Classification of major species in the sericite–Artemisia desert grassland using hyperspectral images and spectral feature identification
Background The species composition of and changes in grassland communities are important indices for inferring the number, quality and community succession of grasslands, and accurate monitoring is the foundation for evaluating, protecting, and utilizing grassland resources. Remote sensing technology provides a reliable and powerful approach for measuring regional terrain information, and the identification of grassland species by remote sensing will improve the quality and effectiveness of grassland monitoring. Methods Ground hyperspectral images of a sericite–Artemisia desert grassland in different seasons were obtained with a Soc710 VP imaging spectrometer. First-order differential processing was used to calculate the characteristic parameters. Analysis of variance was used to extract the main species, namely, Seriphidium transiliense (Poljak), Ceratocarpus arenarius L., Petrosimonia sibirica (Pall), bare land and the spectral characteristic parameters and vegetation indices in different seasons. On this basis, Fisher discriminant analysis was used to divide the samples into a training set and a test set at a ratio of 7:3. The spectral characteristic parameters and vegetation indices were used to identify the three main plants and bare land. Results The selection of parameters with significant differences (P < 0.05) between the recognition objects effectively distinguished different land features, and the identification parameters also differed due to differences in growth period and species. The overall accuracy of the recognition model established by the vegetation index decreased in the following order: June (98.87%) > September (91.53%) > April (90.37%). The overall accuracy of the recognition model established by the feature parameters decreased in the following order: September (89.77%) > June (88.48%) > April (85.98%). Conclusions The recognition models based on vegetation indices in different months are superior to those based on feature parameters, with overall accuracies ranging from 1.76% to 9.40% higher. Based on hyperspectral image data, the use of vegetation indices as identification parameters can enable the identification of the main plants in sericite–Artemisia desert grassland, providing a basis for further quantitative classification of the species in community images.
Liu et al. (2024) Classification of major species in the sericite–Artemisia desert grassland using hyperspectral images and spectral feature identification. PeerJ 12:e17663 https://doi.org/10.7717/peerj.17663
Associations between SNPs and vegetation indices: unraveling molecular insights for enhanced cultivation of tea plant (Camellia sinensis (L.) O. Kuntze)
Background Breeding programs for nutrient-efficient tea plant varieties could be advanced by the combination of genotyping and phenotyping technologies. This study was aimed to search functional SNPs in key genes related to the nitrogen-assimilation in the collection of tea plant Camellia sinensis (L.) Kuntze. In addition, the objective of this study was to reveal efficient vegetation indices for phenotyping of nitrogen deficiency response in tea collection. Methods The study was conducted on the tea plant collection of Camellia sinensis (L.) Kuntze of Western Caucasus grown without nitrogen fertilizers. Phenotypic data was collected by measuring the spectral reflectance of leaves in the 350–1100 nm range calculated as vegetation indices by the portable hyperspectral spectrometer Ci710s. Single nucleotide polymorphisms were identified in 30 key genes related to nitrogen assimilation and tea quality. For this, pooled amplicon sequencing, SNPs annotation and effect prediction with SnpEFF tool were used. Further, a linear regression model was applied to reveal associations between the functional SNPs and the efficient vegetation indices. Results PCA and regression analysis revealed significant vegetation indices with high R2 values (more than 0.5) and the most reliable indices to select ND-tolerant genotypes were established: ZMI, CNDVI, RENDVI, VREI1, GM2, GM1, PRI, and Ctr2, VREI3, VREI2. The largest SNPs frequency was observed in several genes, namely F3’5’Hb, UFGTa, UFGTb, 4Cl, and AMT1.2. SNPs in NRT2.4, PIP, AlaDC, DFRa, and GS1.2 were inherent in ND-susceptible genotypes. Additionally, SNPs in AlaAT1, MYB4, and WRKY57, were led to alterations in protein structure and were observed in ND-susceptible tea genotypes. Associations were revealed between flavanol reflectance index (FRI) and SNPs in ASNb and PIP, that change the amino acids. In addition, two SNPs in 4Cl were associated with water band index (WBI). Conclusions The results will be useful to identify tolerant and susceptible tea genotypes under nitrogen deficiency. Revealed missense SNPs and associations with vegetation indices improve our understanding of nitrogen effect on tea quality. The findings in our study would provide new insights into the genetic basis of tea quality variation under the N-deficiency and facilitate the identification of elite genes to enhance tea quality.
Kuzmina et al. (2024) Associations between SNPs and vegetation indices: unraveling molecular insights for enhanced cultivation of tea plant (Camellia sinensis (L.) O. Kuntze). PeerJ 12:e17689 https://doi.org/10.7717/peerj.17689
Treatment gap and barriers to access mental healthcare among women with postpartum depression symptoms in Pakistan
Background and Objectives Postpartum depression (PPD) is prevalent among women after childbirth, but accessing mental healthcare for PPD is challenging. This study aimed to assess the treatment gap and barriers to mental healthcare access for women with PPD symptoms living in Punjab, Pakistan. Methods A multicenter cross-sectional study was conducted in five populous cities of Punjab from January to June 2023 by administering the questionnaire to the women using stratified random sampling. A total of 3,220 women in first 6 months postpartum were screened using the Edinburgh Postnatal Depression Scale. Of them, 1,503 women scored thirteen or above, indicating potential depressive disorder. Interviews were conducted to explore help-seeking behavior and barriers to accessing mental healthcare. Descriptive statistics along with nonparametric tests (e.g., Kruskal–Wallis, Mann–Whitney U) were used and group differences were examined. Scatter plot matrices with fitted lines were used to explore associations between variables. Classification and regression tree methods were used to classify the importance and contribution of different variables for the intensity of PPD. Results Only 2% of women (n = 33) with high PPD symptoms sought mental healthcare, and merely 5% of women (n = 75) had been in contact with a health service since the onset of their symptoms. 92.80% of women with PPD symptoms did not seek any medical attention. The majority of women, 1,215 (81%), perceived the need for mental health treatment; however, 91.23% of them did not seek treatment from healthcare services. Women who recently gave birth to a female child had higher mean depression scores compared to those who gave birth to a male child. Age, education, and birth location of newborn were significantly associated (p < 0.005) with mean barrier scores, mean social support scores, mean depression scores and treatment gap. The results of classification and regression decision tree model showed that instrumental barrier scores are the most important in predicting mean PPD scores. Conclusion Women with PPD symptoms encountered considerable treatment gap and barriers to access mental health care. Integration of mental health services into obstetric care as well as PPD screening in public and private hospitals of Punjab, Pakistan is critically needed to overcome the treatment gap and barriers.
Sajjad et al. (2024) Treatment gap and barriers to access mental healthcare among women with postpartum depression symptoms in Pakistan. PeerJ 12:e17711 https://doi.org/10.7717/peerj.17711
Monitoring deforestation, forest health, and environmental criticality in a protected area periphery using Geospatial Techniques
Protected areas in South Asia face significant challenges due to human disturbance and deforestation. The ongoing debate surrounds the recent surge in illegal encroachment of forest buffer zones in the Musali divisional secretariat division (DSD), which has led to a significant loss of forest cover over the past three decades. In this context, detecting changes in forest cover, assessing forest health, and evaluating environmental quality are crucial for sustainable forest management. As such, our efforts focused on assessing forest cover dynamics, forest health, and environmental conditions in the DSD from 1988 to 2022. We employed standardized image processing techniques, utilizing Landsat-5 (TM) and Landsat-8 (OLI) images. However, the forest area in the DSD has shown minimal changes, and environmental conditions and forest health have illustrated considerable spatial-temporal variations over the 34 years. The results indicated that 8.5 km2 (1.9%) of forest cover in the DSD has been converted to other land use classes. Overall, the Normalized Difference Vegetation Index (NDVI) has declined over time, while Land Surface Temperature (LST) exhibits an increasing trend. The regression results demonstrated a robust inverse relationship between LST and NDVI. The declining vegetation conditions and the increasing LST contribute to an increase in environmental criticality. The derived maps and indices will be beneficial for forest authorities in identifying highly sensitive locations. Additionally, they could enable land use planners to develop sustainable land management strategies.
Spatial and Geographic Information Science
Withanage et al. (2024) Monitoring deforestation, forest health, and environmental criticality in a protected area periphery using Geospatial Techniques. PeerJ 12:e17714 https://doi.org/10.7717/peerj.17714
Flowering-associated gene expression and metabolic characteristics in adzuki bean (Vigna angularis L.) with different short-day induction periods
Background The adzuki bean is a typical short-day plant and an important grain crop that is widely used due to its high nutritional and medicinal value. The adzuki bean flowering time is affected by multiple environmental factors, particularly the photoperiod. Adjusting the day length can induce flower synchronization in adzuki bean and accelerate the breeding process. In this study, we used RNA sequencing analysis to determine the effects of different day lengths on gene expression and metabolic characteristics related to adzuki bean flowering time. Methods ‘Tangshan hong xiao dou’ was used as the experimental material in this study and field experiments were conducted in 2022 using a randomized block design with three treatments: short-day induction periods of 5 d (SD-5d), 10 d (SD-10d), and 15 d (SD-15d). Results A total of 5,939 differentially expressed genes (DEGs) were identified, of which 38.09% were up-regulated and 23.81% were down-regulated. Gene ontology enrichment analysis was performed on the target genes to identify common functions related to photosystems I and II. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified two pathways involved in the antenna protein and circadian rhythm. Furthermore, florescence was promoted by down-regulating genes in the circadian rhythm pathway through the blue light metabolic pathway; whereas, antenna proteins promoted flowering by enhancing the reception of light signals and accelerating electron transport. In these two metabolic pathways, the number of DEGs was the greatest between the SD-5d VS SD-15d groups. Real-time reverse transcription‒quantitative polymerase chain reaction analysis results of eight DEGs were consistent with the sequencing results. Thus, the sequencing results were accurate and reliable and eight genes were identified as candidates for the regulation of short-day induction at the adzuki bean seedling stage. Conclusions Short-day induction was able to down-regulate the expression of genes related to flowering according to the circadian rhythm and up-regulate the expression of certain genes in the antenna protein pathway. The results provide a theoretical reference for the molecular mechanism of short-day induction and multi-level information for future functional studies to verify the key genes regulating adzuki bean flowering.
Dong et al. (2024) Flowering-associated gene expression and metabolic characteristics in adzuki bean (Vigna angularis L.) with different short-day induction periods. PeerJ 12:e17716 https://doi.org/10.7717/peerj.17716
Comparing and characterizing scapular muscle activation ratios in males and females during execution of common functional movements
Background The shoulder complex relies on scapular movement controlled by periscapular muscles for optimal arm function. However, minimal research has explored scapular muscle activation ratios during functional tasks, nor how they might be influenced by biological sex. This investigation aims to characterize how sex impacts scapular muscle activation ratios during functional tasks. Methods Twenty participants (ten females, ten males) were assessed with surface electromyography (EMG) and motion tracking during seven functional tasks. Activation ratios were calculated from normalized EMG for the three trapezius muscles and serratus anterior. Scapular angles were calculated using a YXZ Euler sequence. Two-way mixed methods ANOVAs (p < .05) were used to assess the effects of sex and humeral elevation level on ratios and angles. Results Sex-based differences were present in the Tie Apron task, with males exhibiting higher upper trapezius/lower trapezius and upper trapezius/middle trapezius ratios than females. Males also demonstrated decreased internal rotation in this task. Other tasks showcased significant sex-based differences in scapular upward rotation but not in activation ratios. Humeral elevation generally demonstrated an inverse relationship with scapular muscle activation ratios. Conclusions This study highlights sex-based differences in scapular muscle activation ratios during specific functional tasks, emphasizing the need to consider sex in analyses of shoulder movements. Normative activation ratios for functional tasks were provided, offering a foundation for future comparisons with non-normative groups. Further research is warranted to confirm and explore additional influencing factors, advancing our understanding of shoulder activation and movement in diverse populations.
Lang et al. (2024) Comparing and characterizing scapular muscle activation ratios in males and females during execution of common functional movements. PeerJ 12:e17728 https://doi.org/10.7717/peerj.17728
Examination of reliability and validity of the Self-Assessment Burden Scale-Motor for community-dwelling older adults in Japan: a validation study
Background The aging society in Japan is progressing rapidly compared with that in the United States and European countries. Aging limits activities of daily living (ADL) in older adults, declining their lives and functions at home. Therefore, improving their ADL to effectively support their functioning at home for as long as possible is vital. Consequently, supporters need to have a common understanding, be promptly aware of the decline in ADL, and quickly introduce rehabilitation. The Functional Independence Measure (FIM) and Barthel Index (BI) are the main scales used to quantitatively assess ADL. However, previous studies have reported that FIM requires specialized knowledge for evaluation, and BI does not appropriately capture changes in ADL. The Self-Assessment Burden Scale-Motor (SAB-M) was developed as a scale for family caregivers to appropriately assess changes in ADL in older adults. Previous studies using the SAB-M have confirmed its reliability and validity in hospitalized patients as assessed by their family caregivers. Therefore, this study aimed to investigate the reliability and validity of the SAB-M among community-dwelling older adults as assessed by their family caregivers. Methods This study included community-dwelling older adults who received home-visit rehabilitation at the first author’s facility between October 2020 and December 2020 in Japan. Following previous studies, the SAB-M was used by family caregivers to assess 20 older adults twice for intra-rater reliability. Furthermore, 168 older adults were evaluated by family caregivers for internal consistency using the SAB-M. For criterion validity, the SAB-M was used for the assessment by family caregivers, and therapists used the FIM-Motor (FIM-M). This study used the weighted kappa, Cronbach’s alpha, and Spearman’s rank correlation coefficients for the statistical analysis of intra-rater reliability, internal consistency, and criterion validity, respectively. Results The weighted kappa coefficient for the total score was 0.98 (p < 0.01) and individual item, it was 0.93 for feeding (p < 0.01), 0.91 for bathing (p < 0.01), 0.98 for dressing (p < 0.01), 0.94 for transfer (p < 0.01), 0.94 for walking/wheelchair (p < 0.01), 0.95 for stairs (p < 0.01), and 0.96 for bladder management (p < 0.01). The Cronbach’s alpha was 0.93 for the seven items. The Spearman’s rank correlation coefficient between the SAB-M and FIM-M scores was 0.91 (p < 0.01). Conclusion The SAB-M has sufficient reliability and validity among community-dwelling older adults. Family caregivers can routinely assess changes in the ADL of community-dwelling older adults using the SAB-M, enabling them to promptly consider introducing rehabilitation when older adults’ ADL declines. Therefore, implementing SAB-M helps older adults live and function at home for as long as possible.
Warabino et al. (2024) Examination of reliability and validity of the Self-Assessment Burden Scale-Motor for community-dwelling older adults in Japan: a validation study. PeerJ 12:e17730 https://doi.org/10.7717/peerj.17730
Assembly and evolutionary analysis of the complete mitochondrial genome of Trichosanthes kirilowii, a traditional Chinese medicinal plant
Trichosanthes kirilowii (T. kirilowii) is a valuable plant used for both medicinal and edible purposes. It belongs to the Cucurbitaceae family. However, its phylogenetic position and relatives have been difficult to accurately determine due to the lack of mitochondrial genomic information. This limitation has been an obstacle to the potential applications of T. kirilowii in various fields. To address this issue, Illumina and Nanopore HiFi sequencing were used to assemble the mitogenome of T. kirilowii into two circular molecules with sizes of 245,700 bp and 107,049 bp, forming a unique multi-branched structure. The mitogenome contains 61 genes, including 38 protein-coding genes (PCGs), 20 tRNAs, and three rRNAs. Within the 38 PCGs of the T. kirilowii mitochondrial genome, 518 potential RNA editing sites were identified. The study also revealed the presence of 15 homologous fragments that span both the chloroplast and mitochondrial genomes. The phylogenetic analysis strongly supports that T. kirilowii belongs to the Cucurbitaceae family and is closely related to Luffa. Collinearity analysis of five Cucurbitaceae mitogenomes shows a high degree of structural variability. Interestingly, four genes, namely atp1, ccmFC, ccmFN, and matR, played significant roles in the evolution of T. kirilowii through selection pressure analysis. The comparative analysis of the T. kirilowii mitogenome not only sheds light on its functional and structural features but also provides essential information for genetic studies of the genus of Cucurbitaceae.
Jiang et al. (2024) Assembly and evolutionary analysis of the complete mitochondrial genome of Trichosanthes kirilowii, a traditional Chinese medicinal plant. PeerJ 12:e17747 https://doi.org/10.7717/peerj.17747
Exploring the technological dimension of Autonomous sensory meridian response-induced physiological responses
Background In recent years, the scientific community has been captivated by the intriguing Autonomous sensory meridian response (ASMR), a unique phenomenon characterized by tingling sensations originating from the scalp and propagating down the spine. While anecdotal evidence suggests the therapeutic potential of ASMR, the field has witnessed a surge of scientific interest, particularly through the use of neuroimaging techniques including functional magnetic resonance imaging (fMRI) as well as electroencephalography (EEG) and physiological measures such as eye tracking (Pupil Diameter), heart rate (HR), heartbeat-evoked potential (HEP), blood pressure (BP), pulse rates (PR), finger photoplethysmography (PPG), and skin conductance (SC). This article is intended to provide a comprehensive overview of technology’s contributions to the scientific elucidation of ASMR mechanisms. Methodology A meticulous literature review was undertaken to identify studies that have examined ASMR using EEG and physiological measurements. The comprehensive search was conducted across databases such as PUBMED, SCOPUS, and IEEE, using a range of relevant keywords such as ‘ASMR’, ‘Autonomous sensory meridian response’, ‘EEG’, ‘fMRI’, ‘electroencephalography’, ‘physiological measures’, ‘heart rate’, ‘skin conductance’, and ‘eye tracking’. This rigorous process yielded a substantial number of 63 PUBMED and 166 SCOPUS-related articles, ensuring the inclusion of a wide range of high-quality research in this review. Results The review uncovered a body of research utilizing EEG and physiological measures to explore ASMR’s effects. EEG studies have revealed distinct patterns of brain activity associated with ASMR experiences, particularly in regions implicated in emotional processing and sensory integration. In physiological measurements, a decrease in HR and an increase in SC and pupil diameter indicate relaxation and increased attention during ASMR-triggered stimuli. Conclusions The findings of this review underscore the significance of EEG and physiological measures in unraveling the psychological and physiological effects of ASMR. ASMR experiences have been associated with unique neural signatures, while physiological measures provide valuable insights into the autonomic responses elicited by ASMR stimuli. This review not only highlights the interdisciplinary nature of ASMR research but also emphasizes the need for further investigation to elucidate the mechanisms underlying ASMR and explore its potential therapeutic applications, thereby paving the way for the development of novel therapeutic interventions.
Seifzadeh et al. (2024) Exploring the technological dimension of Autonomous sensory meridian response-induced physiological responses. PeerJ 12:e17754 https://doi.org/10.7717/peerj.17754
Secretomic changes of amyloid beta peptides on Alzheimer’s disease related proteins in differentiated human SH-SY5Y neuroblastoma cells
Alzheimer’s disease (AD) is a neurodegenerative disease that causes physical damage to neuronal connections, leading to brain atrophy. This disruption of synaptic connections results in mild to severe cognitive impairments. Unfortunately, no effective treatment is currently known to prevent or reverse the symptoms of AD. The aim of this study was to investigate the effects of three synthetic peptides, i.e., KLVFF, RGKLVFFGR and RIIGL, on an AD in vitro model represented by differentiated SH-SY5Y neuroblastoma cells exposed to retinoic acid (RA) and brain-derived neurotrophic factor (BDNF). The results demonstrated that RIIGL peptide had the least significant cytotoxic activity to normal SH-SY5Y while exerting high cytotoxicity against the differentiated cells. The mechanism of RIIGL peptide in the differentiated SH-SY5Y was investigated based on changes in secretory proteins compared to another two peptides. A total of 380 proteins were identified, and five of them were significantly detected after treatment with RIIGL peptide. These secretory proteins were found to be related to microtubule-associated protein tau (MAPT) and amyloid-beta precursor protein (APP). RIIGL peptide acts on differentiated SH-SY5Y by regulating amyloid-beta formation, neuron apoptotic process, ceramide catabolic process, and oxidative phosphorylation and thus has the potentials to treat AD.
Roytrakul et al. (2024) Secretomic changes of amyloid beta peptides on Alzheimer’s disease related proteins in differentiated human SH-SY5Y neuroblastoma cells. PeerJ 12:e17732 https://doi.org/10.7717/peerj.17732