Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps
We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences (TMO)) in an automated procedure. We compare these results with data combined from two major public databases (DB): the Ocean Biodiversity Information System (OBIS), and the Global Biodiversity Information Facility (GBIF). Using DB and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined DB and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for extant cheilostomes for the first time, with peaks in the temperate zones. A total of 79% of the georeferenced species we retrieved from TMO (N = 1,408) and DB (N = 4,549) are non-overlapping. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that many marine latitudinal species richness patterns deviate from the canonical latitudinal diversity gradient (LDG). Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.
Kopperud et al. (2022) Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps. PeerJ 10:e13921 https://doi.org/10.7717/peerj.13921
A cholesterogenic gene signature for predicting the prognosis of young breast cancer patients
Purpose We aimed to establish a cholesterogenic gene signature to predict the prognosis of young breast cancer (BC) patients and then verified it using cell line experiments. Methods In the bioinformatic section, transcriptional data and corresponding clinical data of young BC patients (age ≤ 45 years) were downloaded from The Cancer Genome Atlas (TCGA) database for training set. Differentially expressed genes (DEGs) were compared between tumour tissue (n = 183) and normal tissue (n = 30). By using univariate Cox regression and multi COX regression, a five-cholesterogenic-gene signature was established to predict prognosis. Subgroup analysis and external validations of GSE131769 from the Gene Expression Omnibus (GEO) were performed to verify the signature. Subsequently, in experiment part, cell experiments were performed to further verify the biological roles of the five cholesterogenic genes in BC. Results In the bioinformatic section, a total of 97 upregulated genes and 124 downregulated cholesterogenic genes were screened as DEGs in the TCGA for training the model. A risk scoring signature contained five cholesterogenic genes (risk score = −1.169 × GRAMD1C −0.992 × NFKBIA + 0.432 × INHBA + 0.261 × CD24 −0.839 × ACSS2) was established, which could differentiate the prognosis of young BC patients between high-risk and low-risk group (<0.001). The prediction value of chelesterogenic gene signature in excellent with AUC was 0.810 in TCGA dataset. Then the prediction value of the signature was verified in GSE131769 with P = 0.033. In experiment part, although the downregulation of CD24, GRAMD1C and ACSS2 did not significantly affect cell viability, NFKBIA downregulation promoted the viability, colony forming ability and invasion capability of BC cells, while INHBA downregulation had the opposite effects. Conclusion The five-cholesterogenic-gene signature had independent prognostic value and robust reliability in predicting the prognosis of young BC patients. The cell experiment results suggested that NFKBIA played a protective role, while INHBA played the pro-cancer role in breast cancer.
Li et al. (2022) A cholesterogenic gene signature for predicting the prognosis of young breast cancer patients. PeerJ 10:e13922 https://doi.org/10.7717/peerj.13922
Levels and correlates of knowledge of teething among Saudi Arabian families
Background Parental knowledge of teething has been repeatedly investigated; however, little emphasis has been made on the associated sociodemographic factors with good knowledge of the parents and whether or not good knowledge is translated into adopting proper pain-relieving practices. The present study aims to firstly assess the knowledge level and practices of Saudi parents regarding teething and then explore associated sociodemographic variables with good knowledge of teething to determine the relation between parents’ knowledge of teething and their adoption of pain-relieving practices. Methods This cross-sectional study recruited parents from the social networking sites Facebook, Twitter, Instagram, and WhatsApp, and they were asked to answer a pretested three-part internationally accepted questionnaire. Data were examined using descriptive statistics, chi-square analysis, multivariate logistic regression analysis, and Spearman rank-order correlation coefficient analysis. Results One thousand four hundred ninety-nine parents responded and returned completed questionnaires. Of those, only 11.2% had good knowledge of teething. The majority of parents did not have basic knowledge of the teething period as well as believed that teething was associated with a runny nose (87.5%), diarrhea (77.9%), and sleep disturbance (72%). The results of multivariate logistic regression analysis indicated that parents with no primary school education (Odds Ratio: 0.29), or those who had an intermediate or secondary education level (OR: 0.55 and 0.78) were less likely to have good knowledge compared with parents who had a university degree. However, parents who earned intermediate monthly income (OR: 6.63) were more likely to have good knowledge of teething. With regards to practices used to relieve teething pain, inappropriate practices were observed regarding bottle feeding at night to soothe the child’s pain (72%) and applying topical analgesics to rub the gum (72.4%). A significant positive correlation was found between the knowledge score and the practice score of both fathers and mothers (r = 0.22 and 0.13, p < 0.0001). Conclusion A very low percentage of Saudi parents, mainly those with the highest education level and intermediate monthly income, had good knowledge of teething, which translated into appropriate practices to soothe the child’s pain regardless of the parent’s gender. Saudi parents should receive anticipatory guidance related to teething from all health professionals to ensure an uneventful teething period for their children.
Alkhozaim et al. (2022) Levels and correlates of knowledge of teething among Saudi Arabian families. PeerJ 10:e13948 https://doi.org/10.7717/peerj.13948
Exploring the anticancer and antioxidant properties of Vicia faba L. pods extracts, a promising source of nutraceuticals
Background Pulse crops are considered the major sources of proteins, dietary fiber, micronutrients, and bioactive phytochemicals. Among the numerous pulse crops, broad beans (Vicia faba L.) have received particular attention due to their nutraceutical, functional and economic importance. Our attention was mainly focused on the broad bean pods (VFs), which are the primary by-product of the domestic and industrial processing of broad beans and an attractive source of valuable ingredients. Methods In order to investigate the VFs properties, the flours from broad beans of three different harvest periods were extracted with acetone, methanol and 70% aqueous ethanol and the dried extracts were analyzed, qualitatively and quantitatively, and tested for their antioxidant through DPPH and ABTS assay and anticancer activities using the MTT assay and immunofluorescence analysis. Results The VF extracts demonstrated a good in vitro radical scavenging activity from the first stage of collection of all the V. faba L. extracts. Additionally, the extracts were tested for their cytotoxicity against a panel of cancer and normal cells and the outcomes indicated the ethanol extract as the most active against the melanoma cell line Sk-Mel-28, without affecting the viability of the normal cells. Finally, we found out that the ethanol extract interfered with the microtubules organization, leading to the cancer cells death by apoptosis.
Ceramella et al. (2022) Exploring the anticancer and antioxidant properties of Vicia faba L. pods extracts, a promising source of nutraceuticals. PeerJ 10:e13683 https://doi.org/10.7717/peerj.13683
Growth promotion and mycorrhizal colonization of Argan (Argania spinosa (L.) Skeels) inoculated with the edible desert truffle Tirmania nivea (Desf.) Trappe
This study presents the first evidence of the mycorrhizal compatibility between the edible desert truffle Tirmania nivea and the valuable fruit tree Argania spinosa. Seed germination trials demonstrated that soaking pre-treatment of argan seeds in hydrogen peroxide (9%) for five days combined with the application of a fungicide treatment on an inert sowing material maximized the seed germination of this tree species. The mycorrhizal synthesis was conducted under greenhouse conditions by inoculating, in vivo, the host plant seedlings with spores of T. nivea. The growth and mycorrhizal status of A. spinosa was assessed 15.5 months after inoculation. The desert truffle mycorrhization significantly promoted all the investigated morphological parameters of growth and improved the physiological performances of the host plant through enhancing plant water status and chlorophyll concentration. The mycorrhizal symbiosis led to the formation of typical desert truffle endomycorrhizae with intracellular coils. The resistance of A. spinosa to the harsh environmental conditions of desert habitats makes it a potential candidate for cultivation of desert truffles.
Khrizi et al. (2022) Growth promotion and mycorrhizal colonization of Argan (Argania spinosa (L.) Skeels) inoculated with the edible desert truffle Tirmania nivea (Desf.) Trappe. PeerJ 10:e13769 https://doi.org/10.7717/peerj.13769
Phosphate solubilizing microorganisms isolated from medicinal plants improve growth of mint
The current research project involves isolation and characterization of PSM (phosphate solubilizing microorganisms) from the rhizospheric soil of certain medicinal plants and to determine their effect on plant growth. Medicinal plants, Aloe vera, Bauhinia variegata, Cannabis sativa, Lantana camara and Mentha viridis were selected for the isolation of PSMs. Soil status of the selected medicinal plants was also checked. Phosphate solubilizing bacteria (PSB) were observed under stereomicroscope for their morphological characteristics and Gram’s staining. Phosphate solubilizing fungi (PSF) were also identified microscopically. Colony diameter, halo zone diameter and solubilization index were determined on PVK agar plates. TLC results indicated that citric acid was the most common acid produced by PSM strains. All strains were found to be non-pathogenic in pathogenicity test. A positive plant growth response to PSM inoculation was observed in all studies. In study 1, individual inoculation of PSM showed a significant increased effect on plant growth parameter i.e., fresh and dry weight, plant height and root and shoot length as compared to control. In study2, composite inoculation of PSM along with different P sources revealed that rock phosphate (RP) with PSM increased growth of plants significantly. The present study suggests that PSM inoculation along with RP amendment can be used as biofertilizer.
Tariq et al. (2022) Phosphate solubilizing microorganisms isolated from medicinal plants improve growth of mint. PeerJ 10:e13782 https://doi.org/10.7717/peerj.13782
Acute effects of variable resistance training on force, velocity, and power measures: a systematic review and meta-analysis
Objective Acute effects of variable resistance training (VRT) and constant resistance training (CRT) on neuromuscular performance are still equivocal. We aimed to determine the differences between VRT and CRT in terms of force, velocity, and power outcomes. Methods We searched PubMed, Web of Science, and SPORTDiscus electronic databases for articles until June 2021. Crossover design studies comparing force, velocity, and power outcomes while performing VRT and CRT were included. Two reviewers independently applied the modified version of the Cochrane Collaboration’s tool to assess the risk of bias. A three-level random effects meta-analyses and meta-regressions were used to compute standardized mean differences (SMDs) and 95% confidence intervals. Results We included 16 studies with 207 participants in the quantitative synthesis. Based on the pooled results, VRT generated greater mean velocity (SMD = 0.675; moderate Grading of Recommendations Assessment, Development and Evaluation (GRADE) quality evidence) and mean power (SMD = 1.022; low) than CRT. Subgroup analyses revealed that VRT considerably increased the mean velocity (SMD = 0.903; moderate) and mean power (SMD = 1.456; moderate) in the equated loading scheme and the mean velocity (SMD = 0.712; low) in the CRT higher loading scheme. However, VRT marginally significantly reduced peak velocity (SMD = −0.481; low) in the VRT higher loading scheme. Based on the meta-regression analysis, it was found that mean power (p = 0.014–0.043) was positively moderated by the contribution of variable resistance and peak velocity (p = 0.018) and peak power (p = 0.001–0.004) and RFD (p = 0.003) were positively moderated by variable resistance equipment, favoring elastic bands. Conclusions VRT provides practitioners with the means of emphasizing specific force, velocity, and power outcomes. Different strategies should be considered in context of an individual’s needs. Systematic review registration: PROSPERO CRD42021259205.
Shi et al. (2022) Acute effects of variable resistance training on force, velocity, and power measures: a systematic review and meta-analysis. PeerJ 10:e13870 https://doi.org/10.7717/peerj.13870
Complex interactions between p.His558Arg and linked variants in the sodium voltage-gated channel alpha subunit 5 (NaV1.5)
Common genetic polymorphisms may modify the phenotypic outcome when co-occurring with a disease-causing variant, and therefore understanding their modulating role in health and disease is of great importance. The polymorphic p.His558Arg variant of the sodium voltage-gated channel alpha subunit 5 (NaV1.5) encoded by the SCN5A gene is a case in point, as several studies have shown it can modify the clinical phenotype in a number of cardiac diseases. To evaluate the genetic backgrounds associated with this modulating effect, we reanalysed previous electrophysiological findings regarding the p.His558Arg variant and further assessed its patterns of genetic diversity in human populations. The NaV1.5 p.His558Arg variant was found to be in linkage disequilibrium with six other polymorphic variants that previously were also associated with cardiac traits in GWAS analyses. On account of this, incongruent reports that Arg558 allele can compensate, aggravate or have no effect on NaV1.5, likely might have arose due to a role of p.His558Arg depending on the additional linked variants. Altogether, these results indicate a major influence of the epistatic interactions between SCN5A variants, revealing also that phenotypic severity may depend on the polymorphic background associated to each individual genome.
Lopes-Marques et al. (2022) Complex interactions between p.His558Arg and linked variants in the sodium voltage-gated channel alpha subunit 5 (NaV1.5). PeerJ 10:e13913 https://doi.org/10.7717/peerj.13913
Aluminum phosphate sludge as a phosphorus source for maize production under low soil phosphorus availability
Background With increasing food demand as a consequence of the growing world population, there is a corresponding demand for additional sources of phosphorus (P). Alum-phosphate (Al-P) sludge is a by-product of wastewater treatment and can be a good source of P. In this study, the response of maize (Zea mays L.) to Al-P sludge was tested. Maize was chosen as the test crop due to its prevalent use as human and animal food and as a source of biofuel. The objective of the study was to investigate Al-P sludge as a source of P compared to a commercial fertilizer (monoammonium phosphate, MAP). Methods A growth chamber assay was conducted over four cropping cycles (45 d each). The application rate was 9.7, 19.4, 29.1 and 38.8 mg P kg−1 dry soil. Amendments were applied once at the start of the first cropping cycle. Plants were harvested after each cycle and pots were re-seeded. Dry matter yield (DMY), total P uptake, Al-P uptake, soil total P and Olsen-P concentrations, pH, and EC were measured. Results DMY was significantly greater in pots amended with Al-P sludge than in pots treated with MAP. There was a significant rate × cropping cycle interaction effect on DMY with the differences among rates in cycle 1 different from those in cycle 4. Phosphorus uptake depended on cropping cycle, P source and P application rate. With sludge uptake higher than MAP in all cycles, the highest P uptake was observed at the highest application rate except for cycle 2 where this was observed at the rate of 29.1 mg kg−1. For MAP, phosphorus recovery efficiency (PRE) at the highest rate was significantly greater than that at the lowest rate whereas PRE in cycle 1 was significantly higher than that in cycle 4. In the first two cycles, aluminum uptake was negligible in both MAP and Al-P sludge treatments; however, in cycles 3 and 4, there was significantly more Al in maize from sludge amended pots. Our results show that Al-P sludge was as effective as MAP in supplying enough P for biomass yield. We, therefore, conclude that Al-P sludge could be an alternative source of P, especially for growing maize as feedstock for bioenergy.
Environmental Contamination and Remediation
Tolofari et al. (2022) Aluminum phosphate sludge as a phosphorus source for maize production under low soil phosphorus availability. PeerJ 10:e13885 https://doi.org/10.7717/peerj.13885
The blunted vascular endothelial growth factor-A (VEGF-A) response to high-altitude hypoxia and genetic variants in the promoter region of the VEGFA gene in Sherpa highlanders
Background Sherpa highlanders demonstrate extraordinary tolerance to hypoxia at high altitudes, which may be achieved by mechanisms promoting microcirculatory blood flow and capillary density at high altitudes for restoring oxygen supply to tissues. Vascular endothelial growth factors (VEGFs) are important signaling proteins involved in vasculogenesis and angiogenesis which are stimulated by hypoxia. We hypothesize that the VEGF-A, the major member of the VEGF family, and the gene encoding VEGF-A (VEGFA) play a part in the adaptation to high-altitude hypoxia in Sherpa highlanders. Methods Fifty-one Sherpa highlanders in Namche Bazaar village at a high altitude of 3,440 meters (m) above sea level and 76 non-Sherpa lowlanders in Kathmandu city at 1,300 m in Nepal were recruited for the study. Venous blood was sampled to obtain plasma and extract DNA from each subject. The plasma VEGF-A concentrations were measured and five single-nucleotide polymorphisms (SNPs, rs699947, rs833061, rs1570360, rs2010963, and rs3025039) in the VEGFA were genotyped. The VEGF-A levels and allelic frequencies of the SNPs were compared between the two populations. Results A significant difference in oxygen saturation (SpO2) was observed between the two ethnic groups locating at different elevations (93.7 ± 0.2% in Sherpas at 3,440 m vs. 96.7 ± 0.2% in non-Sherpas at 1,300 m, P < 0.05). The plasma VEGF-A concentration in the Sherpas at high altitude was on the same level as that in the non-Sherpas at low altitude (262.8 ± 17.9 pg/ml vs. 266.8 ± 21.8 pg/ml, P = 0.88). This result suggested that the plasma VEGF-A concentration in Sherpa highlanders was stable despite a high-altitude hypoxic stimulus and that therefore the Sherpas exhibited a phenotype of blunted response to hypoxic stress. Moreover, the allele frequencies of the SNPs rs699947, rs833061, and rs2010963 in the promoter region of the VEGFA were different between the Sherpa highlanders and non-Sherpa lowlanders (corrected P values = 3.30 ×10−5, 4.95 ×10−4, and 1.19 ×10−7, respectively). Conclusions Sherpa highlanders exhibited a blunted VEGF-A response to hypoxia at high altitudes, which was speculated to be associated with the distinctive genetic variations of the SNPs and haplotype in the promoter region of VEGFA in Sherpa highlanders.
Droma et al. (2022) The blunted vascular endothelial growth factor-A (VEGF-A) response to high-altitude hypoxia and genetic variants in the promoter region of the VEGFA gene in Sherpa highlanders. PeerJ 10:e13893 https://doi.org/10.7717/peerj.13893