Multilingual validation of the short form of the Unesp-Botucatu Feline Pain Scale (UFEPS-SF)
Background Pain is the leading cause of animal suffering, hence the importance of validated tools to ensure its appropriate evaluation and treatment. We aimed to test the psychometric properties of the short form of the Unesp-Botucatu Feline Pain Scale (UFEPS-SF) in eight languages. Methods The original scale was condensed from ten to four items. The content validation was performed by five specialists in veterinary anesthesia and analgesia. The English version of the scale was translated and back-translated into Chinese, French, German, Italian, Japanese, Portuguese and Spanish by fluent English and native speaker translators. Videos of the perioperative period of 30 cats submitted to ovariohysterectomy (preoperative, after surgery, after rescue analgesia and 24 h after surgery) were randomly evaluated twice (one-month interval) by one evaluator for each language unaware of the pain condition. After watching each video, the evaluators scored the unidimensional, UFEPS-SF and Glasgow composite multidimensional feline pain scales. Statistical analyses were carried out using R software for intra and interobserver reliability, principal component analysis, criteria concurrent and predictive validities, construct validity, item-total correlation, internal consistency, specificity, sensitivity, the definition of the intervention score for rescue analgesia and diagnostic uncertainty zone, according to the receiver operating characteristic (ROC) curve. Results UFEPS-SF intra- and inter-observer reliability were ≥0.92 and 0.84, respectively, for all observers. According to the principal component analysis, UFEPS-SF is a unidimensional scale. Concurrent criterion validity was confirmed by the high correlation between UFEPS-SF and all other scales (≥0.9). The total score and all items of UFEPS-SF increased after surgery (pain), decreased to baseline after analgesia and were intermediate at 24 h after surgery (moderate pain), confirming responsiveness and construct validity. Item total correlation of each item (0.68–0.83) confirmed that the items contributed homogeneously to the total score. Internal consistency was excellent (≥0.9) for all items. Both specificity (baseline) and sensitivity (after surgery) based on the Youden index was 99% (97–100%). The suggestive cut-off score for the administration of analgesia according to the ROC curve was ≥4 out of 12. The diagnostic uncertainty zone ranged from 3 to 4. The area under the curve of 0.99 indicated excellent discriminatory capacity of UFEPS-SF. Conclusions The UFEPS-SF and its items, assessed by experienced evaluators, demonstrated very good repeatability and reproducibility, content, criterion and construct validities, item-total correlation, internal consistency, excellent sensitivity and specificity and a cut-off point indicating the need for rescue analgesia in Chinese, French, English, German, Italian, Japanese, Portuguese and Spanish.
Luna et al. (2022) Multilingual validation of the short form of the Unesp-Botucatu Feline Pain Scale (UFEPS-SF). PeerJ 10:e13134 https://doi.org/10.7717/peerj.13134
Knowledge, attitudes and perceptions regarding human papillomavirus among university students in Hail, Saudi Arabia
Background Human papillomavirus (HPV) is a well-known cause of cervical cancer. The prevalence of HPV, insufficient preventive services, inadequate treatment access, socioeconomic conditions, certain cultural causes and values and opinions regarding cervical cancer have been established as factors contributing to the occurrence of cervical cancer in various parts of the world. Objective To determine university students’ knowledge, attitudes and perceptions regarding HPV and its vaccine. Material and Methods The present cross-sectional study included students enrolled at the University of Hail, Saudi Arabia. Data were collected from January to May 2020 using a previously validated 26-item questionnaire. Results A total of 386 participants responded to the survey; the response rate was 80%. The majority of the respondents (63%) were male and 332 (86%) respondents were single among the overall study population. Most respondents were aged 21–25 years (75.6%), followed by 26–30 years (12.7%). In total, 130 (33.7%) respondents reported that they had heard of HPV before, while 174 (45.1%) reported that HPV infections are rare in Saudi Arabia. Furthermore, 102 (26.4%) respondents thought that HPV causes genital warts, while almost 29.5% believed that HPV infection is a sexually transmitted disease. Nearly 76.2% of the respondents did not believe that HPV infection can occur without symptoms. Moreover, 53.4% of the respondents stated that they did not know the health problems associated with HPV infection, while 148 (38.8%) stated that cervical cancer is a health problem associated with HPV infection. When asked about their understanding of the HPV vaccine, nearly 267 (62.2%) respondents believed that there is no vaccine for HPV, while 239 (61.9%) believed that the vaccine does not minimise the risk of cervical cancer. In addition, the respondents reported that they would be far more likely to get an HPV vaccine if recommended by their doctors [relative importance index (RII) = 0.745], followed by their friends (RII = 0.675). Conclusion The present findings provide a clear understanding of university students’ knowledge, perceptions and attitudes regarding HPV; this information can be used to raise awareness by developing an effective educational strategy. However, further research with a larger sample size is recommended; such efforts would also aid in the development of educational services for various age ranges.
Alshammari et al. (2022) Knowledge, attitudes and perceptions regarding human papillomavirus among university students in Hail, Saudi Arabia. PeerJ 10:e13140 https://doi.org/10.7717/peerj.13140
RapidHRV: an open-source toolbox for extracting heart rate and heart rate variability
Heart rate and heart rate variability have enabled insight into a myriad of psychophysiological phenomena. There is now an influx of research attempting using these metrics within both laboratory settings (typically derived through electrocardiography or pulse oximetry) and ecologically-rich contexts (via wearable photoplethysmography, i.e., smartwatches). However, these signals can be prone to artifacts and a low signal to noise ratio, which traditionally are detected and removed through visual inspection. Here, we developed an open-source Python package, RapidHRV, dedicated to the preprocessing, analysis, and visualization of heart rate and heart rate variability. Each of these modules can be executed with one line of code and includes automated cleaning. In simulated data, RapidHRV demonstrated excellent recovery of heart rate across most levels of noise (>=10 dB) and moderate-to-excellent recovery of heart rate variability even at relatively low signal to noise ratios (>=20 dB) and sampling rates (>=20 Hz). Validation in real datasets shows good-to-excellent recovery of heart rate and heart rate variability in electrocardiography and finger photoplethysmography recordings. Validation in wrist photoplethysmography demonstrated RapidHRV estimations were sensitive to heart rate and its variability under low motion conditions, but estimates were less stable under higher movement settings.
Kirk et al. (2022) RapidHRV: an open-source toolbox for extracting heart rate and heart rate variability. PeerJ 10:e13147 https://doi.org/10.7717/peerj.13147
ATP11A promotes EMT by regulating Numb PRRL in pancreatic cancer cells
Purpose The Numb protein plays a vital role in tumor development. The main aim of this study was to identify ATP11A, which is associated with the biological behavior of pancreatic cancer, and elucidate its relationship with Numb and the underlying mechanism behind this relationship. Methods First, data retrieved from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEX) databases was used to investigate the expression of ATP11A mRNA and its relationship with Numb mRNA in pancreatic cancer. Western blot assays on 31 pairs of pancreatic cancer tissues and paracancerous tissues, and immunohistochemical assays on 81 pancreatic cancer specimens were performed in order to verify the expression of ATP11A in pancreatic cancer at the protein level. Next, ATP11A was overexpressed or knocked down to observe its effects on the invasion and migration ability of pancreatic cancer cells and the changes of downstream proteins. Rescue assays were conducted to determine the mechanism through which ATP11A affects Numb, ZEB1, Snail2 and other proteins. Furthermore, immunoprecipitation assays were performed to explore the interaction between ATP11A and Numb. Finally, pancreatic cancer cells were stimulated with TGFB1 and ATP11A expression was examined to explore whether the effect of ATP11A on EMT was TGFB dependent. Results At the mRNA level, the expression of ATP11A in pancreatic cancer tissues was significantly higher than in normal pancreatic tissues (P < 0.001). ATP11A expression was also highly correlated with Numb expression (R = 0.676). At the protein level, ATP11A expression in pancreatic cancer tissues was significantly higher than that in paracancerous tissues (P = 0.0009), and high ATP11A expression was also correlated with a worse prognosis. Moreover, our results showed that ATP11A can promote the invasion and migration of pancreatic cancer cells. Additionally, ATP11A could positively regulate the expression of Numb PRRL, Snail2 and ZEB1 proteins. The rescue experiment results showed that the enhancement effect of ATP11A on ZEB1/Snail2 was suppressed by the specific knockdown of Numb PRRL. In addition, the immunoprecipitation results showed that ATP11A could specifically bind to Numb PRRL. The expression of ATP11A was also upregulated after TGFB stimulation, suggesting that the effect of ATP11A on EMT is TGFB dependent. Conclusion ATP11A is significantly upregulated in pancreatic cancer tissues, where it promotes the invasion and migration ability of pancreatic cancer cells. It is also associated with adverse prognosis in pancreatic cancer. Furthermore, ATP11A affects the epithelial-to-mesenchymal transition (EMT) of pancreatic cancer by regulating the TGFB dependent Numb PRRL-ZEB1/Snail2 pathway.
Chen et al. (2022) ATP11A promotes EMT by regulating Numb PRRL in pancreatic cancer cells. PeerJ 10:e13172 https://doi.org/10.7717/peerj.13172
Novel decorating behaviour of silk retreats in a challenging habitat
Many ecological interactions of spiders with their potential prey and predators are affected by the visibility of their bodies and silk, especially in habitats with lower structural complexity that expose spiders. For instance, the surface of tree trunks harbours relatively limited structures to hide in and may expose residents to visual detection by prey and predators. Here we provide the first detailed description of the novel retreat building strategy of the tree trunk jumping spider Arasia mullion. Using fields surveys, we monitored and measured over 115 spiders and 554 silk retreats. These spiders build silk retreats on the exposed surface of tree trunks, where they remain as sedentary permanent residents. Furthermore, the spiders decorate the silk retreats with bark debris that they collect from the immediate surrounding. We discuss the role of silk decoration in the unusual sedentary behaviour of these spiders and the potential mechanisms that allow A. mullion to engineer their niche in a challenging habitat.
Aceves-Aparicio et al. (2022) Novel decorating behaviour of silk retreats in a challenging habitat. PeerJ 10:e12839 https://doi.org/10.7717/peerj.12839
Upside-down in volcanic ash: crown reconstruction of the early Permian seed fern Medullosa stellata with attached foliated fronds
Our understanding of fossil floras through geological time is mainly based on various differently preserved plant parts, often found isolated under restricted taphonomic circumstances. Preservation of whole plants is exceptionally rare in the geological record but provides the most reliable proof of ancient plants, especially those lacking a nearest living relative like the late Paleozoic pteridosperms. Among them, the medullosan seed ferns represent the largest and most essential systematic group. Medullosaleans are well known from the large Euramerican tropical swamp forests of Carboniferous age, but also from seasonally dry, clastic-soil habitats of Late Pennsylvanian–early Permian intramontane basins in central Europe. An exceptional taphonomic window that offered three-dimensional preservation of early Permian plants is located in Chemnitz, eastern Germany. Here, a forest ecosystem had been buried by pyroclastic deposits in a geological instant, 291 ± 2 Ma ago. Medullosaleans are both abundant and diverse in this striking autochthonous assemblage. The upper part of a Medullosa stellata var. typica individual broke at its top resulting from the overload of volcanic ash and was buried upside-down in the basal pyroclastics. The tree crown consists of the anatomically preserved apical stem, ten attached Alethopteris schneideri foliated fronds with Myeloxylon-type petioles and rachises. Though already discovered during the scientific excavation in 2010, the remarkable find required several years of preparation work, documentation, and reconstruction. The fronds were up to 3.5 m long, bifurcating, and bore numerous bipinnately compound pinnae preserved pulvinated in life position. The apical stem vascular system consists of a cylindrical peripheral vascular segment and up to 87 central accessory strands, each surrounded by manoxylic wood and secondary phloem. The reconstructed tree is supposed to have been self-supporting and of slender stature. Its architectural model is comparable to modern tree ferns or cycads and adapted to have grown in light-deficient lower-storey (sub-) tropical forests, usually not exceeding 15 m in height. Apical meristematic growth dominated, whereas only minor secondary growth occurred during ontogenesis. The densely attached frond bases followed a 3/8 phyllotaxis and were most likely abscised shortly after becoming photosynthetically inactive. A high water-conducting potential is assumed due to the tree’s cauline, petiolar and leaf vascular anatomies. Concerning the extensive leaf surface of the densely foliated fronds, considerable transpiration is hypothesised. Alethopteris schneideri foliage is stratigraphically significant for lower Permian (Asselian–Sakmarian) continental strata of central Europe, preferring habitats of wet clastic soils in sub-humid, seasonal palaeoclimate. The new insights provide a substantial step towards the first whole-plant concept of intramontane medullosaleans.
Luthardt et al. (2022) Upside-down in volcanic ash: crown reconstruction of the early Permian seed fern Medullosa stellata with attached foliated fronds. PeerJ 10:e13051 https://doi.org/10.7717/peerj.13051
Mutation breeding of Aspergillus niger by atmospheric room temperature plasma to enhance phosphorus solubilization ability
Background Phosphorus (P) is abundant in soils, including organic and inorganic forms. Nevertheless, most of P compounds cannot be absorbed and used by plants. Aspergillus niger v. Tiegh is a strain that can efficiently degrade P compounds in soils. Methods In this study, A. niger xj strain was mutated using Atmospheric Room Temperature Plasma (ARTP) technology and the strains were screened by Mo-Sb Colorimetry with strong P-solubilizing abilities. Results Compared with the A. niger xj strain, setting the treatment time of mutagenesis to 120 s, four positive mutant strains marked as xj 90–32, xj120–12, xj120–31, and xj180–22 had higher P-solubilizing rates by 50.3%, 57.5%, 55.9%, and 61.4%, respectively. Among them, the xj120–12 is a highly efficient P solubilizing and growth-promoting strain with good application prospects. The growth characteristics such as plant height, root length, and dry and fresh biomass of peanut (Arachis hypogaea L.) increased by 33.5%, 43.8%, 43.4%, and 33.6%, respectively. Besides available P, the chlorophyll and soluble protein contents also vary degrees of increase in the P-solubilizing mutant strains. Conclusions The results showed that the ARTP mutagenesis technology can improve the P solubilization abilities of the A. niger mutant strains and make the biomass of peanut plants was enhanced of mutant strains.
Peng et al. (2022) Mutation breeding of Aspergillus niger by atmospheric room temperature plasma to enhance phosphorus solubilization ability. PeerJ 10:e13076 https://doi.org/10.7717/peerj.13076
E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces
Background The SARS-CoV-2 pandemic reverberated, posing health and social hygiene obstacles throughout the globe. Mutant lineages of the virus have concerned scientists because of convergent amino acid alterations, mainly on the viral spike protein. Studies have shown that mutants have diminished activity of neutralizing antibodies and enhanced affinity with its human cell receptor, the ACE2 protein. Methods Hence, for real-time measuring of the impacts caused by variant strains in such complexes, we implemented E-Volve, a tool designed to model a structure with a list of mutations requested by users and return analyses of the variant protein. As a proof of concept, we scrutinized the spike-antibody and spike-ACE2 complexes formed in the variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma), by using contact maps depicting the interactions made amid them, along with heat maps to quantify these major interactions. Results The results found in this study depict the highly frequent interface changes made by the entire set of mutations, mainly conducted by N501Y and E484K. In the spike-Antibody complex, we have noticed alterations concerning electrostatic surface complementarity, breaching essential sites in the P17 and BD-368-2 antibodies. Alongside, the spike-ACE2 complex has presented new hydrophobic bonds. Discussion Molecular dynamics simulations followed by Poisson-Boltzmann calculations corroborate the higher complementarity to the receptor and lower to the antibodies for the K417T/E484K/N501Y (Gamma) mutant compared to the wild-type strain, as pointed by E-Volve, as well as an intensification of this effect by changes at the protein conformational equilibrium in solution. A local disorder of the loop α1′/β1′, as well its possible effects on the affinity to the BD-368-2 antibody were also incorporated to the final conclusions after this analysis. Moreover, E-Volve can depict the main alterations in important biological structures, as shown in the SARS-CoV-2 complexes, marking a major step in the real-time tracking of the virus mutant lineages. E-Volve is available at http://bioinfo.dcc.ufmg.br/evolve.
Dos Santos et al. (2022) E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. PeerJ 10:e13099 https://doi.org/10.7717/peerj.13099
The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia
Background Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics. Objectives We aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia. Methods Nasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT). Results We successfully identified 16 lineages and six clades out of 202 samples (male n = 116, female n = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave (n = 48, 23.8%) while Delta variants (AY.23, AY.24, AY.39, AY.42, AY.43 dan AY.79) were dominant during the second wave (n = 53, 26.2%) following the highest number of confirmed cases in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 (n = 44) and B.1.470 (n = 1). Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general. Conclusions We demonstrated a shift in SARS-CoV-2 variants from the first wave of COVID-19 to Delta variants in the second wave, during which the number of confirmed cases surpassed those in the first wave of COVID-19 pandemic. Higher proportion of unique mutations detected in Delta variants compared to the first wave variants indicated potential mutational effects on viral transmissibility that correlated with a higher incidence of confirmed cases. Genomic surveillance of circulating variants, especially those with higher transmissibility, should be continuously conducted to rapidly inform decision making and support outbreak preparedness, prevention, and public health response.
Prasetyoputri et al. (2022) The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. PeerJ 10:e13132 https://doi.org/10.7717/peerj.13132
The prognostic and clinicopathological significance of desmoglein 2 in human cancers: a systematic review and meta-analysis
Objective The survival and clinicopathological significance of desmoglein 2 (DSG2) in various cancers is controversial. Thus, we performed this systematic review and meta-analysis to explore the preliminary prognostic value of DSG2. Methods Eligible studies were identified from databases including PubMed, the Cochrane Library, Embase, Web of Science and Scopus. Hand searches were also conducted in relevant bibliographies. We then extracted and pooled hazard ratio (HR) of overall survival (OS) and odds ratio (OR) of clinicopathological features. Results A total of 11 eligible studies containing 1,488 patients were included. Our results demonstrated that in non-small cell lung cancer (NSCLC), high DSG2 expression is associated with poor OS. However, in digestive system cancer and female reproductive system cancer, there were no statistically significant associations between OS and DSG2. Conclusions Based on the findings of this study, high DSG2 expression is associated with worse prognosis in patients with NSCLC, and thus DSG2 expression could be a biomarker for prognosis in NSCLC.
Wang et al. (2022) The prognostic and clinicopathological significance of desmoglein 2 in human cancers: a systematic review and meta-analysis. PeerJ 10:e13141 https://doi.org/10.7717/peerj.13141