Habitat suitability of four threatened Himalayan species: Asiatic black bear, common leopard, musk deer, and snow leopard
Background Biodiversity conservation is becoming challenging day by day. For this, it is essential to understand the distribution, habitat, and impact of anthropogenic activities on animals at risk. We assessed the suitable habitats and anthropogenic impacts on Asiatic black bears, common leopards, musk deer, and snow leopards in and outside the protected areas of Gandaki Province, Nepal. Methods We collected the presence locations of Asiatic black bears, common leopards, musk deer, and snow leopards based on scats and other signs. We employed the Maximum Entropy (MaxEnt) tool to identify suitable habitats of our studied species and their anthropogenic impacts on them. Results The total suitable habitat of the common leopard was found to be 6,052 km2, followed by the Asiatic black bear (5,819 km2), snow leopard (4,447 km2), and musk deer (1,690 km2) in Gandaki Province. Most of the areas of suitable habitat for common leopards and Asiatic black bears were outside the protected areas, and for musk deer and snow leopards were inside the protected areas. Elevation was the most important variable determining habitat suitability of Asiatic black bear, common leopard, and musk deer, whereas the distance to water was the most important variable determining habitat suitability of snow leopard. Asiatic black bears, common leopards, and musk deer face significant anthropogenic impacts, but snow leopards face some anthropogenic impacts. Conclusion Managing these animals’ habitats inside and outside protected areas is essential. Hence, biodiversity conservation and livelihood opportunities should be balanced in the Himalayas on a win-win basis.
Malla et al. (2023) Habitat suitability of four threatened Himalayan species: Asiatic black bear, common leopard, musk deer, and snow leopard. PeerJ 11:e16085 https://doi.org/10.7717/peerj.16085
Exploring the relationship between nutritional intake and menstrual cycle in elite female athletes
This study aimed to examine potential variations in nutritional intake among female athletes, including top-level, throughout the menstrual cycle. A total 122 female athletes participated in the study, documenting their food consumption over a 3-day period. The menstrual status of female athletes was also assessed, and using the survey results, the phase of the menstrual cycle (the follicular, early luteal, or late luteal) during which each meal was recorded was determined. Consequently, the meal records were categorized into the respective three phases. The findings of this study indicated that there were no notable disparities in nutritional intake, encompassing energy, protein, fat, carbohydrate, calcium, iron, and fiber, across the three phases of the menstrual cycle. The results imply that female athletes may experience comparatively smaller variations in nutrient intake related to the menstrual cycle. This could be attributed to the higher energy requirements of female athletes because of their rigorous training. This study underscores the significance of accounting for the population when examining nutrient intake changes associated with the menstrual cycle.
Miyamoto et al. (2023) Exploring the relationship between nutritional intake and menstrual cycle in elite female athletes. PeerJ 11:e16108 https://doi.org/10.7717/peerj.16108
DeepMethylation: a deep learning based framework with GloVe and Transformer encoder for DNA methylation prediction
DNA methylation is a crucial topic in bioinformatics research. Traditional wet experiments are usually time-consuming and expensive. In contrast, machine learning offers an efficient and novel approach. In this study, we propose DeepMethylation, a novel methylation predictor with deep learning. Specifically, the DNA sequence is encoded with word embedding and GloVe in the first step. After that, dilated convolution and Transformer encoder are utilized to extract the features. Finally, full connection and softmax operators are applied to predict the methylation sites. The proposed model achieves an accuracy of 97.8% on the 5mC dataset, which outperforms state-of-the-art methods. Furthermore, our predictor exhibits good generalization ability as it achieves an accuracy of 95.8% on the m1A dataset. To ease access for other researchers, our code is publicly available at https://github.com/sb111169/tf-5mc.
Wang et al. (2023) DeepMethylation: a deep learning based framework with GloVe and Transformer encoder for DNA methylation prediction. PeerJ 11:e16125 https://doi.org/10.7717/peerj.16125
Seroprevalence of SARS-CoV-2 anti-spike IgG antibody among COVID-19 vaccinated individuals residing in Surabaya, East Java, Indonesia
Background To limit the SARS-CoV-2 transmission, the Indonesian government launched a COVID-19 vaccination program in January 2021. Studies on the clinical treatment and implementation of COVID-19 vaccination have shown promising results; however, it is necessary to estimate the effectiveness of the vaccines. With the ongoing COVID-19 pandemic, studies have highlighted the impact of COVID-19 vaccines, especially CoronaVac, on Indonesian healthcare workers. To get a better picture of how the vaccines work in Indonesia, it is necessary to estimate the prevalence of SARS-CoV-2 anti-S IgG antibody induced by the COVID-19 vaccine in individuals who have already received two-to-three doses of vaccines. Materials and Methods Four-hundred and ninety-six whole-blood samples were collected from participants residing in Surabaya, East Java, Indonesia, who received a minimum of a two-dose COVID-19 vaccine. Serums were then isolated from the blood and subjected to detect SARS-CoV-2 anti-S IgG antibodies using a lateral flow immunochromatographic assay. Results The prevalence of positive anti-S-IgG antibodies was 91.7% (455/496) in all participants receiving a minimum of a two-dose COVID-19 vaccine. As many as 209 (85.3%) and 141 (96.6%) participants were seropositive for receiving CoronaVac and AstraZeneca, respectively. Meanwhile, all participants receiving two-dose CoronaVac with one booster dose of Moderna (105/100%) were seropositive (p < 0.05). Age, comorbidity, and time after the last vaccine were significantly correlated with seropositivity (p < 0.05). Conclusion Different vaccines might produce different antibody responses. Adopting a stronger policy regarding the administration of booster doses might be beneficial to elicit positive anti-S-IgG antibodies, especially among older individuals, those with comorbid diseases, and those with a longer time after the second vaccination dose.
Megasari et al. (2023) Seroprevalence of SARS-CoV-2 anti-spike IgG antibody among COVID-19 vaccinated individuals residing in Surabaya, East Java, Indonesia. PeerJ 11:e16142 https://doi.org/10.7717/peerj.16142
Classification and prediction of Klebsiella pneumoniae strains with different MLST allelic profiles via SERS spectral analysis
The Gram-negative non-motile Klebsiella pneuomoniae is currently a major cause of hospital-acquired (HA) and community-acquired (CA) infections, leading to great public health concern globally, while rapid identification and accurate tracing of the pathogenic bacterium is essential in facilitating monitoring and controlling of K. pneumoniae outbreak and dissemination. Multi-locus sequence typing (MLST) is a commonly used typing approach with low cost that is able to distinguish bacterial isolates based on the allelic profiles of several housekeeping genes, despite low resolution and labor intensity of the method. Core-genome MLST scheme (cgMLST) is recently proposed to sub-type and monitor outbreaks of bacterial strains with high resolution and reliability, which uses hundreds or thousands of genes conserved in all or most members of the species. However, the method is complex and requires whole genome sequencing of bacterial strains with high costs. Therefore, it is urgently needed to develop novel methods with high resolution and low cost for bacterial typing. Surface enhanced Raman spectroscopy (SERS) is a rapid, sensitive and cheap method for bacterial identification. Previous studies confirmed that classification and prediction of bacterial strains via SERS spectral analysis correlated well with MLST typing results. However, there is currently no similar comparative analysis in K. pneumoniae strains. In this pilot study, 16 K. pneumoniae strains with different sequencing typings (STs) were selected and a phylogenetic tree was constructed based on core genome analysis. SERS spectra (N = 45/each strain) were generated for all the K. pneumoniae strains, which were then comparatively classified and predicted via six representative machine learning (ML) algorithms. According to the results, SERS technique coupled with the ML algorithm support vector machine (SVM) could achieve the highest accuracy (5-Fold Cross Validation = 100%) in terms of differentiating and predicting all the K. pneumoniae strains that were consistent to corresponding MLSTs. In sum, we show in this pilot study that the SERS-SVM based method is able to accurately predict K. pneumoniae MLST types, which has the application potential in clinical settings for tracing dissemination and controlling outbreak of K. pneumoniae in hospitals and communities with low costs and high rapidity.
Zhang et al. (2023) Classification and prediction of Klebsiella pneumoniae strains with different MLST allelic profiles via SERS spectral analysis. PeerJ 11:e16161 https://doi.org/10.7717/peerj.16161
Systematic and meta-based evaluation of the relationship between the built environment and physical activity behaviors among older adults
Objectives Existing assertions about the relationship between various factors of the built environment and physical activity behaviors are inconsistent and warrant further exploration and analysis. Methods This study systematically searched PubMed, Embase, Web of Science, Scopus, the Cochrane Library and Google Scholar for the effect of the built environment on the physical activity behaviors of older adults. R software was used to calculate the meta-estimated odds ratio with a 95% confidence interval. Simultaneously, the quality of included studies was evaluated using an observational study quality evaluation standard recommended by American health care quality and research institutions. Results A total of 16 original researches were included in this meta-analysis and eight factors of the built environment were evaluated. These factors which ranked from high to low according to their impact were traffic safety (OR = 1.58, 95% CI [1.14–2.20]), destination accessibility (OR = 1.24, 95% CI [1.06–1.44]), aesthetics of sports venues (OR = 1.21, 95% CI [1.07–1.37]), virescence of sports venues (OR = 1.14, 95% CI [1.06–1.23]), building density (OR = 1.07, 95% CI [1.02–1.13]). Additionally, it seemed that there was no potential association between mixed land use (OR = 1.01, 95% CI [0.92–1.10]), the quality of pedestrian facilities (OR = 1.00, 95% CI [0.92–1.08]) or commercial facilities (OR = 0.94, 95% CI [0.88–1.00]) and physical activity behaviors of older adults. Conclusions The built environment has been found to exhibit a significant relationship with the physical activity behaviors of older adults. It is proposed that factors such as traffic safety, destination accessibility, aesthetics of sports venues, virescence of sports venues, and building density be given more consideration when aiming to promote physical activity levels among older adults.
You et al. (2023) Systematic and meta-based evaluation of the relationship between the built environment and physical activity behaviors among older adults. PeerJ 11:e16173 https://doi.org/10.7717/peerj.16173
Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers
Background The non-recombining region of the human Y chromosome (NRY) is a strictly paternally inherited genetic marker and the best material to trace the paternal lineages of populations. Y chromosomal short tandem repeat (Y-STR) is characterized by high polymorphism and paternal inheritance pattern, so it has been widely used in forensic medicine and population genetic research. This study aims to understand the genetic distribution of Y-STRs in the Guizhou Dong population, provide reference data for forensic application, and explore the phylogenetic relationships between the Guizhou Dong population and other comparison populations. Methods Based on the allele profile of 44 Y-markers in the Guizhou Dong group, we estimate their allele frequencies and haplotype frequencies. In addition, we also compare the forensic application efficiency of different Y-STR sets in the Guizhou Dong group. Finally, genetic relationships among Guizhou Dong and other reference populations are dissected by the multi-dimensional scaling and the phylogenetic tree. Results A total of 393 alleles are observed in 312 Guizhou Dong individuals for these Y-markers, with allele frequencies ranging from 0.0032 to 0.9679. The haplotype diversity and discriminatory capacity for these Y-markers in the Guizhou Dong population are 0.99984 and 0.97440, respectively. The population genetic analyses of the Guizhou Dong group and other reference populations show that the Guizhou Dong group has the closest genetic relationship with the Hunan Dong population, and followed by the Guizhou Tujia population. Conclusions In conclusion, these 44 Y-markers can be used as an effective tool for male differentiation in the Guizhou Dong group. The haplotype data in this study not only enrich the Y-STR data of different ethnic groups in China, but also have important significance for population genetics and forensic research.
Zhang et al. (2023) Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers. PeerJ 11:e16183 https://doi.org/10.7717/peerj.16183
Age and socio-economic status affect dengue and COVID-19 incidence: spatio-temporal analysis of the 2020 syndemic in Buenos Aires City
In early 2020, Argentina experienced the worst dengue outbreak in its history, concomitant with first-to-date increasing COVID-19 cases. Dengue epidemics in temperate Argentina have already been described as spatially heterogeneous; in the previous 2016 outbreak, transmission occurred 7.3 times more frequently in slums compared to the rest of Buenos Aires City (CABA). These informal settlements have deficient sanitary conditions, precarious housing and high incidence of social vulnerabilities. The purpose of this work was to study the spatio-temporal patterns of the 2020 dengue epidemic in CABA in relation to socio-economic living conditions of its inhabitants and its interaction with the onset of COVID-19. The study considered the period between Jan 1st and May 30th 2020. Dengue and COVID-19 databases were obtained from the National Health Surveillance System; each record was anonymized and geo-localized. The city was divided according to census tracts and grouped in four socio-economic strata: slums, high, mid and low residential. An aligned-rank transform ANOVA was performed to test for differences in the incidence of dengue and COVID-19, and age at death due to COVID-19, among socio-economic strata, four age categories and their interaction. The incidence by cluster was calculated with a distance matrix up to 600 m from the centroid. Spatial joint dengue and COVID-19 risk was estimated by multiplying the nominal risk for each disease, defined from 1 (low) to 5 (high) according to their quantiles. During the study period, 7,175 dengue cases were registered in CABA (incidence rate 23.3 cases per 10,000 inh), 29.2% of which occurred in slums. During the same period, 8,809 cases of COVID-19 were registered (28.6 cases per 10,000 inh); over half (51.4%) occurred in slums, where the median age of cases (29 years old) was lower than in residential areas (42 years old). The mean age of the deceased was 58 years old in slums compared to 79 years old outside. The percentage of deaths in patients under 60 years old was 56% in slums compared to 8% in the rest of the city. The incidence of both diseases was higher in slums than in residential areas for most age categories. Spatial patterns were heterogeneous: dengue presented higher incidence values in the southern sector of the city and the west, and low values in highly urbanized quarters, whereas COVID-19 presented higher values in the east, south, high populated areas and slums. The lowest joint risk clusters were located mainly in high residential areas, whereas high joint risk was observed mainly in the south, some western clusters, the historical part of the city and center north. The social epidemiological perspective of dengue and COVID-19 differed, given that socio environmental heterogeneity influenced the burden of both viruses in a different manner. Despite the overwhelming effect of the COVID-19 pandemic, health care towards other diseases, especially in territories with pre-existing vulnerabilities, should not be unattended.
Carbajo et al. (2023) Age and socio-economic status affect dengue and COVID-19 incidence: spatio-temporal analysis of the 2020 syndemic in Buenos Aires City. PeerJ 11:e14735 https://doi.org/10.7717/peerj.14735
Research on the coupling coordination and driving role of urbanization and ecological resilience in the middle and lower reaches of the Yangtze River
Background The growth of urbanization in the 20th and 21st centuries has resulted in unprecedented ecological security issues. The imbalance between urban development and internal ecological security is a growing concern. Methods Based on the urban development process and the characteristics of ecosystem resilience, the corresponding urbanization evaluation system (“scale-structure-benefit”) and ecosystem resilience assessment model (“resistance-adaptability-restoring”) were constructed to explore the changes in each dimension as well as to analyze the spatial and temporal changes and driving effects of the coupled coordination level of urbanization and ecological resilience using the coupled coordination degree (CCD) model and geographically and temporally weighted regression (GTWR). Results (1) From 2005 to 2020, urbanization levels increased (from 0.204 to 0.264, respectively), whereas the level of ecological resilience gradually decreased (from 0.435 to 0.421, respectively). The spatial distribution of urbanization is rather steady, with a “high-northeast low-southwest” pattern of regional distribution; however, the spatial distribution pattern of ecological resilience is essentially the reverse. (2) During the study period, there was an improvement in the level of coordination between urbanization and ecological resilience, with an increase from 0.524 to 0.540. However, the main coordination type remained the same, with over 46% being at the basic coordination stage. The relative development type was dominated by the lagging urbanization stage, with the lagging ecological resilience and synchronous development stages accounting for a smaller proportion, and the space was distributed in a block-like cluster. (3) The running results of the GTWR show that the core dimensions of the whole region are scale, benefit, and structure, and the impact of each dimension shows obvious spatial heterogeneity. Cities with different levels of relative development also have different central dimensions. This research will provide support for the coordination of urban development in areas where economic construction and ecological resilience are not coordinated, and will contribute to the sustainable development of urban areas.
Spatial and Geographic Information Science
Xiao et al. (2023) Research on the coupling coordination and driving role of urbanization and ecological resilience in the middle and lower reaches of the Yangtze River. PeerJ 11:e15869 https://doi.org/10.7717/peerj.15869
Genome-wide analysis of the heat shock transcription factor family reveals saline-alkali stress responses in Xanthoceras sorbifolium
The heat shock transcription factor (HSF) family is involved in regulating growth, development, and abiotic stress. The characteristics and biological functions of HSF family member in X. sorbifolium, an important oil and ornamental plant, have never been reported. In this study, 21 XsHSF genes were identified from the genome of X. sorbifolium and named XsHSF1-XsHSF21 based on their chromosomal positions. Those genes were divided into three groups, A, B, and C, containing 12, one, and eight genes, respectively. Among them, 20 XsHSF genes are located on 11 chromosomes. Protein structure analysis suggested that XsHSF proteins were conserved, displaying typical DNA binding domains (DBD) and oligomerization domains (OD). Moreover, HSF proteins within the same group contain specific motifs, such as motif 5 in the HSFC group. All XsHSF genes have one intron in the CDS region, except XsHSF1 which has two introns. Promoter analysis revealed that in addition to defense and stress responsiveness elements, some promoters also contained a MYB binding site and elements involved in multiple hormones responsiveness and anaerobic induction. Duplication analysis revealed that XsHSF1 and XsHSF4 genes were segmentally duplicated while XsHSF2, XsHSF9, and XsHSF13 genes might have arisen from transposition. Expression pattern analysis of leaves and roots following salt-alkali treatment using qRT-PCR indicated that five XsHSF genes were upregulated and one XsHSF gene was downregulated in leaves upon NaCl treatment suggesting these genes may play important roles in salt response. Additionally, the expression levels of most XsHSFs were decreased in leaves and roots following alkali-induced stress, indicating that those XsHSFs may function as negative regulators in alkali tolerance. MicroRNA target site prediction indicated that 16 of the XsHSF genes may be regulated by multiple microRNAs, for example XsHSF2 might be regulated by miR156, miR394, miR395, miR408, miR7129, and miR854. And miR164 may effect the mRNA levels of XsHSF3 and XsHSF17, XsHSF9 gene may be regulated by miR172. The expression trends of miR172 and miR164 in leaves and roots on salt treatments were opposite to the expression trend of XsHSF9 and XsHSF3 genes, respectively. Promoter analysis showed that XsHSFs might be involved in light and hormone responses, plant development, as well as abiotic stress responses. Our results thus provide an overview of the HSF family in X. sorbifolium and lay a foundation for future functional studies to reveal its roles in saline-alkali response.
Li et al. (2023) Genome-wide analysis of the heat shock transcription factor family reveals saline-alkali stress responses in Xanthoceras sorbifolium. PeerJ 11:e15929 https://doi.org/10.7717/peerj.15929