bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan
Authors: Marghoob Muhammad Usama , Rodriguez-Sanchez Alejandro , Imran Asma , Mubeen Fathia , Hoagland Lori
Published: November 2022

Soil salinization and heavy metal (HM) contamination are major challenges facing agricultural systems worldwide. Determining how soil microbial communities respond to these stress factors and identifying individual phylotypes with potential to tolerate these conditions while promoting plant growth could help prevent negative impacts on crop productivity. This study used amplicon sequencing and several bioinformatic programs to characterize differences in the composition and potential functional capabilities of soil bacterial, fungal, and archaeal communities in five agricultural fields that varied in salinity and HM concentrations within the Indus basin region of Pakistan. The composition of bacteria with the potential to fix atmospheric nitrogen (N) and produce the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase were also determined. Microbial communities were dominated by: Euryarchaeota (archaea), Actinobacteria, Proteobacteria, Planctomycetota, Firimicutes, Patescibacteria and Acidobacteria (bacteria), and Ascomycota (fungi), and all soils contained phylotypes capable of N-fixation and ACC-deaminase production. Salinity influenced bacterial, but not archaeal or fungal communities. Both salinity and HM altered the relative abundance of many phylotypes that could potentially promote or harm plant growth. These stress factors also appeared to influence the potential functional capabilities of the microbial communities, especially in their capacity to cycle phosphorous, produce siderophores, and act as symbiotrophs or pathotrophs. Results of this study confirm that farms in this region are at risk due to salinization and excessive levels of some toxic heavy metals, which could negatively impact crop and human health. Changes in soil microbial communities and their potential functional capabilities are also likely to affect several critical agroecosystem services related to nutrient cycling, pathogen suppression, and plant stress tolerance. Many potentially beneficial phylotypes were identified that appear to be salt and HM tolerant and could possibly be exploited to promote these services within this agroecosystem. Future efforts to isolate these phylotypes and determine whether they can indeed promote plant growth and/or carry out other important soil processes are recommended. At the same time, identifying ways to promote the abundance of these unique phylotypes either through modifying soil and crop management practices, or developing and applying them as inoculants, would be helpful for improving crop productivity in this region.
Loss of CAPS2/Cadps2 leads to exocrine pancreatic cell injury and intracellular accumulation of secretory granules in mice
Authors: Sato Yotaroh , Tsuyusaki Miho , Takahashi-Iwanaga Hiromi , Fujisawa Rena , Masamune Atsushi , Hamada Shin , Matsumoto Ryotaro , Tanaka Yu , Kakuta Yoichi , Yamaguchi-Kabata Yumi , Furuse Tamio , Wakana Shigeharu , Shimura Takuya , Kobayashi Rika , Shinoda Yo , Goitsuka Ryo , Maezawa So , Sadakata Tetsushi , Sano Yoshitake , Furuichi Teiichi
Published: November 2022

The type 2 Ca2+-dependent activator protein for secretion (CAPS2/CADPS2) regulates dense-core vesicle trafficking and exocytosis and is involved in the regulated release of catecholamines, peptidergic hormones, and neuromodulators. CAPS2 is expressed in the pancreatic exocrine acinar cells that produce and secrete digestive enzymes. However, the functional role of CAPS2 in vesicular trafficking and/or exocytosis of non-regulatory proteins in the exocrine pancreas remains to be determined. Here, we analyzed the morpho-pathological indicators of the pancreatic exocrine pathway in Cadps2-deficient mouse models using histochemistry, biochemistry, and electron microscopy. We used whole exosome sequencing to identify CADPS2 variants in patients with chronic pancreatitis (CP). Caps2/Cadps2-knockout (KO) mice exhibited morphophysiological abnormalities in the exocrine pancreas, including excessive accumulation of secretory granules (zymogen granules) and their amylase content in the cytoplasm, deterioration of the fine intracellular membrane structures (disorganized rough endoplasmic reticulum, dilated Golgi cisternae, and the appearance of empty vesicles and autophagic-like vacuoles), as well as exocrine pancreatic cell injury, including acinar cell atrophy, increased fibrosis, and inflammatory cell infiltration. Pancreas-specific Cadps2 conditional KO mice exhibited pathological abnormalities in the exocrine pancreas similar to the global Cadps2 KO mice, indicating that these phenotypes were caused either directly or indirectly by CAPS2 deficiency in the pancreas. Furthermore, we identified a rare variant in the exon3 coding region of CADPS2 in a non-alcoholic patient with CP and showed that Cadps2-dex3 mice lacking CAPS2 exon3 exhibited symptoms similar to those exhibited by the Cadps2 KO and cKO mice. These results suggest that CAPS2 is critical for the proper functioning of the pancreatic exocrine pathway, and its deficiency is associated with a risk of pancreatic acinar cell pathology.
Aberrant N-glycolylneuraminic acid in breast MCF-7 cancer cells and cancer stem cells
Authors: Yang Wenqian , Jiang Yuan , Guo Qulian , Tian Zhixin , Cheng Zhigang
Published: November 2022

N-Glycolylneuraminic acid (Neu5Gc) is not normally detected in humans because humans lack the hydroxylase enzyme that converts cytidine-5′-monophosphate-N-acetylneuraminic acid (CMP-Neu5Ac) to CMP-Neu5Gc; thus, any Neu5Gc appearing in the human body is aberrant. Neu5Gc has been observed in human cancer cells and tissues. Moreover, antibodies against Neu5Gc have been detected in healthy humans, which are obstacles to clinical xenotransplantation and stem cell therapies. Thus, the study of Neu5Gc in humans has important pathological and clinical relevance. Here, we report the N-glycoproteomics characterization of aberrant Neu5Gc in breast MCF-7 cancer cells and cancer stem cells (CSCs) at the molecular level of intact N-glycopeptides, including comprehensive information (peptide backbones, N-glycosites, N-glycan monosaccharide compositions, and linkage structures) based on a target-decoy theoretical database search strategy and a spectrum-level false discovery rate (FDR) control ≤1%. The existence of Neu5Gc on N-glycan moieties was further confirmed according to its characteristic oxonium fragment ions in the MS/MS spectra of either m/z 308.09816 (Neu5Gc) or 290.08759 (Neu5Gc-H2O). The results are an important addition to previously reported Neu5Ac data and can be further validated with targeted MS methods such as multiple and parallel reaction monitoring and biochemical methods such as immunoassays. This MS-based N-glycoproteomics method can be extended to the discovery and characterization of putative aberrant Neu5Gc in other biological and clinical systems.
The expression and prognostic value of transporter 1, ATP binding cassette subfamily B member in clear cell renal cell cancer with experimental validation
Authors: Wang Zhen-Da , Tian Xi , Wang Yue , Wang Jun-Jie , Ye Shi-Qi , Huang Yong-Qiang , Qu Yuan-Yuan , Chang Kun , Shi Guo-Hai , Ye Ding-Wei , Gu Cheng-Yuan
Published: November 2022

Transporter associated with antigen processing 1(TAP1) serves as a protein to transport antigenic peptides from the surface of the endoplasmic reticulum to the lumen of the endoplasmic reticulum when the antigens are presented by major histocompatibility complex type I (MHC-I), which has been identified to play a critical role in antigen presentation in innate immunity. In tumors, the role of TAP1 seems to remain controversial. On the one hand, given the role of TAP1 in antigen presentation, it is indicated that high TAP1 expression corresponds to the emergence of more neoantigens epitopes that facilitate the recognition for phagocytes, T cells and other cells. On the other hand, the genetic ablation of transporter associated with antigen processing (TAP) results in the presentation of new class I-restricted epitopes encoded in house-keeping products. Opposite result has been revealed by studies in other tumors suggest, which implies a more complex function of TAP1. Therefore, it’s significant to clarify the role of TAP1 in clear cell renal cell carcinoma (ccRCC). In this study, we found the elevated expression levels in mRNA and protein of TAP1 in ccRCC tissues, which indicated a relatively worse prognosis. Transwell assay and Scratch assayin vitrodemonstrated the promotive role of TAP1 in ccRCC migration as well as a significant role in metastasis. And the increased expression of TAP1 resulted in more immune cells infiltrated in cancer tissues. TAP1 was also demonstrated to be related to immune regulator genes, as gene set enrichment analysis (GSEA) indicated its significant role in immune regulation. The results of CancerSEA indicated the positive association of the high-level TAP1 expression with epithelial–mesenchymal transition (EMT) and the inverse association with Cell Cycle. The effective drugs were also predicted based on TAP1 expression, of which the high level was indeed associated with resistance to multiple drugs, but some effective drugs still identified based on high TAP1 expression. According to the analysis of various databases, the role of TAP1 in ccRCC was explored, especially in relationship of TAP1 with tumor microenvironment. These results indicate that TAP1 can serve as a potential target for treatment of ccRCC.
PET/CT-based radiomics analysis may help to predict neoadjuvant chemotherapy outcomes in breast cancer
Authors: Yang Liping , Chang Jianfei , He Xitao , Peng Mengye , Zhang Ying , Wu Tingting , Xu Panpan , Chu Wenjie , Gao Chao , Cao Shaodong , Kang Shi
Published: November 2022

Background

The aim of this study was to evaluate the clinical usefulness of radiomics signature-derived 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography–computed tomography (PET-CT) for the early prediction of neoadjuvant chemotherapy (NAC) outcomes in patients with (BC).

Methods

A total of 124 patients with BC who underwent pretreatment PET-CT scanning and received NAC between December 2016 and August 2019 were studied. The dataset was randomly assigned in a 7:3 ratio to either the training or validation cohort. Primary tumor segmentation was performed, and radiomics signatures were extracted from each PET-derived volume of interest (VOI) and CT-derived VOI. Radiomics signatures associated with pathological treatment response were selected from within a training cohort (n = 85), which were then applied to generate different classifiers to predict the probability of pathological complete response (pCR). Different models were then independently tested in the validation cohort (n = 39) regarding their accuracy, sensitivity, specificity, and area under the curve (AUC).

Results

Thirty-five patients (28.2%) had pCR to NAC. Twelve features consisting of five PET-derived signatures, four CT-derived signatures, and three clinicopathological variables were candidates for the model’s development. The random forest (RF), k-nearest neighbors (KNN), and decision tree (DT) classifiers were established, which could be utilized to predict pCR to NAC with AUC ranging from 0.819 to 0.849 in the validation cohort.

Conclusions

The PET/CT-based radiomics analysis might provide efficient predictors of pCR in patients with BC, which could potentially be applied in clinical practice for individualized treatment strategy formulation.
Prognostic and diagnostic value of circRNA expression in prostate cancer: A systematic review and meta-analysis
Authors: Xie Jingling , Jiang Hui , Zhao Yuanqing , Jin Xin rui , Li Baolin , Zhu Zixin , Zhang Limei , Liu Jinbo
Published: November 2022

Background

Circular RNAs (circRNAs) are receiving increasing attention as novel biomarkers. Our goal was to investigate the diagnostic, clinicopathological, and prognostic utility of circRNAs in prostate cancer (PCa).

Methods

Relevant literature was searched in PubMed, Web of Science, and EMBASE. Sensitivity, specificity, diagnostic odds ratio (DOR), negative likelihood ratio (NLR), positive likelihood ratio (PLR), and the area under the curve (AUC) were calculated to evaluate the diagnostic accuracy of circRNA expression. circRNAs’ clinical, pathological, and prognostic value was examined using pooled odds ratios (ORs) and hazard ratios (HRs).

Results

This meta-analysis included 23 studies, with 5 for diagnosis, 16 for clinicopathological parameters, and 10 for prognosis. For diagnostic value, the pooled sensitivity, pooled specificity, PLR, NLR, DOR, and AUC were 0.82, 0.62, 2.17, 0.29, 7.37, and 0.81, respectively. Upregulation of carcinogenic circRNAs was associated with poor clinical parameters (Gleason score: OR = 0.222, 95% CI: 0.145–0.340; T classification: OR = 0.274, 95% CI: 0.175–0.430; lymph node metastasis: OR = 0.353, 95% CI: 0.175–0.716; tumor size: OR = 0.226, 95% CI: 0.099–0.518) and could predict poor survival outcomes (HR = 2.408, 95% CI: 1.559–3.720, p < 0.001). Conversely, downregulation of tumor-suppressor circRNAs was also associated with poor clinical parameters (Gleason score: OR = 1.689, 95% CI: 1.144–2.493; T classification: OR = 2.586, 95% CI: 1.779–3.762) and worse prognosis (HR = 1.739, 95% CI: 1.147–2.576, p = 0.006).

Conclusion

Our results showed that circRNAs might be useful biomarkers for the diagnosis and prognosis of PCa.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier CRD42021284785.
Signatures of illness in children requiring unplanned intubation in the pediatric intensive care unit: A retrospective cohort machine-learning study
Authors: Spaeder Michael C. , Moorman J. Randall , Moorman Liza P. , Adu-Darko Michelle A. , Keim-Malpass Jessica , Lake Douglas E. , Clark Matthew T.
Published: November 2022

Acute respiratory failure requiring the initiation of invasive mechanical ventilation remains commonplace in the pediatric intensive care unit (PICU). Early recognition of patients at risk for respiratory failure may provide clinicians with the opportunity to intervene and potentially improve outcomes. Through the development of a random forest model to identify patients at risk for requiring unplanned intubation, we tested the hypothesis that subtle signatures of illness are present in physiological and biochemical time series of PICU patients in the early stages of respiratory decompensation. We included 116 unplanned intubation events as recorded in the National Emergency Airway Registry for Children in 92 PICU admissions over a 29-month period at our institution. We observed that children have a physiologic signature of illness preceding unplanned intubation in the PICU. Generally, it comprises younger age, and abnormalities in electrolyte, hematologic and vital sign parameters. Additionally, given the heterogeneity of the PICU patient population, we found differences in the presentation among the major patient groups – medical, cardiac surgical, and non-cardiac surgical. At four hours prior to the event, our random forest model demonstrated an area under the receiver operating characteristic curve of 0.766 (0.738 for medical, 0.755 for cardiac surgical, and 0.797 for non-cardiac surgical patients). The multivariable statistical models that captured the physiological and biochemical dynamics leading up to the event of urgent unplanned intubation in a PICU can be repurposed for bedside risk prediction.
Clinical features and prognostic factors of children with profound sudden sensorineural hearing loss
Authors: Xiao Ling , Su Shuping , Liang Jia , Jiang Ying , Shu Yan , Yao Hongbing , Ding Ling
Published: November 2022

Objective

To investigate the clinical features and factors affecting the prognosis of children with profound sudden sensorineural hearing loss (SSNHL).

Methods

We retrospectively analyzed the clinical data of 147 children with profound SSNHL who received inpatient treatment at our department from January 2016 to January 2021. All children were administered with systemic steroid therapy and/or intratympanic steroid (ITS) treatment for 2 weeks. Statistical analyses were performed for the clinical features, treatment effectiveness, and factors affecting the prognosis using SPSS 23.0.

Results

The median age of the study population was 8 (6–10) years. The median treatment onset time was 8 (4–20) days. The most common concomitant symptom was tinnitus (45.58%). Laboratory findings showed that the percentages of children with abnormal leukocytes was 25.85%, abnormal platelet counts was 17.01%, abnormal cytomegalovirus IgG antibodies was 36.73% and abnormal Epstein–Barr (EB) virus IgG antibodies was 41.50%. The overall recovery rate of the treatment was 20.04%. The univariate analysis showed that age, treatment onset time, tinnitus, and ITS treatment were associated with the prognosis (p < 0.05). Regarding laboratory findings, the neutrophil count, lymphocyte count, and neutrophil-to-lymphocyte ratio differed significantly between the effective and invalid treatment effect groups (p < 0.05). The multivariable logistic regression analysis showed that treatment onset time [odds ratio (OR) = 0.936, 95% confidence interval (CI): 0.881–0.994] and ITS treatment (OR = 0.174, 95% CI: 0.044–0.0687) correlated with hearing recovery (p < 0.05).

Conclusion

In this study, the earlier the treatment start time of children with profound SSNHL, the better was the prognosis. Further, ITS could be an effective treatment option.
Correlation of systemic immune-inflammation Index with surgical necrotizing enterocolitis
Authors: Feng Wei , Hou Jinping , Xiang Chenzhu , Die Xiaohong , Sun Jing , Guo Zhenhua , Liu Wei , Wang Yi
Published: November 2022

Background

Systemic Immune-Inflammation Index (SII), known as an easy, economical and useful marker, correlates with the severity of inflammatory response. However, the usefulness of SII in necrotizing enterocolitis (NEC) remains unclear. Therefore, we evaluated the correlation of SII at NEC diagnosis and subsequent surgery.

Methods

Retrospective review of 131 neonates with NEC in a tertiary-level pediatric referral hospital was conducted with assessments of demographic data, general blood examination results at NEC diagnosis, treatment strategies and clinical outcomes. The receiver operating characteristic (ROC) curve determined the optimal cut-off values of SII, platelet-to-lymphocyte ratio (PLR), and neutrophil-to-lymphocyte ratio. Univariate/multivariate logistic regression analysis and ROC curve were conducted to evaluate the predictive significance of SII in identifying the patients who eventually received surgery. Additionally, NEC-related deaths were assessed.

Results

Overall, 49 (37.4%) cases received surgical intervention and mortality was 12.3% (14/131). The area under ROC curve of SII at NEC diagnosis to predict subsequent surgery was 0.833 (optimal cut-off value: 235.85). The SII value in surgical intervention group was significantly higher than that in medical treatment group (332.92 ± 158.52 vs. 158.84 ± 106.82, P < 0.001). Independent influencing factors for surgical NEC were SII (95% confidence interval [CI]: 4.568∼36.449, odds ratio [OR]:12.904, P < 0.001) and PLR (95% CI: 1.071∼7.356, OR:2.807, P = 0.036). SII ≤ 235.85 could identify patients at high risk for surgery, with 87.76% sensitivity, 73.17% specificity, outperformed PLR. Furthermore, mortality was significantly higher in patients with SII ≤ 235.85 than those with SII > 235.85 (20.0% vs. 1.5%, P < 0.001).

Conclusion

SII and PLR at NEC diagnosis were independent influencing factors for subsequent surgery. SII ≤ 235.85 may be a useful predictive marker for the identification of surgical NEC and mortality.
Co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model
Authors: Yu Xuefei , Liu Ziyun , Pan Yuqing , Cui Xuewei , Zhao Xinyi , Li Danni , Xue Xindong , Fu Jianhua
Published: November 2022

Background

Bronchopulmonary dysplasia (BPD) is the most common neonatal chronic lung disease. However, its exact molecular pathogenesis is not understood. We aimed to identify relevant gene modules that may play crucial roles in the occurrence and development of BPD by weighted gene co-expression network analysis (WGCNA).

Methods

We used RNA-Seq data of BPD and healthy control rats from our previous studies, wherein data from 30 samples was collected at days 1, 3, 7, 10, and 14. Data for preprocessing analysis included 17,613 differentially expressed genes (DEGs) with false discovery rate <0.05.

Results

We grouped the highly correlated genes into 13 modules, and constructed a network of mRNA gene associations, including the 150 most associated mRNA genes in each module. Lgals8, Srpra, Prtfdc1, and Thap11 were identified as the key hub genes. Enrichment analyses revealed Golgi vesicle transport, coated vesicle, actin-dependent ATPase activity and endoplasmic reticulum pathways associated with these genes involved in the pathological process of BPD in module.

Conclusions

This is a study to analyze data obtained from BPD animal model at different time-points using WGCNA, to elucidate BPD-related susceptibility modules and disease-related genes.
Myocardial extracellular volume is a non-invasive tissue marker of heart failure in patients with transposition of the great arteries and systemic right ventricle
Authors: Al-Wakeel-Marquard Nadya , Ferreira da Silva Tiago , Berger Felix , Kuehne Titus , Messroghli Daniel R.
Published: November 2022

Background

Focal myocardial fibrosis in the systemic right ventricle (RV) is related to ventricular dysfunction and adverse outcome in patients with d-transposition of the great arteries (dTGA) post atrial redirection and those with congenitally corrected TGA (ccTGA). The role of diffuse fibrotic lesions in these conditions remains poorly understood. Our study aimed to investigate diffuse myocardial fibrosis by measuring extracellular volume (ECV) with cardiovascular magnetic resonance (CMR) and to explore correlations between ECV and clinical as well as functional markers of heart failure in patients with TGA and systemic RV.

Methods

We prospectively included dTGA and ccTGA patients aged ≥14 years and compared them to healthy controls. Standardized CMR included modified Look-Locker Inversion recovery T1 mapping to quantify diffuse myocardial fibrosis in the systemic RV and the subpulmonary left ventricle (LV). The centerline of RV and LV myocardium was marked with a line of interest tool to determine native and post-contrast T1 for quantification of ECV.

Results

In total, 13 patients (dTGA: n  =  8, ccTGA: n = 5) with a median age of 30.3 years were enrolled. LV ECV was higher in patients than in controls [34% (30%–41%) vs. 26% (23%–27%), p < 0.001], with values increased above the upper limit of normal in 10/13 patients (77%). RV ECV tended to be higher in patients than in controls, albeit without statistical significance [29% (27%–32%) vs. 28% (26%–29%), p = 0.316]. Patients with elevated LV ECV had lower LV ejection fraction than those with normal ECV (52 ± 5% vs. 65 ± 4%, p = 0.007). Correlations with clinical parameters were not observed. LV ECV was significantly higher than RV ECV (p = 0.016) in the patient group.

Conclusions

In this study, LV ECV was significantly increased in TGA patients compared to controls, and was associated with LV dysfunction. Our data suggest that ECV may serve as a non-invasive tissue marker of heart failure in TGA with systemic RV. Further research is necessary to evaluate the prognostic implications and the potential role of ECV in monitoring disease progression and guiding therapy, aiming to maintain LV function or train the LV for subaortic location in TGA patients from infancy to adulthood.
Suitability of botanical extracts as components of complex mixtures used in herbal tea infusions—challenges and opportunities
Authors: Brendler T. , Brinckmann J. A. , Daoust M. , He H. , Masé G. , Steffan K. , Williams M.
Published: November 2022

Herbal tea is a mainstay dosage form in practically all systems of traditional medicine and widely used in modern alternative and complementary medicine. Incorporating botanical extracts into herbal tea formulations is of vital interest to manufacturers as it allows for the use of herbal ingredients that would otherwise not be suitable for the dosage form, for instance, dosing requirements, solubility in water, sensory constraints etc. Furthermore, reducing the amount of ingredients in a formula increases compliance with dosing recommendations and thus therapeutic benefit. However, formulating with botanical extracts comes with challenges, ranging from sourcing ingredients of appropriate quality, developing suitable methods for quality control with combinations of (herbal) ingredients, processing constraints such as hygroscopicity, solubility, dispersibility, homogeneity of distribution, and packaging machinability, all the way to stability required for hot-water infusion. We report on experiences with overcoming such challenges in a set of examples and provide guidance to the extract industry on how to tap into the bagged tea sector with better suited or tailor-made solutions for the formulator.
Arbuscular mycorrhiza mitigates zinc stress on Eucalyptus grandis through regulating metal tolerance protein gene expression and ionome uptake
Authors: Han Li-Na , Wang Si-Jia , Chen Hui , Ren Ying , Xie Xian-An , Wang Xing-Yang , Hu Wen-Tao , Tang Ming
Published: November 2022

Arbuscular mycorrhizal (AM) fungi are symbionts of most terrestrial plants and enhance their adaptability in metal-contaminated soils. In this study, mycorrhized and non-mycorrhized Eucalyptus grandis were grown under different Zn treatments. After 6 weeks of treatment, the growing status and ionome content of plants as well as the expression patterns of metal tolerance proteins and auxin biosynthesis–related genes were measured. In this study, mycorrhized E. grandis showed higher biomass and height at a high level of Zn compared with non-mycorrhized plants. In addition, AM plants accumulated P, Mg, and Mn in roots and P, Fe, and Cu in shoots, which indicate that AM fungi facilitate the uptake of ionome nutrients to promote plant growth. In addition, mycorrhiza upregulated the expression of EgMTP1 and EgMTP7, whose encoding proteins were predicted to be located at the vacuolar membrane. Meanwhile, Golgi membrane transporter EgMTP5 was also induced in AM shoot. Our results suggest that AM likely mitigates Zn toxicity through sequestrating excess Zn into vacuolar and Golgi. Furthermore, the expression of auxin biosynthesis–related genes was facilitated by AM, and this is probably another approach for Zn tolerance.
Seedling maize counting method in complex backgrounds based on YOLOV5 and Kalman filter tracking algorithm
Authors: Li Yang , Bao Zhiyuan , Qi Jiangtao
Published: November 2022

Maize population density is one of the most essential factors in agricultural production systems and has a significant impact on maize yield and quality. Therefore, it is essential to estimate maize population density timely and accurately. In order to address the problems of the low efficiency of the manual counting method and the stability problem of traditional image processing methods in the field complex background environment, a deep-learning-based method for counting maize plants was proposed. Image datasets of the maize field were collected by a low-altitude UAV with a camera onboard firstly. Then a real-time detection model of maize plants was trained based on the object detection model YOLOV5. Finally, the tracking and counting method of maize plants was realized through Hungarian matching and Kalman filtering algorithms. The detection model developed in this study had an average precision mAP@0.5 of 90.66% on the test dataset, demonstrating the effectiveness of the SE-YOLOV5m model for maize plant detection. Application of the model to maize plant count trials showed that maize plant count results from test videos collected at multiple locations were highly correlated with manual count results (R2 = 0.92), illustrating the accuracy and validity of the counting method. Therefore, the maize plant identification and counting method proposed in this study can better achieve the detection and counting of maize plants in complex backgrounds and provides a research basis and theoretical basis for the rapid acquisition of maize plant population density.
Regulation of Na+/H+ exchangers, Na+/K+ transporters, and lignin biosynthesis genes, along with lignin accumulation, sodium extrusion, and antioxidant defense, confers salt tolerance in alfalfa
Authors: Rahman Md Atikur , Woo Jae Hoon , Lee Sang-Hoon , Park Hyung Soo , Kabir Ahmad Humayan , Raza Ali , El Sabagh Ayman , Lee Ki-Won
Published: November 2022

Accumulation of high sodium (Na+) leads to disruption of metabolic processes and decline in plant growth and productivity. Therefore, this study was undertaken to clarify how Na+/H+ exchangers and Na+/K+ transporter genes contribute to Na+ homeostasis and the substantial involvement of lignin biosynthesis genes in salt tolerance in alfalfa (Medicago sativa L.), which is poorly understood. In this study, high Na+ exhibited a substantial reduction of morphophysiological indices and induced oxidative stress indicators in Xingjiang Daye (XJD; sensitive genotype), while Zhongmu (ZM; tolerant genotype) remained unaffected. The higher accumulation of Na+ and the lower accumulation of K+ and K+/(Na+ + K+) ratio were found in roots and shoots of XJD compared with ZM under salt stress. The ZM genotype showed a high expression of SOS1 (salt overly sensitive 1), NHX1 (sodium/hydrogen exchanger 1), and HKT1 (high-affinity potassium transporter 1), which were involved in K+ accumulation and excess Na+ extrusion from the cells compared with XJD. The lignin accumulation was higher in the salt-adapted ZM genotype than the sensitive XJD genotype. Consequently, several lignin biosynthesis–related genes including 4CL2, CCoAOMT, COMT, CCR, C4H, PAL1, and PRX1 exhibited higher mRNA expression in salt-tolerant ZM compared with XJD. Moreover, antioxidant enzyme (catalase, superoxide dismutase, ascorbate peroxidase, and glutathione reductase) activity was higher in ZM relative to XJD. This result suggests that high antioxidant provided the defense against oxidative damages in ZM, whereas low enzyme activity with high Na+ triggered the oxidative damage in XJD. These findings together illustrate the ion exchanger, antiporter, and lignin biosysthetic genes involving mechanistic insights into differential salt tolerance in alfalfa.
Changes in root chemical diversity along an elevation gradient of Changbai Mountain, China
Authors: Wu Shihua , Wang Ruili , Zhu Haihua , Wang Yuan , Du Yanyan , Zhu Sihao , Zhao Ning
Published: November 2022

Root chemical traits play a critical role in plant resource use strategies and ecosystem nutrient cycling; however, the chemical diversity of multiple elements of fine root and community chemical assembly belowground are poorly understood. Here, we measured 13 elements (C, N, K, Ca, Mg, S, P, Al, Fe, Na, Mn, Zn, and Cu) in the fine roots of 204 plant species along elevational transect from 540 to 2357 m of Changbai Mountain, China to explore the variation, diversity, and community assembly of root chemical traits. At the species level, the concentrations of macronutrients (N, K, Ca, Mg, S, and P) decreased, whereas the trace metals (Fe, Mn, and Zn) increased with elevation. Root chemical traits at the community level systematically shifted along elevational gradients showing a pattern similar to that at the species level, which were mainly influenced by climate and soil rather than species diversity. In general, the interactions of climate and soil were the main drivers of root chemical assembly for woody layers, whereas soil factors played significant role for root chemical assembly for herb layer. The chemical assembly of rock-derived element P was mainly driven by soil factors. Meanwhile, root chemical diversities were mainly regulated by species diversity, the interactions of climate and soil, and soil factors in the tree, shrub, and herb layers, respectively. A better understanding of plant root chemical diversity and community chemical assembly will help to reveal the role of chemical traits in ecosystem functioning.
A tale of two metals: Biofortification of rice grains with iron and zinc
Authors: Wairich Andriele , Ricachenevsky Felipe K. , Lee Sichul
Published: November 2022

Iron (Fe) and zinc (Zn) are essential micronutrients needed by virtually all living organisms, including plants and humans, for proper growth and development. Due to its capacity to easily exchange electrons, Fe is important for electron transport in mitochondria and chloroplasts. Fe is also necessary for chlorophyll synthesis. Zn is a cofactor for several proteins, including Zn-finger transcription factors and redox metabolism enzymes such as copper/Zn superoxide dismutases. In humans, Fe participates in oxygen transport, electron transport, and cell division whereas Zn is involved in nucleic acid metabolism, apoptosis, immunity, and reproduction. Rice (Oryza sativa L.) is one of the major staple food crops, feeding over half of the world’s population. However, Fe and Zn concentrations are low in rice grains, especially in the endosperm, which is consumed as white rice. Populations relying heavily on rice and other cereals are prone to Fe and Zn deficiency. One of the most cost-effective solutions to this problem is biofortification, which increases the nutritional value of crops, mainly in their edible organs, without yield reductions. In recent years, several approaches were applied to enhance the accumulation of Fe and Zn in rice seeds, especially in the endosperm. Here, we summarize these attempts involving transgenics and mutant lines, which resulted in Fe and/or Zn biofortification in rice grains. We review rice plant manipulations using ferritin genes, metal transporters, changes in the nicotianamine/phytosiderophore pathway (including biosynthetic genes and transporters), regulators of Fe deficiency responses, and other mutants/overexpressing lines used in gene characterization that resulted in Fe/Zn concentration changes in seeds. This review also discusses research gaps and proposes possible future directions that could be important to increase the concentration and bioavailability of Fe and Zn in rice seeds without the accumulation of deleterious elements. We also emphasize the need for a better understanding of metal homeostasis in rice, the importance of evaluating yield components of plants containing transgenes/mutations under field conditions, and the potential of identifying genes that can be manipulated by gene editing and other nontransgenic approaches.
Exogenous nitric oxide promotes salinity tolerance in plants: A meta-analysis
Authors: Tahjib-Ul-Arif Md. , Wei Xiangying , Jahan Israt , Hasanuzzaman Md. , Sabuj Zahid Hasan , Zulfiqar Faisal , Chen Jianjun , Iqbal Rashid , Dastogeer Khondoker M. G. , Sohag Abdullah Al Mamun , Tonny Sadia Haque , Hamid Imran , Al-Ashkar Ibrahim , Mirzapour Mohsen , El Sabagh Ayman , Murata Yoshiyuki
Published: November 2022

Nitric oxide (NO) has received much attention since it can boost plant defense mechanisms, and plenty of studies have shown that exogenous NO improves salinity tolerance in plants. However, because of the wide range of experimental settings, it is difficult to assess the administration of optimal dosages, frequency, timing, and method of application and the overall favorable effects of NO on growth and yield improvements. Therefore, we conducted a meta-analysis to reveal the exact physiological and biochemical mechanisms and to understand the influence of plant-related or method-related factors on NO-mediated salt tolerance. Exogenous application of NO significantly influenced biomass accumulation, growth, and yield irrespective of salinity stress. According to this analysis, seed priming and foliar pre-treatment were the most effective methods of NO application to plants. Moreover, one-time and regular intervals of NO treatment were more beneficial for plant growth. The optimum concentration of NO ranges from 0.1 to 0.2 mM, and it alleviates salinity stress up to 150 mM NaCl. Furthermore, the beneficial effect of NO treatment was more pronounced as salinity stress was prolonged (>21 days). This meta-analysis showed that NO supplementation was significantly applicable at germination and seedling stages. Interestingly, exogenous NO treatment boosted plant growth most efficiently in dicots. This meta-analysis showed that exogenous NO alleviates salt-induced oxidative damage and improves plant growth and yield potential by regulating osmotic balance, mineral homeostasis, photosynthetic machinery, the metabolism of reactive oxygen species, and the antioxidant defense mechanism. Our analysis pointed out several research gaps, such as lipid metabolism regulation, reproductive stage performance, C4 plant responses, field-level yield impact, and economic profitability of farmers in response to exogenous NO, which need to be evaluated in the subsequent investigation.
Key role of reactive oxygen species-scavenging system in nitric oxide and hydrogen sulfide crosstalk-evoked thermotolerance in maize seedlings
Authors: Sun Yu-Ying , Wang Jia-Qi , Xiang Ru-Hua , Li Zhong-Guang
Published: November 2022

Nitric oxide (NO) and hydrogen sulfide (H2S) are novel signaling molecules, which participate in plant growth, development, and response to stress. In this study root-irrigation with 0.15 mM sodium nitroprusside (SNP, NO donor) up-regulated gene expression of L-CYSTEINE DESULFHYDRASE1 (LCD1), activities of L-cysteine desulfhydrase (LCD) and D-cysteine desulfhydrase (DCD), as well as an endogenous H2S level, compared to control seedlings. The SNP-up-regulated effects were enhanced by 0.5 mM sodium hydrosulfide (NaHS, H2S donor), but weakened by NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO) and H2S scavenger hypotaurine (HT) alone. NaHS had no significant effect on gene expression and activity of nitrate reductase (NR, a NO candidate producing enzyme). These data indicate that NO could trigger the LCD/H2S signaling pathway in maize seedlings. To further investigate the effect of NO and H2S crosstalk on thermotolerance in maize seedlings, thermotolerance parameters and reactive oxygen species (ROS)-scavenging system were estimated. The results show that SNP increased survival rate and tissue viability, decreased malondialdehyde (MDA) accumulation, and electrolyte leakage in maize seedlings under heat stress (HS), implying NO could improve thermotolerance in maize seedlings. The NO-improved thermotolerance was impaired by H2S inhibitor DL-propargylglycine (PAG) and scavenger HT alone. Similarly, SNP up-regulated the gene expression of DEHYDROASCORBATE REDUCTASE (DHAR) and GLUTATHIONE REDUCTASE1 (GR1); activities of ascorbate peroxidase, glutathione reductase, and catalase; as well as levels of ascorbic acid, glutathione, flavonoids, carotenoids, and total phenols. SNP also reduced hydrogen peroxide and superoxide radical accumulation in maize seedlings under HS compared to the control. The effects of SNP on ROS and their scavenger system were weakened by PAG and HT alone. These data hint that NO could evoke thermotolerance in maize seedlings by triggering the LCD/H2S signaling pathway, and the ROS-scavenging system played a key role in the NO and H2S crosstalk-evoked thermotolerance.
The associations between smartphone addiction and self-esteem, self-control, and social support among Chinese adolescents: A meta-analysis
Authors: Ding Yueming , Wan Xiao , Lu Guangli , Huang Haitao , Liang Yipei , Yu Jingfen , Chen Chaoran
Published: November 2022

Background

Smartphone addiction has become a social problem that affects the healthy growth of adolescents, and it is frequently reported to be correlated with self-esteem, self-control, and social support among adolescents.

Methods

A meta-analysis was conducted by searching the PubMed, Web of Science, Embase, PsycINFO, PsycArticles, China National Knowledge Infrastructure (CNKI), WANFANG DATA, and Chongqing VIP Information Co., Ltd. (VIP) databases. Stata 16.0 was used to analyse the overall effect and test the moderating effect.

Results

Fifty-six studies were included, involving a total of 42,300 participants. Adolescents' smartphone addiction had a moderately negative correlation with self-esteem (r = −0.25, 95% CI = −0.29 to −0.22, p < 0.001), a strong negative correlation with self-control (r = −0.48, 95% CI = −0.53 to −0.42, p < 0.001), and a weak negative correlation with social support (r = −0.16, 95% CI = −0.23 to −0.09, p < 0.001). Moderation analysis revealed that the correlation between adolescents' smartphone addiction and self-esteem was strongest when smartphone addiction was measured with the Mobile Phone Addiction Tendency Scale for College Students (MPATS; r = −0.38). The correlation between adolescents' smartphone addiction and self-control was strongest when self-control was measured with the Middle school students' Self-control Ability Questionnaire (MSAQ; r = −0.62). The effect of dissertations on smartphone addiction, self-control, and social support among adolescents was significantly larger than that of journal articles. The correlation between adolescents' smartphone addiction and social support was strongest when smartphone addiction was measured with the Mobile Phone Addiction Index (MPAI; r = −0.24). However, the correlations between adolescents' smartphone addiction and self-esteem, self-control, and social support were not affected by age or gender.

Conclusion

There was a strong relationship between smartphone addiction and self-esteem, self-control, and social support among adolescents. In the future, longitudinal research should be carried out to better investigate the dynamic changes in therelationship between smartphone addiction and self-esteem, self-control, and social support.

Systematic review registration

https://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42022300061.
The knowledge produced through student drawings
Authors: Hatisaru Vesife
Published: November 2022

Drawings have been extensively used as a research method to gather data from research participants including school students regarding their perceptions of mathematics and its teaching and learning. What is valued in drawing-based research in mathematics education, and what kind of knowledge is produced through student drawings, however, is not known. This study examines drawing-based research studies to understand these questions by applying a novel framework – the legitimation code theory (LCT). The study focuses on two cases: one of which looked at middle school students’ images of mathematicians (draw a mathematician) and the other examined the same age group students’ descriptions of mathematics classrooms (draw a mathematics classroom). Within both studies, greater emphases are on the students’ perceptions relating to the discipline-related issues such as teaching and learning of mathematics, mathematics classroom experiences, and practices and tools of mathematicians. Students’ perceptions of the mathematics discipline and their attitudes toward mathematics and perceptions of the attributes of mathematicians are also a focus. The study offers the LCT approach to critically analyze the drawing-based research in the mathematics education field to contribute to the production of significant and needed knowledge in the field.
Relationship Between Perceived Parental Academic Expectations and Students' Self-Regulated Learning Ability: A Cross-Sectional Study
Authors: Xu Ling , Ma Lijun , Duan Peng
Published: November 2022

In the field of self-regulated learning ability for college students, prior research usually neglected the role of parents when considering the physical distance between college and home. Indeed, an underlying describable driving force of learning remains embedded in the relationship between parents and students, even at the college stage. This study aimed to explore the relationships among perceived parental academic expectations, mastery goal orientation, self-reflection, and self-regulated learning ability of college students. Mediation and moderated mediation analyses were employed to analyze a sample of 691 college students. The results indicate that mastery goal orientation partially mediates the relationship between perceived parental academic expectations and self-regulated learning. In addition, self-reflection moderates the relationship between perceived parental academic expectations and self-regulated learning. The positive correlation between perceived parental academic expectation and self-regulated learning is stronger for students with low self-reflection than those with high self-reflection.
A deep learning-based model for detecting depression in senior population
Authors: Lin Yunhan , Liyanage Biman Najika , Sun Yutao , Lu Tianlan , Zhu Zhengwen , Liao Yundan , Wang Qiushi , Shi Chuan , Yue Weihua
Published: November 2022

Objectives

With the attention paid to the early diagnosis of depression, this study tries to use the biological information of speech, combined with deep learning to build a rapid binary-classification model of depression in the elderly who use Mandarin and test its effectiveness.

Methods

Demographic information and acoustic data of 56 Mandarin-speaking older adults with major depressive disorder (MDD), diagnosed with the Mini-International Neuropsychiatric Interview (MINI) and the fifth edition of Diagnostic and Statistical Manual of Mental Disorders (DSM-5), and 47 controls was collected. Acoustic data were recorded using different smart phones and analyzed by deep learning model which is developed and tested on independent validation set. The accuracy of the model is shown by the ROC curve.

Results

The quality of the collected speech affected the accuracy of the model. The initial sensitivity and specificity of the model were respectively 82.14% [95%CI, (70.16–90.00)] and 80.85% [95%CI, (67.64–89.58)].

Conclusion

This study provides a new method for rapid identification and diagnosis of depression utilizing deep learning technology. Vocal biomarkers extracted from raw speech signals have high potential for the early diagnosis of depression in older adults.
Greater variability in daily sleep efficiency predicts depression and anxiety in young adults: Estimation of depression severity using the two-week sleep quality records of wearable devices
Authors: Lim Jae-A , Yun Je-Yeon , Choi Soo-Hee , Park Susan , Suk Hye Won , Jang Joon Hwan
Published: November 2022

Objectives

Sleep disturbances are associated with both the onset and progression of depressive disorders. It is important to capture day-to-day variability in sleep patterns; irregular sleep is associated with depressive symptoms. We used sleep efficiency, measured with wearable devices, as an objective indicator of daily sleep variability.

Materials and methods

The total sample consists of 100 undergraduate and graduate students, 60% of whom were female. All were divided into three groups (with major depressive disorder, mild depressive symptoms, and controls). Self-report questionnaires were completed at the beginning of the experiment, and sleep efficiency data were collected daily for 2 weeks using wearable devices. We explored whether the mean value of sleep efficiency, and its variability, predicted the severity of depression using dynamic structural equation modeling.

Results

More marked daily variability in sleep efficiency significantly predicted levels of depression and anxiety, as did the average person-level covariates (longer time in bed, poorer quality of life, lower extraversion, and higher neuroticism).

Conclusion

Large swings in day-to-day sleep efficiency and certain clinical characteristics might be associated with depression severity in young adults.