modified: 2021-04-26 description: BackgroundThe Fear of COVID-19 Scale (FCV-19S) is a brief self-report measure developed at the beginning of the coronavirus pandemic. The scale evaluates the emotional responses to COVID-19. To date, the FCV-19S has been translated and validated in about 20 languages and has been used in many published research. The current study aimed to validate the Polish version of the FCV-19S.MethodThe FCV-19S was translated into Polish using forward- and back-translation. From May 15th to June 15th 2020, a total of 708 community members (Sample 1: 383 persons, 209 females, Sample 2: 325 persons, 198 females) participated in the online study. The participants were recruited using online advertisements in social media. Participation was anonymous, voluntary, and without compensation. A confirmatory factor analysis was performed to test the one-factor structure of the FCV-19S. Then, measurement invariance was analyzed across samples, gender and age groups. To assess the validity of the scale, correlations between the FCV-19S and the remaining scales were computed.ResultsInternal consistency of the FCV-19S was good in both samples (Cronbach’s alpha 0.89 and 0.85). The CFA showed that the one-factor model fits the data well (RMSEA = 0.067, 90% CI [0.059–0.094], CFI = 0.977, TLI = 0.965, GFI = 0.986). The criteria for configural, metric, scalar and strict invariance were met for all models tested. The FCV-19S scores correlated significantly with age, subjective vulnerability to the disease, neuroticism, self-reported compliance with the pandemic measures, and three kinds of preventive behavior (i.e., social distancing, hand hygiene, and disinfecting things).ConclusionThe Polish version of the FCV-19S had a unidimensional structure, good reliability, and correlated as predicted with other variables. With the FCV-19S and the obtained results, healthcare professionals, researchers, and the government can gain more valuable information about people who may be at risk for negative psychological outcomes during the pandemic or who are not implementing protective behavior. The tool can be used in hospitals to quickly screen the level of fear in patients and minimize its severe adverse consequences. creator: Irena Pilch creator: Zofia Kurasz creator: Agnieszka Turska-Kawa uri: https://doi.org/10.7717/peerj.11263 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pilch et al. title: NFIB promotes the migration and progression of kidney renal clear cell carcinoma by regulating PINK1 transcription link: https://peerj.com/articles/10848 last-modified: 2021-04-23 description: Kidney renal clear cell carcinoma (KIRC) is the most common and aggressive type of renal cell carcinoma. Due to high mortality rate, high metastasis rate and chemical resistance, the prognosis of KIRC patients is poor. Therefore, it is necessary to study the mechanisms of KIRC development and to develop more effective prognostic molecular biomarkers to help clinical patients. In our study, we used The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to investigate that the expression of nuclear factor I B (NFIB) is significantly higher in KIRC than in adjacent tissues. Moreover, NFIB expression levels are associated with multiple clinical pathological parameters of KIRC, and KIRC patients with high NFIB expression have poor prognosis, suggesting that NFIB may play vital roles in the malignant development of KIRC. Further studies demonstrated that NFIB could promote the progression and metastasis of KIRC and participate in the regulation of PTEN induced kinase 1 (PINK1). Furthermore, we used chromatin immunoprecipitation (ChIP) experiments to confirm that NFIB binds to the PINK1 promoter and regulates its expression at the transcriptional level. Further experiments also confirmed the important roles of PINK1 in promoting the development of tumors by NFIB. Hence, our data provide a new NFIB-mediated regulatory mechanism for the tumor progression of KIRC and suggest that NFIB can be applied as a new predictor and therapeutic target for KIRC. creator: Ninghua Wang creator: Jing Yuan creator: Fei Liu creator: Jun Wei creator: Yu Liu creator: Mei Xue creator: Rui Dong uri: https://doi.org/10.7717/peerj.10848 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Soil fertility evaluation and spatial distribution of grasslands in Qilian Mountains Nature Reserve of eastern Qinghai-Tibetan Plateau link: https://peerj.com/articles/10986 last-modified: 2021-04-23 description: The study assessed the overall soil characteristics of grasslands on Qilian Mountains and rated the soil nutrient status with classification standard of the second national soil survey of China. Nemerow index method was used to evaluate the soil fertility of different grassland types. GIS was used to analyze the spatial distribution of the soil nutrients and provided a database for the grassland’s ecological protection and restoration. The study graded the soil organic matter (SOM), total N, and available K at level 2 (high) or above for most regions, available soil-P at level 4, while the soil bulk density, total porosity and pH were 0.77–1.32 g cm−3, 35.36–58.83% and 7.63–8.54, respectively. The rank of comprehensive soil fertility index was temperate steppe (TS) > alpine meadow (AM) > alpine steppe (AS) >upland meadow (UM) >alpine desert (AD)> lowland meadow (LM)> temperate desert steppe (TDS)> temperate desert (TD). The areas with high, medium and low soil fertility accounted for 63.19%, 34.24% and 2.57% of the total grassland area. Soil fertility of different grassland types had different main limiting factors, for instance, the pH, total N and SOM were the main factors limiting soil fertility in LM, while pH and available P were the main factors limiting soil fertility in UM, AM, TS and AS. In summary, the grassland soil fertility was generally at the mid-upper level, and the main limiting factors were found in the different types of the grasslands and their spatial distributions were figured out. Our findings also indicated that the typical grasslands and meadows may require phosphorus application, while for desert grasslands, both nitrogen and phosphorus were required to improve their comprehensive soil fertility and grassland productivity. creator: Qiang Li creator: Junyin Yang creator: Wenhao Guan creator: Zhigang Liu creator: Guoxing He creator: Degang Zhang creator: Xiaoni Liu uri: https://doi.org/10.7717/peerj.10986 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Porphyromonas gingivalis lipopolysaccharide promotes T-hel per17 cell differentiation by upregulating Delta-like ligand 4 expression on CD14+ monocytes link: https://peerj.com/articles/11094 last-modified: 2021-04-23 description: BackgroudTo investigate the effect and mechanism of Porphyromonas gingivalis (P. gingivalis) lipopolysaccharide (LPS) on Th17 cell differentiation mediated by CD14+ monocytes. Methods P. gingivalis LPS-activated CD14+ monocytes were co-cultured with CD4+T cells in different cell ratios. An indirect co-culture system was also established using transwell chambers. Furthermore, anti- Delta-like ligand 4 (Dll-4) antibody was used to investigate the role of Dll-4 in Th17 cell response. The mRNA expression was analyzed using quantitative reverse transcription-polymerase chain reaction, and secreted cytokines in culture supernatant were detected using enzyme-linked immunosorbent assay. Flow cytometry was used to determine the frequencies of Th17 cells. IL-17 protein expression levels were determined using western blotting assay. ResultsP. gingivalis LPS increased the expressions of interleukin (IL)-1β, IL-6, IL-23 and transforming growth factor (TGF)-β in CD14+ monocytes. Th17 cell frequency upregulated, which is not solely cytokine-dependent but rather requires cell-cell contact with activated monocytes, particularly in the 1:10 cell ratio. Furthermore, P. gingivalis LPS increased t he expression of Dll-4 on CD14+ monocytes, whereas the anti- Dll-4 a ntibody decreased the response of Th17 cells. The results suggest that P. gingivalis LPS enhances Th17 cell response via Dll-4 upregulation on CD14+ monocytes. creator: Chi Zhang creator: Chenrong Xu creator: Li Gao creator: Xiting Li creator: Chuanjiang Zhao uri: https://doi.org/10.7717/peerj.11094 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Re-positive of SARS-CoV-2 test is common in COVID-19 patients after hospital discharge. Data from high standard post-discharge quarantined patients in Macao SAR, China link: https://peerj.com/articles/11170 last-modified: 2021-04-23 description: During the pandemic of COVID-19, Macau faces tremendous pressure because it is a famous gambling and tourism city with the world’s highest population density. The Macau government implemented decisive public health intervention to control the transmission of COVID-19, and there were only two independent outbreaks in Macau. In the second outbreak, all 35 cases were infected in foreign countries. They were quarantined in airborne infection isolation rooms for at least 14 days with reverse transcription-polymerase chain reaction (RT-PCR) tests after hospital discharge. Twelve (34.3%) of them had re-positive SARS-CoV-2 test results, and none of them presented any COVID-19 signs or symptoms during the entire quarantine period. In this study, the re-positive patients were more likely to be diagnosed in the early stage of the disease with a longer hospital stay. Virus re-infection is impossible in this high standard isolation setting, and reactivation is also unlikely, so that residual virus nucleic acid should be the possible reason for this phenomenon. Due to limited data about the risk of re-positive patients, it is better to quarantine patients after discharge for a prolonged period with repeat RT-PCR tests to minimize the community’s potential risk, particularly in the regions with relative plenty of resources and low community infection rate such as Macau. creator: Chi Leong Wong creator: Sao Kuan Lei creator: Chin Ion Lei creator: Iek Long Lo creator: Chong Lam creator: Iek Hou Leong uri: https://doi.org/10.7717/peerj.11170 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wong et al. title: A molecular dynamics simulation study of the ACE2 receptor with screened natural inhibitors to identify novel drug candidate against COVID-19 link: https://peerj.com/articles/11171 last-modified: 2021-04-23 description: Background & ObjectivesThe massive outbreak of Novel Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has turned out to be a serious global health issue worldwide. Currently, no drugs or vaccines are available for the treatment of COVID-19. The current computational study was attempted to identify a novel therapeutic inhibitor against novel SARS-CoV-2 using in silico drug discovery pipeline.MethodsIn the present study, the human angiotensin-converting enzyme 2 (ACE2) receptor was the target for the designing of drugs against the deadly virus. The 3D structure of the receptor was modeled & validated using a Swiss-model, Procheck & Errat server. A molecular docking study was performed between a group of natural & synthetic compounds having proven anti-viral activity with ACE2 receptor using Autodock tool 1.5.6. The molecular dynamics simulation study was performed using Desmond v 12 to evaluate the stability and interaction of the ACE2 receptor with a ligand.ResultsBased on the lowest binding energy, confirmation, and H-bond interaction, cinnamic acid (−5.20 kcal/mol), thymoquinone (−4.71 kcal/mol), and andrographolide (Kalmegh) (−4.00 kcal/mol) were screened out showing strong binding affinity to the active site of ACE2 receptor. MD simulations suggest that cinnamic acid, thymoquinone, and andrographolide (Kalmegh) could efficiently activate the biological pathway without changing the conformation in the binding site of the ACE2 receptor. The bioactivity and drug-likeness properties of compounds show their better pharmacological property and safer to use.Interpretation & ConclusionsThe study concludes the high potential of cinnamic acid, thymoquinone, and andrographolide against the SARS-CoV-2 ACE2 receptor protein. Thus, the molecular docking and MD simulation study will aid in understanding the molecular interaction between ligand and receptor binding site, thereby leading to novel therapeutic intervention. creator: Neha Srivastava creator: Prekshi Garg creator: Prachi Srivastava creator: Prahlad Kishore Seth uri: https://doi.org/10.7717/peerj.11171 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Srivastava et al. title: Marine microalgae co-cultured with floc-forming bacterium: Insight into growth and lipid productivity link: https://peerj.com/articles/11217 last-modified: 2021-04-23 description: This study investigated the effect of co-culturing microalgae with a floc-forming bacterium. Of the six microalgae isolated from a biofloc sample, only Thalassiosira weissflogii, Chlamydomonas sp. and Chlorella vulgaris were propagated successfully in Conway medium. Hence, these species were selected for the experiment comparing microalgae axenic culture and co-culture with the floc-forming bacterium, Bacillus infantis. Results obtained showed that the co-culture had higher microalgae biomass compared to the axenic culture. A similar trend was also observed concerning the lipid content of the microalgae-bacterium co-cultures. The cell number of B. infantis co-cultured with T. weissflogii increased during the exponential stage until the sixth day, but the other microalgae species experienced a significant early reduction in cell density of the bacteria at the exponential stage. This study represents the first attempt at co-culturing microalgae with B. infantis, a floc-forming bacterium, and observed increased biomass growth and lipid accumulation compared to the axenic culture. creator: Chin Sze Yee creator: Victor Tosin Okomoda creator: Fakriah Hashim creator: Khor Waiho creator: Siti Rozaimah Sheikh Abdullah creator: Cosmas Alamanjo creator: Hassimi Abu Hasan creator: Emienour Muzalina Mustafa creator: Nor Azman Kasan uri: https://doi.org/10.7717/peerj.11217 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yee et al. title: Subterranean movement inferred by temporary emigration in Barton Springs salamanders (Eurycea sosorum) link: https://peerj.com/articles/11246 last-modified: 2021-04-23 description: Movement behavior is an important aspect of animal ecology but is challenging to study in species that are unobservable for some portion of their lives, such as those inhabiting subterranean environments. Using four years of robust-design capture-recapture data, we examined the probability of movement into subterranean habitat by a population of endangered Barton Springs salamanders (Eurycea sosorum), a species that inhabits both surface and subterranean groundwater habitats. We tested the effects of environmental variables and body size on survival and temporary emigration, using the latter as a measure of subterranean habitat use. Based on 2,046 observations of 1,578 individuals, we found that temporary emigration was higher for larger salamanders, 79% of which temporarily emigrated into subterranean habitat between primary sampling intervals, on average. Body size was a better predictor of temporary emigration and survival compared to environmental covariates, although coefficients from lower ranked models suggested turbidity and dissolved oxygen may influence salamander movement between the surface and subsurface. Surface population dynamics are partly driven by movement below ground and therefore surface abundance estimates represent a fraction of the superpopulation. As such, while surface habitat management remains an important conservation strategy for this species, periodic declines in apparent surface abundance do not necessarily indicate declines of the superpopulation associated with the spring habitat. creator: Nathan F. Bendik creator: Dee Ann Chamberlain creator: Thomas J. Devitt creator: Sarah E. Donelson creator: Bradley Nissen creator: Jacob D. Owen creator: Donelle Robinson creator: Blake N. Sissel creator: Kenneth Sparks uri: https://doi.org/10.7717/peerj.11246 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Planktonic associations between medusae (classes Scyphozoa and Hydrozoa) and epifaunal crustaceans link: https://peerj.com/articles/11281 last-modified: 2021-04-23 description: Jellyfish are known to carry various epibionts, including many of the subphylum Crustacea. However, the associations between gelatinous zooplankton and other invertebrates have been chronically overlooked. Crustacea, a massive clade of economically, ecologically, and culturally important species, includes many taxa that utilize gelatinous zooplankton for food, transport, and protection as both adults and juveniles. Here we compile 211 instances of epifaunal crustaceans recorded on Hydromedusae and Scyphomedusae from a century of literature. These include 78 identified crustacean species in 65 genera across nine orders found upon 37 Hydromedusa species and 48 Scyphomedusae. The crustacean life stage, location, nature of the association with the medusa, years, months, and depths are compiled to form a comprehensive view of the current state of the literature. Additionally, this review highlights areas where the current literature is lacking, particularly noting our poor understanding of the relationships between juvenile crabs of commercially valuable species and medusae. creator: Kaden Muffett creator: Maria Pia Miglietta uri: https://doi.org/10.7717/peerj.11281 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Muffett and Miglietta title: Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision link: https://peerj.com/articles/11310 last-modified: 2021-04-23 description: Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis). creator: Petr G. Garibian creator: Dmitry P. Karabanov creator: Anna N. Neretina creator: Derek J. Taylor creator: Alexey A. Kotov uri: https://doi.org/10.7717/peerj.11310 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Garibian et al.