Development of the breastfeeding support scale to measure breastfeeding support from lay and professional persons, and its predictive validity in Japan
Background International and national organizations recommend exclusive breastfeeding for the first 6 months of life, but many women stop earlier. Lay and professional persons can support mothers’ efforts to overcome breastfeeding difficulties. Considering breastfeeding support to comprise emotional support, practical help, and information offered to women who desire to breastfeed (by professionals, family members, and others), we developed and tested a scale to measure it in Japan. Methods A total of 31 items were generated by literature review and from the authors’ clinical experiences. Those items were tested with 243 mothers who visited public health centers in Tokyo for their infant’s health check-up 3 months after birth. Breastfeeding support and infant feeding status were then assessed 5 months after birth. All the data were collected by using self-administered questionnaires. Results On the basis of the results of factor analysis, the number of items was reduced to 11. There were three factors: support from breastfeeding peers and from people in specifically named healthcare professions, practical help, and support from people the mother can rely on to help meet emotional needs and address breastfeeding concerns. Internal-consistency reliability (alpha) of scores on the 11-item scale was 0.83 when measured 3 months postpartum and 0.85 when measured 5 months postpartum. Higher scores on the 11-item scale 3 months postpartum were associated with more breastfeeding exclusivity both at that time (Kruskal–Wallis test, chi-squared = 14.871, df = 3, n = 211, p = 0.002, eta-squared = 0.071) and also 5 months postpartum (Kruskal–Wallis test, chi-squared = 8.556, df = 3, n = 159, p = 0.036, eta-squared = 0.054). Further, the area under the Receiver Operating Characteristic curve was 0.73 (95% CI [0.57–0.88]), which indicates that scores on the 11-item scale 3 months postpartum may be useful to predict which mothers will be less exclusive in breastfeeding 5 months postpartum. In conclusion, scores on this 11-item scale were reasonably reliable and valid for measuring breastfeeding support provided by lay and professional persons to mothers in Japan. Further research is required to evaluate this scale’s applicability in other settings.
Nanishi et al. (2021) Development of the breastfeeding support scale to measure breastfeeding support from lay and professional persons, and its predictive validity in Japan. PeerJ 9:e11779 https://doi.org/10.7717/peerj.11779
Relationship between impulsivity and suicide among the rural elderly in China: a case-control psychological autopsy study
Background The relationship between impulsivity and suicide is inconsistent in different populations. Hence, the relationship between impulsivity and suicide still needs to be studied among the elderly population. The present study intends to explore the relationship between impulsivity and suicide among the rural Chinese elderly. Methods A case-control psychological autopsy study was conducted from February 1, 2014 to December 18, 2015 among rural residents over the age of 60 who died by suicide. The sample consisted of 242 suicides as the case group and 242 living individuals as the control group. Data on demographic characteristics, impulsivity, previous history of suicide attempts, social support, negative life events, and suicidal behavior were collected. Results Our study found that impulsivity increased the risk of suicide. The case group showed a higher Barratt Impulsiveness Scale score compared with the control group (p < 0.001), which indicates that impulsivity was higher among the elderly suicides. In addition, regression analyses show that impulsivity (odds ratio: 1.03, 95% confidence interval: 1.01–1.06) is an independent risk factor of suicide, after controlling for the effects of marital status, education, family annual income, being left behind, social support, and negative life events. Finally, compared with elderly who do not have a history of attempted suicide, elderly with a history of attempted suicide showed higher impulsivity (p = 0.001).
Zhou et al. (2021) Relationship between impulsivity and suicide among the rural elderly in China: a case-control psychological autopsy study. PeerJ 9:e11801 https://doi.org/10.7717/peerj.11801
ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review
Antibiotic and herbicide resistance genes are the most common marker genes for plant transformation to improve crop yield and food quality. However, there is public concern about the use of resistance marker genes in food crops due to the risk of potential gene flow from transgenic plants to compatible weedy relatives, leading to the possible development of “superweeds” and antibiotic resistance. Several selectable marker genes such as aph, nptII, aaC3, aadA, pat, bar, epsp and gat, which have been synthesized to generate transgenic plants by genetic transformation, have shown some limitations. These marker genes, which confer antibiotic or herbicide resistance and are introduced into crops along with economically valuable genes, have three main problems: selective agents have negative effects on plant cell proliferation and differentiation, uncertainty about the environmental effects of many selectable marker genes, and difficulty in performing recurrent transformations with the same selectable marker to pyramid desired genes. Recently, a simple, novel, and affordable method was presented for plant cells to convert non-metabolizable phosphite (Phi) to an important phosphate (Pi) for developing cells by gene expression encoding a phosphite oxidoreductase (PTXD) enzyme. The ptxD gene, in combination with a selection medium containing Phi as the sole phosphorus (P) source, can serve as an effective and efficient system for selecting transformed cells. The selection system adds nutrients to transgenic plants without potential risks to the environment. The ptxD/Phi system has been shown to be a promising transgenic selection system with several advantages in cost and safety compared to other antibiotic-based selection systems. In this review, we have summarized the development of selection markers for genetic transformation and the potential use of the ptxD/Phi scheme as an alternative selection marker system to minimize the future use of antibiotic and herbicide marker genes.
Dormatey et al. (2021) ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review. PeerJ 9:e11809 https://doi.org/10.7717/peerj.11809
The importance of spawning behavior in understanding the vulnerability of exploited marine fishes in the U.S. Gulf of Mexico
The vulnerability of a fish stock to becoming overfished is dependent upon biological traits that influence productivity and external factors that determine susceptibility or exposure to fishing effort. While a suite of life history traits are traditionally incorporated into management efforts due to their direct association with vulnerability to overfishing, spawning behavioral traits are seldom considered. We synthesized the existing biological and fisheries information of 28 fish stocks in the U.S. Gulf of Mexico to investigate relationships between life history traits, spawning behavioral traits, management regulations, and vulnerability to fishing during the spawning season. Our results showed that spawning behavioral traits were not correlated with life history traits but improved identification of species that have been historically overfished. Species varied widely in their intrinsic vulnerability to fishing during spawning in association with a broad range of behavioral strategies. Extrinsic vulnerability was high for nearly all species due to exposure to fishing during the spawning season and few management measures in place to protect spawning fish. Similarly, several species with the highest vulnerability scores were historically overfished in association with spawning aggregations. The most vulnerable species included several stocks that have not been assessed and should be prioritized for further research and monitoring. Collectively, the results of this study illustrate that spawning behavior is a distinct aspect of fish ecology that is important to consider for predictions of vulnerability and resilience to fisheries exploitation.
Biggs et al. (2021) The importance of spawning behavior in understanding the vulnerability of exploited marine fishes in the U.S. Gulf of Mexico. PeerJ 9:e11814 https://doi.org/10.7717/peerj.11814
Effect of modified pomace on copper migration via riverbank soil in southwest China
To explore the effects of modified pomace on copper migration via the soil on the banks of the rivers in northern Sichuan and Chongqing, fruit pomace (P) and ethylene diamine tetra-acetic acid (EDTA) modified P (EP) were evenly added (1% mass ratio) to the soil samples of Guanyuan, Nanbu, Jialing, and Hechuan from the Jialing River; Mianyang and Suining from the Fu River; and Guangan and Dazhou from the Qu River. The geochemical characteristics and migration rules of copper in different amended soils were simulated by column experiment. Results showed that the permeation time of copper in each soil column was categorized as EP-amended > P-amended > original soil, and the permeation time of amended soil samples at different locations was Jialing > Suining > Mianyang > Guangan > Dazhou > Nanbu > Guanyuan > Hechuan. Meanwhile, the average flow rate of copper in each soil column showed a reverse trend with the permeation time. Copper in exchangeable, carbonate, and iron–manganese oxide forms decreased with the increase of vertical depth in the soil column, among which the most evident decreases appeared in the carbonate-bonding form. The copper accumulation in different locations presented a trend of Jialing > Suining > Mianyang > Guangan > Dazhou > Nanbu > Guangyuan > Hechuan, and the copper content under the same soil showed EP-amended > P-amended > original soil. The copper proportion of the carbonate form was the highest in each soil sample, followed by the exchangeable form. The proportions of iron-manganese oxide and organic matter forms were relatively small. A significant correlation was observed between the cation exchange capacity and the copper content in exchangeable and carbonate forms. Moreover, total organic carbon and copper contents were negatively correlated.
Environmental Contamination and Remediation
Chen et al. (2021) Effect of modified pomace on copper migration via riverbank soil in southwest China. PeerJ 9:e11844 https://doi.org/10.7717/peerj.11844
PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly
DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets.
Borry et al. (2021) PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly. PeerJ 9:e11845 https://doi.org/10.7717/peerj.11845
Distribution, source, water quality and health risk assessment of dissolved heavy metals in major rivers in Wuhan, China
Heavy metals are released into the water system through various natural processes and anthropogenic activities, thus indirectly or directly endangering human health. The distribution, source, water quality and health risk assessment of dissolved heavy metals (V, Mn, Fe, Co, Ni, Zn, As, Mo, Sb) in major rivers in Wuhan were analyzed by correlation analysis (CA), principal component analysis (PCA), heavy metal pollution index (HPI), hazard index (HI) and carcinogenic risk (CR). The results showed that the spatial variability of heavy metal contents was pronounced. PCA and CA results indicated that natural sources controlled Mn, Fe, Co, Ni and Mo, and industrial emissions were the dominant factor for V, Zn and Sb, while As was mainly from the mixed input of urban and agricultural activities. According to the heavy metal pollution index (HPI, ranging from 23.74 to 184.0) analysis, it should be noted that As and Sb contribute most of the HPI values. The health risk assessment using HI and CR showed that V and Sb might have a potential non-carcinogenic risk and As might have a potential carcinogenic risk to adults and children in the study area (CR value exceeded target risk 10−4). At the same time, it was worth noting that As might have a potential non-carcinogenic risk for children around QLR (HI value exceeded the threshold value 1). The secular variation of As and Sb should be monitor in high-risk areas. The results of this study can provide important data for improving water resources management efficiency and heavy metal pollution prevention in Wuhan.
Zhang et al. (2021) Distribution, source, water quality and health risk assessment of dissolved heavy metals in major rivers in Wuhan, China. PeerJ 9:e11853 https://doi.org/10.7717/peerj.11853
Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan
Background Bread wheat is the most important cereal in Kazakhstan, where it is grown on over 12 million hectares. One of the major constraints affecting wheat grain yield is drought due to the limited water supply. Hence, the development of drought-resistant cultivars is critical for ensuring food security in this country. Therefore, identifying quantitative trait loci (QTLs) associated with drought tolerance as an essential step in modern breeding activities, which rely on a marker-assisted selection approach. Methods A collection of 179 spring wheat accessions was tested under irrigated and rainfed conditions in Northern Kazakhstan over three years (2018, 2019, and 2020), during which data was collected on nine traits: heading date (HD), seed maturity date (SMD), plant height (PH), peduncle length (PL), number of productive spikes (NPS), spike length (SL), number of kernels per spike (NKS), thousand kernel weight (TKW), and kernels yield per m2 (YM2). The collection was genotyped using a 20,000 (20K) Illumina iSelect SNP array, and 8,662 polymorphic SNP markers were selected for a genome-wide association study (GWAS) to identify QTLs for targeted agronomic traits. Results Out of the total of 237 discovered QTLs, 50 were identified as being stable QTLs for irrigated and rainfed conditions in the Akmola region, Northern Kazakhstan; the identified QTLs were associated with all the studied traits except PH. The results indicate that nine QTLs for HD and 11 QTLs for SMD are presumably novel genetic factors identified in the irrigated and rainfed conditions of Northern Kazakhstan. The identified SNP markers of the QTLs for targeted traits in rainfed conditions can be applied to develop new competitive spring wheat cultivars in arid zones using a marker-assisted selection approach.
Amalova et al. (2021) Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan. PeerJ 9:e11857 https://doi.org/10.7717/peerj.11857
Proteomic analysis reveals some common proteins in the kidney stone matrix
Background Proteins are the most abundant component of kidney stone matrices and their presence may reflect the process of the stone’s formation. Many studies have explored the proteomics of urinary stones and crystals. We sought to comprehensively identify the proteins found in kidney stones and to identify new, reliable biomolecules for use in nephrolithiasis research. Methods We conducted bioinformatics research in November 2020 on the proteomics of urinary stones and crystals. We used the ClusterProfiler R package to transform proteins into their corresponding genes and Ensembl IDs. In each study we located where proteomic results intersected to determine the 20 most frequently identified stone matrix proteins. We used the Human Protein Atlas to obtain the biological information of the 20 proteins and conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis to explore their biological functions. We also performed immunohistochemistry to detect the expression of the top five stone matrix proteins in renal tissue. Results We included 19 relevant studies for analysis. We then identified 1,409 proteins in the stone matrix after the duplicates were removed. The 20 most-commonly identified stone matrix proteins were: S100A8, S100A9, uromodulin, albumin, osteopontin, lactotransferrin, vitamin K-dependent protein Z, prothrombin, hemoglobin subunit beta, myeloperoxidase, mannan-binding lectin serine protease 2, lysozyme C, complement C3, serum amyloid P-component, cathepsin G, vitronectin, apolipoprotein A-1, eosinophil cationic protein, fibrinogen alpha chain, and apolipoprotein D. GO and KEGG analysis revealed that these proteins were typically engaged in inflammation and immune response.Immunohistochemistry of the top five stone matrix proteins in renal tissue showed that the expression of S100A8, S100A9, and osteopontin increased, while uromodulin decreased in kidney stone patients. Albumin was rarely expressed in the kidney with no significant difference between healthy controls and kidney stone patients. Conclusion Proteomic analysis revealed some common inflammation-related proteins in the kidney stone matrix. The role of these proteins in stone formation should be explored for their potential use as diagnostic biomarkers and therapeutic targets for urolithiasis.
Yang et al. (2021) Proteomic analysis reveals some common proteins in the kidney stone matrix. PeerJ 9:e11872 https://doi.org/10.7717/peerj.11872
HepGentox: a novel promising HepG2 reportergene-assay for the detection of genotoxic substances in complex mixtures
Background In risk assessment, genotoxicity is a key factor to determine the safety for the consumer. Most in vitro genotoxicity assays were developed for the assessment of pure substances. However, in recent years more attention has been given to complex mixtures, where usually low amounts of a substance are present. For high-throughput screening, a toxicologically sensitive assay should be used, covering a broad range of genotoxic substances and detecting them at low concentrations. HepG2 cells have been recommended as one of the prime candidates for genotoxicity testing, as they are p53 competent, less prone towards cytotoxic effects and tend to have some metabolic activity. Methods A HepG2 liver cell line was characterized for its suitability for genotoxicity assessment. For this, a luciferase based reporter gene assay revolving around the p53 pathway was validated for the analysis of pure substances and of complex mixtures. Further, the cell’s capability to detect genotoxins correctly with and without an exogenous metabolizing system, namely rat liver S9, was assessed. Results The assay proved to have a high toxicological sensitivity (87.5%) and specificity (94%). Further, the endogenous metabolizing system of the HepG2 cells was able to detect some genotoxins, which are known to depend on an enzymatic system. When complex mixtures were added this did not lead to any adverse effects concerning the assays performance and cytotoxicity was not an issue. Discussion The HepGentox proved to have a high toxicological sensitivity and specificity for the tested substances, with similar or even lower lowest effective concentration (LEC) values, compared to other regulatory mammalian assays. This combines some important aspects in one test system, while also being less time and material consuming and covering several genotoxicity endpoints. As the assay performs well with and without an exogenous metabolizing system, no animal liver fractions have to be used, which application is discussed controversially and is considered to be expensive and laborious in sample testing. Because of this, the HepGentox is suitable for a cost-efficient first screening approach to obtain important information with human cells for further approaches, with a relatively fast and easy method. Therefore, the HepGentox is a promising assay to detect genotoxic substances correctly in complex mixtures even at low concentrations, with the potential for a high throughput application. In a nutshell, as part of an in vitro bioassay test battery, this assay could provide valuable information for complex mixtures.
Pinter et al. (2021) HepGentox: a novel promising HepG2 reportergene-assay for the detection of genotoxic substances in complex mixtures. PeerJ 9:e11883 https://doi.org/10.7717/peerj.11883