Obesity phenotypes and their relationships with atrial fibrillation
Background This study assessed the associations of metabolic obesity phenotypes with the risk of atrial fibrillation (Afib). Methods This prospective cohort study categorized Taiwanese adults according to their body mass index (BMI) and metabolic health status at baseline. We assigned the participants to the underweight (BMI < 18.5 kg/m2), normal weight (BMI = 18.5–23.9 kg/m2), and overweight/obesity groups (BMI ≥ 24 kg/m2). Metabolically healthy was defined as absence of hypertension, diabetes, and hyperlipidemia and the presence of healthy metabolic profiles. Results In total, 5,742 adults were included. During a median follow-up of 13.7 years, 148 patients developed Afib. Compared to the metabolically healthy normal weight group, the risk of Afib was significantly higher than those in the metabolically unhealthy overweight/obesity (hazard ratio = 2.20, 95% confidence interval [1.12–4.33]) and metabolically unhealthy normal weight groups (HR = 2.64, 95% CI [1.34–5.17]). Additionally, the point estimate suggested a 1.97-fold greater risk among the metabolically healthy overweight/obesity group, although this difference was not significant given the wide confidence interval (HR = 1.97, 95% CI [0.80–4.86]). Conclusion Our results demonstrated the relationships of metabolic health and weight regarding the risk of Afib in Taiwanese adults. The Afib risk among metabolic and obesity phenotypes is associated with a metabolically unhealthy status. A trend toward a higher Afib risk with obesity among metabolically healthy subjects was observed. However, the result was not robust and it still suggested further study.
Tsai et al. (2021) Obesity phenotypes and their relationships with atrial fibrillation. PeerJ 9:e12342 https://doi.org/10.7717/peerj.12342
The inconsistent microbiota of Budu, the Malaysian fermented anchovy sauce, revealed through 16S amplicon sequencing
Budu is a Malaysian fermented anchovy sauce produced by immersing small fishes into a brine solution for 6 to 18 months. Microbial enzymes are known to contribute to fermentation; however, not much is known about the microbial community in Budu. Therefore, a better understanding of the Budu microbiome is necessary to improve the quality, consistency, and safety of the Budu products. In this study, we collected 60 samples from 20 bottles of Budu produced by seven manufacturers. We analyzed their microbiota using V3–V4 16S rRNA amplicon sequencing when we first opened the bottle (month 0), as well as 3 and 7 months post-opening (months 3 and 7). Tetragenococcus was the dominant genus in many samples, reaching a maximum proportion of 98.62%, but was found in low abundance, or absent, in other samples. When Budu samples were not dominated by a dominant taxa, we observed a wider genera diversity such as Staphylococcus, Acinetobacter, Halanaerobium and Bacillus. While the taxonomic composition was relatively stable across sampling periods, samples from two brands showed a sudden increase in relative abundance of the genus Chromobacterium at month 7. Based on prediction of metagenome functions, non-Tetragenococcus-dominated samples were predicted to have enriched functional pathways related to amino acid metabolism and purine metabolism compared to Tetragenococcus-dominated samples; these two pathways are fundamental to fermentation quality and health attributes of fish sauce. Among the non-Tetragenococcus-dominated samples, contributions towards amino acid metabolism and purine metabolism were biased towards the dominant taxa when species evenness is low, while in samples with higher species evenness, the contributions towards the two pathways were predicted to be evenly distributed between taxa. Our results demonstrated that the utility of 16S sequencing to assess batch variation in fermented food production. The distinct microbiota was shown to correlate with characteristic metagenome function including functions potentially related to fermented food nutrition and quality.
Md Zoqratt et al. (2021) The inconsistent microbiota of Budu, the Malaysian fermented anchovy sauce, revealed through 16S amplicon sequencing. PeerJ 9:e12345 https://doi.org/10.7717/peerj.12345
In silico identification, characterization expression profile of WUSCHEL-Related Homeobox (WOX) gene family in two species of kiwifruit
The WUSCHEL (WUS)-related homeobox (WOX) gene family is a class of plant-specific transcriptional factors and plays a crucial role in forming the shoot apical meristem and embryonic development, stem cell maintenance, and various other developmental processes. However, systematic identification and characterization of the kiwifruit WOX gene family have not been studied. This study identified 17 and 10 WOX genes in A. chinensis (Ac) and A. eriantha (Ae) genomes, respectively. Phylogenetic analysis classified kiwifruit WOX genes from two species into three clades. Analysis of phylogenetics, synteny patterns, and selection pressure inferred that WOX gene families in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in WOX gene number and distribution. Ten conserved motifs were identified in the kiwifruit WOX genes, and motif architectures of WOXs belonging to different clades highly diverged. The cis-element analysis and expression profiles investigation indicated the functional differentiation of WOX genes and identified the potential WOXs in response to stresses. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit WOXs.
Feng et al. (2021) In silico identification, characterization expression profile of WUSCHEL-Related Homeobox (WOX) gene family in two species of kiwifruit. PeerJ 9:e12348 https://doi.org/10.7717/peerj.12348
A novel role for apatinib in enhancing radiosensitivity in non-small cell lung cancer cells by suppressing the AKT and ERK pathways
Background Radioresistance is still the major cause of radiotherapy failure and poor prognosis in patients with non-small cell lung cancer (NSCLC). Apatinib (AP) is a highly selective inhibitor of vascular endothelial growth factor receptor 2 (VEGFR2). Whether and how AP affects radiosensitivity in NSCLC remains unknown. The present study aimed to explore the radiosensitization effect of AP in NSCLC and its underlying mechanism as a radiosensitizer. Methods The NSCLC cell lines A549 and LK2 were treated with AP, ionizing radiation (IR), or both AP and IR. Expression of VEGFR2 was analyzed by western blot and RT-PCR. Cell proliferation was measured using CCK-8 and colony formation assays. Apoptosis and cell cycle distribution in NSCLC cells were analyzed by flow cytometry. Nuclear phosphorylated histone H2AX foci immunofluorescence staining was performed to evaluate the efficacy of the combination treatment. Western blot was used to explore the potential mechanisms of action. Results AP inhibited cell proliferation in a dose- and time-dependent manner. Flow cytometry analysis indicated that AP significantly increased radiation-induced apoptosis. Colony formation assays revealed that AP enhanced the radiosensitivity of NSCLC cells. AP strongly restored radiosensitivity by increasing IR-induced G2/M phase arrest. AP effectively inhibited repair of radiation-induced DNA double-strand breaks. Western blot analysis showed that AP enhanced radiosensitivity by downregulating AKT and extracellular signal-regulated kinase (ERK) signaling. Conclusion Our findings suggest that AP may enhance radiosensitivity in NSCLC cells by blocking AKT and ERK signaling. Therefore, AP may be a potential clinical radiotherapy synergist and a novel small-molecule radiosensitizer in NSCLC. Our study fills a gap in the field of anti-angiogenic drugs and radiosensitivity.
Li et al. (2021) A novel role for apatinib in enhancing radiosensitivity in non-small cell lung cancer cells by suppressing the AKT and ERK pathways. PeerJ 9:e12356 https://doi.org/10.7717/peerj.12356
fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences
Compositionally-biased (CB) regions in biological sequences are enriched for a subset of sequence residue types. These can be shorter regions with a concentrated bias (i.e., those termed ‘low-complexity’), or longer regions that have a compositional skew. These regions comprise a prominent class of the uncharacterized ‘dark matter’ of the protein universe. Here, I report the latest version of the fLPS package for the annotation of CB regions, which includes added consideration of DNA sequences, to label the eight possible biased regions of DNA. In this version, the user is now able to restrict analysis to a specified subset of residue types, and also to filter for previously annotated domains to enable detection of discontinuous CB regions. A ‘thorough’ option has been added which enables the labelling of subtler biases, typically made from a skew for several residue types. In the output, protein CB regions are now labelled with bias classes reflecting the physico-chemical character of the biasing residues. The fLPS 2.0 package is available from: https://github.com/pmharrison/flps2 or in a Supplemental File of this paper.
Harrison (2021) fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences. PeerJ 9:e12363 https://doi.org/10.7717/peerj.12363
Using historical dip net data to infer absence of flatwoods salamanders in stochastic environments
Local extinction and undetected presence are two very different biological phenomena, but they can be challenging to differentiate. Stochastic environments hamper the development of standardized monitoring schemes for wildlife, and make it more challenging to plan and evaluate the success of conservation efforts. To avoid reintroductions of species at risk that could jeopardize extant populations, managers attempting translocation events require a higher level of confidence that a failure to confirm presence represents a true absence. For many pond breeding amphibians, monitoring of the breeding population occurs indirectly through larval surveys. Larval development and successful recruitment only occurs after a sequence of appropriate environmental conditions, thus it is possible for a breeding population of adults to exist at a site but for detectability of the species to be functionally zero. We investigate how annual variability in detection influences long-term monitoring efforts of Reticulated Flatwoods Salamanders (Ambystoma bishopi) breeding in 29 wetlands in Florida. Using 8 years of historic dip net data, we simulate plausible monitoring scenarios that incorporate environmental stochasticity into estimates of detection probability. We found that annual variation in environmental conditions precluded a high degree of certainty in predicting site status for low-intensity monitoring schemes. Uncertainty was partly alleviated by increasing survey effort, but even at the highest level of sampling intensity assessed, multiple years of monitoring are required to confidently determine presence/absence at a site. Combined with assessments of habitat quality and landscape connectivity, our results can be used to identify sites suitable for reintroduction efforts. Our methodologies can be generally applied to increase the effectiveness of surveys for diverse organisms for which annual variability in detectability is known.
Brooks et al. (2021) Using historical dip net data to infer absence of flatwoods salamanders in stochastic environments. PeerJ 9:e12388 https://doi.org/10.7717/peerj.12388
Rapid authenticity testing of artificially bred green turtles (Chelonia mydas) using microsatellite and mitochondrial DNA markers
Sea turtles are threatened by climate change and human activity, and their global populations continue to decline sharply. The Chinese government encourages artificial breeding of sea turtles to reduce the use of wild populations. However, artificial breeding of sea turtles is still fairly difficult, and some facilities may illegally purchase wild turtle eggs and then sell incubated turtles by marketing them as artificially bred turtles, which adds another threat to an already endangered species. Therefore, it is necessary to find a reliable method to distinguish the authenticity of artificially bred individuals. In this study, we investigated a turtle farm in southern China, that contained more than 400 green turtles, which were claimed to have been bred in captivity. Parentage testing of turtles from this farm was successfully conducted using two nuclear microsatellites combined with a mitochondrial D-loop DNA marker. Genetic matching of all 19 adults and randomly selected 16 juvenile turtles revealed that none of the juvenile turtles had a matching parent combination among the adult turtles. Therefore, we speculated that the green turtles in this farm were from the wild and that their origin of birth was mainly the Sulu Sea. The methods and molecular markers used in this study could be a reference for rapid authenticity testing of green turtles in future forensic enforcement and population management.
Zhang et al. (2021) Rapid authenticity testing of artificially bred green turtles (Chelonia mydas) using microsatellite and mitochondrial DNA markers. PeerJ 9:e12410 https://doi.org/10.7717/peerj.12410
Psychometric evaluation of an Italian custom 4-item short form of the PROMIS anxiety item bank in immune-mediated inflammatory diseases: an item response theory analysis
Background There has recently been growing interest in the roles of inflammation in contributing to the development of anxiety in people with immune-mediated inflammatory diseases (IMID). Patient-reported outcome measures can facilitate the assessment of physical and psychological functioning. The National Institutes of Health (NIH)’s Patient-Reported Outcomes Measurement Information System (PROMIS®) is a set of Patient-Reported Outcomes (PROs) that cover physical appearance, mental health, and social health. The PROMIS has been built through an Item Response Theory approach (IRT), a model-based measurement in which trait level estimates depend on both persons’ responses and on the properties of the items that were administered. The aim of this study is to test the psychometric properties of an Italian custom four-item Short Form of the PROMIS Anxiety item bank in a cohort of outpatients with IMIDs. Methods We selected four items from the Italian standard Short Form Anxiety 8a and administered them to consecutive outpatients affected by Inflammatory Bowel disease (n = 246), rheumatological (n = 100) and dermatological (n = 43) diseases, and healthy volunteers (n = 280). Data was analyzed through an Item Response Theory (IRT) analysis in order to evaluate the psychometric properties of the Italian adaptation of the PROMIS anxiety short form. Results Taken together, Confirmatory Factor Analysis and Exploratory Factor analysis suggest that the unidimensionality assumption of the instrument holds. The instrument has excellent reliability from a Classical Theory of Test (CTT) standpoint (Cronbach’s α = 0.93, McDonald’s ω = 0.92). The 2PL Graded Response Model (GRM) model provided showed a better goodness of fit as compared to the 1PL GRM model, and local independence assumption appears to be met overall. We did not find signs of differential item functioning (DIF) for age and gender, but evidence for uniform (but not non-uniform) DIF was found in three out of four items for the patient vs. control group. Analysis of the test reliability curve suggested that the instrument is most reliable for higher levels of the latent trait of anxiety. The groups of patients exhibited higher levels of anxiety as compared to the control group (ps < 0.001, Bonferroni-corrected). The groups of patients were not different between themselves (p = 1, Bonferroni-corrected). T-scores based on estimated latent trait and raw scores were highly correlated (Pearson’s r = 0.98) and led to similar results. Discussion The Italian custom four-item short form from the PROMIS anxiety form 8a shows acceptable psychometric properties both from a CTT and an IRT standpoint. The Test Reliability Curve shows that this instrument is mostly informative for people with higher levels of anxiety, making it particularly suitable for clinical populations such as IMID patients.
Liuzza et al. (2021) Psychometric evaluation of an Italian custom 4-item short form of the PROMIS anxiety item bank in immune-mediated inflammatory diseases: an item response theory analysis. PeerJ 9:e12100 https://doi.org/10.7717/peerj.12100
Polycaprolactone nanofibers as an adjuvant strategy for Tamoxifen release and their cytotoxicity on breast cancer cells
Breast cancer is the second leading cause of death in women, and tamoxifen citrate (TMX) is accepted widely for the treatment of hormone receptor–positive breast cancers. Several local drug-delivery systems, including nanofibers, have been developed for antitumor treatment. Nanofibers are biomaterials that mimic the natural extracellular matrix, and they have been used as controlled release devices because they enable highly efficient drug loading. The purpose of the present study was to develop polycaprolactone (PCL) nanofibers incorporating TMX for use in the treatment of breast tumors. Pristine PCL and PCL-TMX nanofibers were produced by electrospinning and characterized physiochemically using different techniques. In addition, an in vitro study of TMX release from the nanofibers was performed. The PCL-TMX nanofibers showed sustained TMX release up to 14 h, releasing 100% of the TMX. The Resazurin reduction assay was used to evaluate the TMX cytotoxicity on MCF-7 breast cancer cell line and PBMCs human. The PCL-TMX nanofiber was cytotoxic toPBMCs and MCF-7. Based on these results, the PCL-TMX nanofibers developed have potential as an alternative for local chronic TMX use for breast cancer treatment, however tissue tests must be done.
Pinzón-García et al. (2021) Polycaprolactone nanofibers as an adjuvant strategy for Tamoxifen release and their cytotoxicity on breast cancer cells. PeerJ 9:e12124 https://doi.org/10.7717/peerj.12124
Land-use change influence soil quality parameters at an ecologically fragile area of YongDeng County of Gansu Province, China
Dry ecosystems, despite their relative levels of aridity, are very diverse, and play a vital role in the livelihoods of many dryland inhabitants. It is therefore critical to investigate the relationship between land-use change and soil quality parameters to offer a scientific basis for optimizing land-use planning and improving soil quality status in dry ecosystems and ecologically vulnerable areas. This study, therefore, analyzed the physicochemical properties of soils in five different land-use types namely farmland, abandoned farmland, natural grassland, artificial lemon forest, and poplar woodland at YongDeng County. The soil quality status of the aforementioned land-use types was also evaluated through Principal component analysis. The results revealed that abandoned farmland and natural grassland recorded the highest average values of soil coarse particles of 24.0% and 23.4% respectively compared to the other land-use types. The highest average value (46.1%) of fine soil particles was recorded in poplar woodland followed by natural grassland (36.6%) and the average value of very fine soil particles was higher in farmland (40.8%) and artificial lemon woodland (38.3%) than in the other land-use types. The average value of clayey particles was highest in farmland (11.1%), followed by artificial lemon woodland (9.3%), and abandoned farmland (6.5%), then poplar woodland which recorded an average value of (4.2%). The average values of Soil water content, soil pH, soil electrical conductivity, and soil total nitrogen content were significantly higher in farmland compared to the other land-use types. Soil organic carbon content was significantly higher in abandoned farmland at (P < 0.03) and lemon woodland at (P < 0.01) than in farmlands, natural grasslands, and poplar stands. The soil quality indicators of the different land-use types were significantly correlated with each other. Among them, the correlation coefficient of each evaluation index was highest in poplar woodland, followed by natural grassland, lower in farmland and artificial lemon woodland, and lowest in abandoned farmland. The overall soil quality scores were in the following order: farmland > abandoned farmland > 0 > grassland > lemon woodland > poplar woodland. In the study area, the soil quality of farmland that has been finely managed and naturally restored to grassland following abandonment is superior, whereas the soil quality of natural grassland, artificial lemon woodland, and poplar forest land is substandard. The comprehensive analysis of soil quality demonstrates that conservation tillage and fine management of water-irrigated farmland, as well as the natural conversion of abandoned farmland to grassland, can significantly improve the soil quality of sandy soils, reduce water and soil loss, increase fertility, and gradually improve regional ecological environmental conditions.
Adingo et al. (2021) Land-use change influence soil quality parameters at an ecologically fragile area of YongDeng County of Gansu Province, China. PeerJ 9:e12246 https://doi.org/10.7717/peerj.12246