bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptome-wide m6A methylome analysis uncovered the changes of m6A modification in oral pre-malignant cells compared with normal oral epithelial cells
Authors: Chen Xun , Chen Liutao , Tang Yuquan , He Yi , Pan Kuangwu , Yuan Linyu , Xie Weihong , Chen Shangwu , Zhao Wei , Yu Dongsheng
Published: September 2022

As the most common post-transcriptional RNA modification, m6A methylation extensively regulates the structure and function of RNA. The dynamic and reversible modification of m6A is coordinated by m6A writers and erasers. m6A reader proteins recognize m6A modification on RNA, mediating different downstream biological functions. mRNA m6A modification and its corresponding regulators play an important role in cancers, but its characteristics in the precancerous stage are still unclear. In this study, we used oral precancerous DOK cells as a model to explore the characteristics of transcriptome-wide m6A modification and major m6A regulator expression in the precancerous stage compared with normal oral epithelial cell HOEC and oral cancer cell SCC-9 through MeRIP-seq and RT-PCR. Compared with HOEC cells, we found 1180 hyper-methylated and 1606 hypo-methylated m6A peaks and 354 differentially expressed mRNAs with differential m6A peaks in DOK cells. Although the change of m6A modification in DOK cells was less than that in SCC-9 cells, mRNAs with differential m6A in both cell lines were enriched into many identical GO terms and KEGG pathways. Among the 20 known m6A regulatory genes, FTO, ALKBH5, METTL3 and VIRMA were upregulated or downregulated in DOK cells, and the expression levels of 10 genes such as METTL14/16, FTO and IGF2BP2/3 were significantly changed in SCC-9 cells. Our data suggest that precancerous cells showed, to some extent, changes of m6A modification. Identifying some key m6A targets and corresponding regulators in precancerous stage may provide potential intervention targets for the prevention of cancer development through epigenetic modification in the future.
Genomic landscape of lung adenocarcinomas in different races
Authors: Shi Huashan , Seegobin Karan , Heng Fei , Zhou Kexun , Chen Ruqin , Qin Hong , Manochakian Rami , Zhao Yujie , Lou Yanyan
Published: September 2022

Background

Lung adenocarcinoma is a molecularly heterogeneous disease. Several studies, including The Cancer Genome Atlas Research Network (TCGA) and Lung Cancer Mutation Consortium (LCMC), explored the genetic alterations among different ethnic groups. However, minority groups are often under-represented in these relevant studies and the genomic alterations among racial groups are not fully understood.

Methods

We analyze genomic characteristics among racial groups to understand the diversities and their impact on clinical outcomes.

Results

Native Americans had significantly higher rates of insertions and deletions than other races (P<0.001). Among patients with lung adenocarcinomas, EGFR and KRAS were the highest discrepancy genes in the different racial groups (P<0.001). The EGFR exon 21 L858R point mutation was three times higher in Asians than in all other races (P<0.001). Asians, Whites, and Blacks had 4.7%, 3.1%, and 1.8% ALK rearrangement, respectively (P<0.001). White patients had the highest rates of reported KRAS G12C (15.51%) than other races (P<0.001). Whites (17.2%), Blacks (15.1%), and Other (15.7%) had higher rates of STK11 mutation than Asians (3.94%) (P<0.001). RET rearrangement and ERBB2 amplification were more common in Asian patients than in Other racial groups. Apart from point mutations, structural variations, and fusion genes, we identified a significant amount of copy number alterations in each race.

Conclusions

The tumor genomic landscape is significantly distinct in different races. This data would shed light on the understanding of molecular alterations and their impacts on clinical management in different lung cancer patients.
NOX4 has the potential to be a biomarker associated with colon cancer ferroptosis and immune infiltration based on bioinformatics analysis
Authors: Yang Xiaoping , Yu Yi , Wang Zirui , Wu Pingfan , Su Xiaolu , Wu Zhiping , Gan Jianxin , Zhang Dekui
Published: September 2022

Background

Colon cancer (CC) is a common tumor, but its pathogenesis is still not well understood. Competitive endogenous RNA (ceRNA) theory, ferroptosis and tumor immune infiltration may be the mechanisms of the development of cancer. The purpose of the study is to seek genes connected with both immunity and ferroptosis, and provide important molecular basis for early noninvasive diagnosis and immunotherapy of CC.

Methods

We extracted messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (lncRNA) data of CC from The Cancer Genome Atlas database (TCGA), identified the differentially expressed mRNA (DEmRNA), miRNA (DEmiRNA) and lncRNA (DElncRNA), then constructed a ceRNA network. Venn overlap analysis was used to identify genes associated with immunity and ferroptosis in ceRNA network. The expression and prognosis of target genes were analyzed via Gene Expression Profiling Interactive Analysis (GEPIA) and PrognoScan database, and we analysed the related functions and signaling pathways of target genes by enrichment analysis. The correlation between target genes and tumor immune infiltrating was explored by CIBERSORT and spearman correlation analysis. Finally, the expression of target genes was detected via quantitative reverse transcription-PCR (qRT-PCR) in CC and normal colon tissues.

Results

Results showed that there were 4 DElncRNA, 4 DEmiRNA and 126 DEmRNA in ceRNA network. NADPH oxidase 4 protein (NOX4) was a DEmRNA associated with immunity and ferroptosis in ceRNA network. NOX4 was highly expressed in CC and connected with unfavourable prognosis. NOX4 was obviously enriched in pathways connected with carcinogenesis and significantly correlated with six kinds of immune cells. Immune checkpoints and NOX4 spearman correlation analysis showed that the expression of NOX4 was positively related to programmed cell death protein 1 (PD-1)-PDCD1, programmed cell death-Ligand 1 (PD-L1)-CD274 and cytotoxic T-lymphocyte-associated protein 4 (CTLA4).

Conclusions

To conclude, our study suggests that NOX4 is associated with both ferroptosis and tumor immunity, and might be a biomarker associated with the carcinogenesis, prognosis of CC and a potential target of CC immunotherapy.
Lenvatinib plus transarterial chemoembolization with or without immune checkpoint inhibitors for unresectable hepatocellular carcinoma: A review
Authors: Sun Liwei , Xu Xuelong , Meng Fanguang , Liu Qian , Wang Hankang , Li Xiaodong , Li Guijie , Chen Feng
Published: September 2022

Lenvatinib plus transarterial chemoembolization (TACE)have become the first choice for patients with hepatocellular carcinoma (HCC) that are unsuitable for TACE. Sorafenib plus TACE therapy for patients with portal vein tumor thrombus (PVTT) achieved positive results. However, Lenvatinib plus TACE appeared to achieve a more advantageous result for these patients based on the phase 3 REFLECT trial. Both TACE and lenvatinib therapy have immune-stimulating effects, so would lenvatinib plus TACE and immune checkpoint inhibitors be an advantageous therapy for unresectable HCC (uHCC)? Thirteen articles from PubMed were explored to determine the efficacy and safety of lenvatinib plus TACE with or without PD-1 inhibitors therapy. Most of the adverse events (AEs) were manageable. Lenvatinib plus TACE therapy was superior to lenvatinib monotherapy with intermediate stage HCC especially beyond up-to-seven criterion and was superior to TACE monotherapy in patients with uHCC or sorafenib plus TACE therapy in patients with PVTT. Objective response rates (ORRs) of 53.1%–75%, median progression free survival (PFS) of 6.15–11.6 months, and median overall survival (OS) of 14.5–18.97 months were achieved in the lenvatinib plus TACE group. Levatinib plus TACE and PD-1 inhibitors achieved ORRs of 46.7% –80.6%, median PFS of 7.3–13.3 months, and median OS of 16.9–24 months. Control studies also confirmed the triple therapy was superior to lenvatinib plus TACE in patients with uHCC. Overall, the triple therapy is a promising treatment for patients with uHCC, including main PVTT and extrahepatic metastasis. Lenvatinib plus TACE therapy was also preferable for intermediate stage HCC beyond up-to-seven criterion and for patients with PVTT.
A new partially hydrolyzed whey-based follow-on formula with age-adapted protein content supports healthy growth during the first year of life
Authors: Billeaud Claude , Adamon Latif , Piloquet Hugues , Hays Nicholas P. , Dupuis Lénaïck , Metreau Isabelle , Léké André
Published: September 2022

Background

Standard infant formulae often have higher protein content than breastmilk in order to compensate for potentially lower digestibility; excess protein intake may promote adverse effects later in life. A new partially hydrolyzed whey-based (pHF-W) follow-on formula (FoF) with age-adapted protein content was evaluated for growth and gastrointestinal (GI) tolerance in healthy infants.

Methods

Formula-fed (FF) infants (n = 108) received standard pHF-W formula (1.9 g protein/100 kcal) from enrollment (age ≤ 30 days) until age 120 days followed by new pHF-W FoF (1.6 g protein/100 kcal) until 360 days. Weight gain velocity (WGV) (mean daily WG from enrollment to age 180 days) was compared to WHO growth standards and a breastfed (BF) reference group (n = 86) (non-inferiority margin –3 g/day). GI tolerance was assessed using a validated questionnaire (scale range 13−65).

Results

WGV in FF infants (mean ± SD 24.0 ± 4.4 g/day) was non-inferior to BF (23.7 ± 3.9 g/day) and WHO standards (all p ≤ 0.013). Weight-for-age, length-for-age, weight-for-length, and head circumference-for-age z-scores of FF infants were not significantly different from BF at any timepoint. Symptoms of GI intolerance were low (≤23) at all timepoints and similar between groups.

Conclusion

A new pHF-W FoF with age-adapted protein content fed sequentially after standard pHF-W infant formula is safe, well-tolerated, and promotes a healthy growth pattern consistent with BF infants and WHO standards during the first year of life.

Clinical trial registration

[https://clinicaltrials.gov/], identifier [NCT03276663].
The value of CT radiomic in differentiating mycoplasma pneumoniae pneumonia from streptococcus pneumoniae pneumonia with similar consolidation in children under 5 years
Authors: Wang Dongdong , Zhao Jianshe , Zhang Ran , Yan Qinghu , Zhou Lu , Han Xiaoyu , Qi Yafei , Yu Dexin
Published: September 2022

Objective

To investigate the value of CT radiomics in the differentiation of mycoplasma pneumoniae pneumonia (MPP) from streptococcus pneumoniae pneumonia (SPP) with similar CT manifestations in children under 5 years.

Methods

A total of 102 children with MPP (n = 52) or SPP (n = 50) with similar consolidation and surrounding halo on CT images in Qilu Hospital and Qilu Children’s Hospital between January 2017 and March 2022 were enrolled in the retrospective study. Radiomic features of the both lesions on plain CT images were extracted including the consolidation part of the pneumonia or both consolidation and surrounding halo area which were respectively delineated at region of interest (ROI) areas on the maximum axial image. The training cohort (n = 71) and the validation cohort (n = 31) were established by stratified random sampling at a ratio of 7:3. By means of variance threshold, the effective radiomics features, SelectKBest and least absolute shrinkage and selection operator (LASSO) regression method were employed for feature selection and combined to calculate the radiomics score (Rad-score). Six classifiers, including k-nearest neighbor (KNN), support vector machine (SVM), extreme gradient boosting (XGBoost), random forest (RF), logistic regression (LR), and decision tree (DT) were used to construct the models based on radiomic features. The diagnostic performance of these models and the radiomic nomogram was estimated and compared using the area under the receiver operating characteristic (ROC) curve (AUC), and the decision curve analysis (DCA) was used to evaluate which model achieved the most net benefit.

Results

RF outperformed other classifiers and was selected as the backbone in the classifier with the consolidation + the surrounding halo was taken as ROI to differentiate MPP from SPP in validation cohort. The AUC value of MPP in validation cohort was 0.822, the sensitivity and specificity were 0.81 and 0.81, respectively.

Conclusion

The RF model has the best classification efficiency in the identification of MPP from SPP in children, and the ROI with both consolidation and surrounding halo is most suitable for the delineation.
Comparative efficacy of Honghua class injections for treating acute ischemic stroke: A Bayesian network meta-analysis of randomized controlled trials
Authors: Li Lan , Shao Chongyu , Liu Zheting , Wu Xiaolong , Yang Jiehong , Wan Haitong
Published: September 2022

Background: Acute ischemic stroke (AIS) is associated with high morbidity, mortality, and disability. Clinical trials have shown that Honghua class injections (HCIs) combined with WM achieve better clinical efficacy than WM alone. In this study, we performed a Bayesian network meta-analysis (NMA) of randomized controlled trials (RCTs) to evaluate the efficacy of different HCIs combined with WM in treating AIS.

Methods: First, the inclusion and exclusion criteria were established. From inception to 1 June 2022, a systematic literature search was conducted in multiple databases for the treatment of AIS with HCIs, including Honghua injection (HI), Safflower Yellow injection (SYI), Guhong injection (GHI), and Danhong injection (DHI). Subsequently, OpenBUGS 3.2.3 was applied to conduct a Bayesian algorithm, and Stata 16.0 was used to prepare the graphs. Multidimensional cluster analysis was performed using the “scatterplot3d” package in R 3.6.1 software.

Results: In this NMA, a total of 120 eligible RCTs were included, involving 12,658 patients, and evaluating the clinical effectiveness rates, activities of daily living (ADL), hemorheological indexes, and adverse reactions (ADRs). DHI + WM was the best intervention for improving the clinical effectiveness rate. Moreover, cluster analysis demonstrated that DHI + WM and SYI + WM had better comprehensive therapeutic effects. As most of the included RCTs did not monitor ADRs, the safety of the HCIs remains to be further explored.

Conclusion: DHI + WM and SYI + WM probably have a better clinical efficacy on AIS patients. Nevertheless, due to the limitation of this NMA, this conclusion may be biased. High-quality RCTs should be performed to validate our findings.

Systematic Review Registration:https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42021229599
Efficacy of single-dose intravitreal dexamethasone implantation for retinal vein occlusion patients with refractory macular edema: A systematic review and meta-analysis
Authors: Yuan Qiongzhen , Gao Yunxia , Liu Yilin , Xu Hanyue , Wang Tong , Zhang Ming
Published: September 2022

Purpose: To assess the functional and anatomical consequences of single-dose dexamethasone (DEX) implants for the treatment of refractory macular edema (ME) secondary to retinal vein occlusion (RVO) after anti-vascular endothelial growth factor agents.

Methods: A literature search of studies on switching therapy to DEX implants from anti-VEGF agents in refractory RVO patients was performed with five electronic databases (PubMed, Embase, Web of Science, MEDLINE, and Cochrane Library) prior to January 2022. The main outcomes included best-corrected visual acuity (BCVA) and central macular thickness (CMT) changes at different follow-up endpoints from baseline. All analyses were performed using Stata version 15.0.

Results: The final analysis included four eligible studies with a total of 99 patients. After single-dose DEX implant application, BCVA improved significantly at 2, 3, and 6 months with an average gain of −0.23 logarithm of the minimum angle of resolution (logMAR) (p = 0.004), −0.20 logMAR (p = 0.027), and -0.09 logMAR (p = 0.021), respectively. Mean CMT reduction was also significant from baseline to 2 months (-241.89 μm, p < 0.001), 3 months (−222.61 μm, p < 0.001), and 6 months (−90.49 μm, p < 0.001). No serious adverse events were observed in any of the included studies.

Conclusion: This meta-analysis showed that RVO patients with refractory ME could benefit significantly from switching therapy to DEX implantation, with efficacy lasting 6 months after a single-dose application. Intravitreal DEX implantation is a safe and effective option for refractory cases.
Particle network EnKF for large-scale data assimilation
Authors: Li Xinjia , Lu Wenlian
Published: September 2022

The Ensemble Kalman filter (EnKF) is a classic method of data assimilation. For distributed sampling, the conventional EnKF usually requires a centralized server to integrate the predictions of all particles or a fully-connected communication network, causing traffic jams and low bandwidth utilization in high-performance computing. In this paper, we propose a novel distributed scheme of EnKF based on network setting of sampling, called Particle Network EnKF. Without a central server, every sampling particle communicates with its neighbors over a sparsely connected network. Unlike the existing work, this method focuses on the distribution of sampling particles instead of sensors and has been proved effective and robust on numerous tasks. The numerical experiments on the Lorenz-63 and Lorenz-96 systems indicate that, with proper communication rounds, even on a sparse particle network, this method achieves a comparable performance to the standard EnKF. A detailed analysis of effects of the network topology and communication rounds is performed. Another experiment demonstrating a trade-off between the particle homogeneity and performance is also provided. The experiments on the whole-brain neuronal network model show promises for applications in large-scale assimilation problems.
Anisotropy in ultrasound shear wave elastography: An add-on to muscles characterization
Authors: Ngo Ha-Hien-Phuong , Poulard Thomas , Brum Javier , Gennisson Jean- Luc
Published: September 2022

Ultrasound shear wave elastography was developed the past decade, bringing new stiffness biomarker in clinical practice. This biomarker reveals to be of primarily importance for the diagnosis of breast cancer or liver fibrosis. In muscle this biomarker become much more complex due to the nature of the muscle itself: an anisotropic medium. In this manuscript we depict the underlying theory of propagating waves in such anisotropic medium. Then we present the available methods that can consider and quantify this parameter. Advantages and drawbacks are discussed to open the way to imagine new methods that can free this biomarker in a daily clinical practice.
Classification of functional and non-functional arm use by inertial measurement units in individuals with upper limb impairment after stroke
Authors: Pohl Johannes , Ryser Alain , Veerbeek Janne Marieke , Verheyden Geert , Vogt Julia Elisabeth , Luft Andreas Rüdiger , Awai Easthope Chris
Published: September 2022

Background:Arm use metrics derived from wrist-mounted movement sensors are widely used to quantify the upper limb performance in real-life conditions of individuals with stroke throughout motor recovery. The calculation of real-world use metrics, such as arm use duration and laterality preferences, relies on accurately identifying functional movements. Hence, classifying upper limb activity intofunctionalandnon-functionalclasses is paramount. Acceleration thresholds are conventionally used to distinguish these classes. However, these methods are challenged by the high inter and intra-individual variability of movement patterns. In this study, we developed and validated a machine learning classifier for this task and compared it to methods using conventional and optimal thresholds.

Methods:Individuals after stroke were video-recorded in their home environment performing semi-naturalistic daily tasks while wearing wrist-mounted inertial measurement units. Data were labeled frame-by-frame following the Taxonomy of Functional Upper Limb Motion definitions, excluding whole-body movements, and sequenced into 1-s epochs. Actigraph counts were computed, and an optimal threshold for functional movement was determined by receiver operating characteristic curve analyses on group and individual levels. A logistic regression classifier was trained on the same labels using time and frequency domain features. Performance measures were compared between all classification methods.

Results:Video data (6.5 h) of 14 individuals with mild-to-severe upper limb impairment were labeled. Optimal activity count thresholds were ≥20.1 for the affected side and ≥38.6 for the unaffected side and showed high predictive power with an area under the curve (95% CI) of 0.88 (0.87,0.89) and 0.86 (0.85, 0.87), respectively. A classification accuracy of around 80% was equivalent to the optimal threshold and machine learning methods and outperformed the conventional threshold by ∼10%. Optimal thresholds and machine learning methods showed superior specificity (75–82%) to conventional thresholds (58–66%) across unilateral and bilateral activities.

Conclusion:This work compares the validity of methods classifying stroke survivors’ real-life arm activities measured by wrist-worn sensors excluding whole-body movements. The determined optimal thresholds and machine learning classifiers achieved an equivalent accuracy and higher specificity than conventional thresholds. Our open-sourced classifier or optimal thresholds should be used to specify the intensity and duration of arm use.
Long-term excessive application of K2SO4 fertilizer alters bacterial community and functional pathway of tobacco-planting soil
Authors: Lu Ya , Cong Ping , Kuang Shuai , Tang Lina , Li Yuyi , Dong Jianxin , Song Wenjing
Published: September 2022

To improve tobacco leaf quality, excessive K2SO4 fertilizers were applied to soils in major tobacco-planting areas in China. However, the effects of K2SO4 application on soil microbial community and functions are still unclear. An eight-year field experiment with three kinds of K2SO4 amounts (low amount, K2O 82.57 kg hm-2, LK; moderate amount, K2O 165.07 kg hm-2, MK; high amount, K2O 247.58 kg hm-2, HK) was established to assess the effects of K2SO4 application on the chemical and bacterial characteristics of tobacco-planting soil using 16S rRNA gene and metagenomic sequencing approaches. Results showed that HK led to lower pH and higher nitrogen (N), potassium (K), sulfur(S) and organic matter contents of the soil than LK. The bacterial community composition of HK was significantly different from those of MK and LK, while these of MK and LK were similar. Compared to LK, HK increased the relative abundance of predicted copiotrophic groups (e.g. Burkholderiaceae, Rhodospirillaceae families and Ellin6067 genus) and potentially beneficial bacteria (e.g. Gemmatimonadetes phylum and Bacillus genus) associated with pathogens and heavy metal resistance, N fixation, dissolution of phosphorus and K. While some oligotrophic taxa (e.g. Acidobacteria phylum) related to carbon, N metabolism exhibited adverse responses to HK. Metagenomic analysis suggested that the improvement of pathways related to carbohydrate metabolism and genetic information processing by HK might be the self-protection mechanism of microorganisms against environmental stress. Besides, the redundancy analysis and variation partitioning analysis showed that soil pH, available K and S were the primary soil factors in shifting the bacterial community and KEGG pathways. This study provides a clear understanding of the responses of soil microbial communities and potential functions to excessive application of K2SO4 in tobacco-planting soil.
Genetic and molecular pathways controlling rice inflorescence architecture
Authors: Chun Yan , Kumar Ashmit , Li Xueyong
Published: September 2022

Rice inflorescence is one of the major organs in determining grain yield. The genetic and molecular regulation on rice inflorescence architecture has been well investigated over the past years. In the present review, we described genes regulating rice inflorescence architecture based on their roles in meristem activity maintenance, meristem identity conversion and branch elongation. We also introduced the emerging regulatory pathways of phytohormones involved in rice inflorescence development. These studies show the intricacies and challenges of manipulating inflorescence architecture for rice yield improvement.
RNA-seq analysis reveals key genes associated with seed germination of Fritillaria taipaiensis P.Y.Li by cold stratification
Authors: Yang Qiu-Xiong , Chen Dan , Zhao Yan , Zhang Xiao-Yu , Zhao Min , Peng Rui , Sun Nian-Xi , Baldwin Timothy Charles , Yang Sheng-Chao , Liang Yan-Li
Published: September 2022

Seed dormancy is an adaptive strategy for environmental evolution. However, the molecular mechanism of the breaking of seed dormancy at cold temperatures is still unclear, and the genetic regulation of germination initiated by exposure to cold temperature requires further investigation. In the initial phase of the current study, the seed coat characteristics and embryo development of Fritillaria taipaiensis P.Y.Li at different temperatures (0°C, 4°C, 10°C & 25°C) was recorded. The results obtained demonstrated that embryo elongation and the dormancy-breaking was most significantly affected at 4°C. Subsequently, transcriptome analyses of seeds in different states of dormancy, at two stratification temperatures (4°C and 25°C) was performed, combined with weighted gene coexpression network analysis (WGCNA) and metabolomics, to explore the transcriptional regulation of seed germination in F. taipaiensis at the two selected stratification temperatures. The results showed that stratification at the colder temperature (4°C) induced an up-regulation of gene expression involved in gibberellic acid (GA) and auxin biosynthesis and the down-regulation of genes related to the abscisic acid (ABA) biosynthetic pathway. Thereby promoting embryo development and the stimulation of seed germination. Collectively, these data constitute a significant advance in our understanding of the role of cold temperatures in the regulation of seed germination in F. taipaiensis and also provide valuable transcriptomic data for seed dormancy for other non-model plant species.
Multi-omic characterization of bifunctional peroxidase 4-coumarate 3-hydroxylase knockdown in Brachypodium distachyon provides insights into lignin modification-associated pleiotropic effects
Authors: Shrestha Him K. , Fichman Yosef , Engle Nancy L. , Tschaplinski Timothy J. , Mittler Ron , Dixon Richard A. , Hettich Robert L. , Barros Jaime , Abraham Paul E.
Published: September 2022

A bifunctional peroxidase enzyme, 4-coumarate 3-hydroxylase (C3H/APX), provides a parallel route to the shikimate shunt pathway for the conversion of 4-coumarate to caffeate in the early steps of lignin biosynthesis. Knockdown of C3H/APX (C3H/APX-KD) expression has been shown to reduce the lignin content in Brachypodium distachyon. However, like many other lignin-modified plants, C3H/APX-KDs show unpredictable pleiotropic phenotypes, including stunted growth, delayed senescence, and reduced seed yield. A system-wide level understanding of altered biological processes in lignin-modified plants can help pinpoint the lignin-modification associated growth defects to benefit future studies aiming to negate the yield penalty. Here, a multi-omic approach was used to characterize molecular changes resulting from C3H/APX-KD associated lignin modification and negative growth phenotype in Brachypodium distachyon. Our findings demonstrate that C3H/APX knockdown in Brachypodium stems substantially alters the abundance of enzymes implicated in the phenylpropanoid biosynthetic pathway and disrupt cellular redox homeostasis. Moreover, it elicits plant defense responses associated with intracellular kinases and phytohormone-based signaling to facilitate growth-defense trade-offs. A deeper understanding along with potential targets to mitigate the pleiotropic phenotypes identified in this study could aid to increase the economic feasibility of lignocellulosic biofuel production.
Daily changes on seasonal ecophysiological responses of the intertidal brown macroalga Lessonia spicata: Implications of climate change
Authors: Celis-Plá Paula S. M. , Trabal Andres , Navarrete Camilo , Troncoso Macarena , Moenne Fabiola , Zúñiga Antonio , Figueroa Félix L. , Sáez Claudio A.
Published: September 2022

Global climate change is expected to have detrimental effects on coastal ecosystems, with impacts observable at the local and regional levels, depending on factors such as light, temperature, and nutrients. Shifts in dominance between primary producers that can capitalize on carbon availability for photosynthesis will have knock-on effects on marine ecosystems, affecting their ecophysiological responses and biological processes. Here, we study the ecophysiological vulnerability, photoacclimation capacity, and tolerance responses as ecophysiological responses of the intertidal kelp Lessonia spicata (Phaeophyceae, Laminariales) during a year through different seasons (autumn, winter, spring, and summer) in the Pacific Ocean (central Chile). Six different daily cycle experiments were carried out within each season. A battery of different biochemical assays associated with antioxidant responses and in-vivo chlorophyll a fluorescence parameter showed that during spring and summer, there was an increase in photosynthetic capacity in the macroalgae, although their responses varied depending on light and nutrient availability in the course of the year. Lessonia spicata showed maximal photosynthesis and a similar photoinhibition pattern in summer compared to the other seasons, and the contents of nitrate and phosphorous in seawater were less in winter. Thus, high irradiance during spring and summer displayed a higher maximal electron transport rate (ETRmax), irradiance of saturation (Ek), non-photochemical quenching (NPQmax), nitrogen and carbon contents, and photoprotector compound levels. Antioxidant activity increased also in summer, the seasonal period with the highest oxidative stress conditions, i.e., the highest level of hydrogen peroxide (H2O2). In contrast, under low irradiance, i.e., wintertime conditions, L. spicata demonstrated lower concentrations of the photosynthetic pigments such as chlorophyll a and carotenoids. Our study suggests that macroalgae that are subjected to increased irradiance and water temperature under lower nutrient availability mediated by seasonal changes (expected to worsen under climate change) respond with higher values of productivity, pigment contents, and photoprotective compounds. Thus, our findings strengthen the available evidence to predict that algae in the order Laminariales, specifically L. spicata (kelp), could better proliferate, with lower vulnerability and greater acclimation, than other marine species subject to future expected conditions associated with climate change.
Arbuscular mycorrhizal fungi enhanced rice proline metabolism under low temperature with nitric oxide involvement
Authors: Liu Zhilei , Bi Shiting , Meng Jingrou , Liu Tingting , Li Pengfei , Yu Cailian , Peng Xianlong
Published: September 2022

Arbuscular mycorrhizal fungi (AMF) are known to improve plant stress tolerance by regulating proline accumulation, and nitric oxide (NO) plays an important signaling role in proline metabolism. Environmental nitrogen (N) affects AMF colonization and its contribution to host plants resistance to stress conditions. However, the relationship between proline metabolism and NO in mycorrhizal rice and the effect of N application on symbiont proline metabolism under low temperature have not been established. Pot culture experiments with different temperature, N and exogenous NO donor treatments were conducted with non-mycorrhizal and mycorrhizal rice. The results showed that AMF enhanced rice proline accumulation under low-temperature stress and decreased glutamate (Glu) and ornithine (Orn) concentrations significantly. In comparison with non-mycorrhizal rice, AMF colonization significantly decreased the Glu concentration, but had little effect on the Orn concentration under low-temperature stress, accompanied by increasing expression of OsP5CS2, OsOAT and OsProDH1. Exogenous application of NO increased proline concentration both under normal and low temperature, which exhibited a higher increase in mycorrhizal rice. NO also triggered the expression of key genes in the Glu and Orn pathways of proline synthesis as well as proline degradation. Higher N application decreased the AMF colonization, and AMF showed greater promotion of proline metabolism at low N levels under low temperature stress by regulating the Glu synthetic pathway. Meanwhile, AMF increased rice nitrate reductase (NR) and nitric oxide synthase (NOS) activities and then enhanced NO accumulation under low N levels. Consequently, it could be hypothesized that one of the mechanisms by which AMF improves plant resistance to low-temperature stress is the accumulation of proline via enhancement of the Glu and Orn synthetic pathways, with the involvement of the signaling molecule NO. However, the contribution of AMF to rice proline accumulation under low-temperature stress was attenuated by high N application.
MtNF-YC6 and MtNF-YC11 are involved in regulating the transcriptional program of arbuscular mycorrhizal symbiosis
Authors: Deng Chen , Li Chun-Jui , Hsieh Chen-Yun , Liu Li-Yu Daisy , Chen Yi-An , Lin Wei-Yi
Published: September 2022

Arbuscular mycorrhizal fungi are obligate symbionts that transfer mineral nutrients to host plants through arbuscules, a fungal structure specialized for exchange for photosynthetic products. MtNF-YC6 and MtNF-YC11, which encode the C subunits of nuclear factor Y (NF-Y) family in Medicago truncatula are induced specifically by arbuscular mycorrhizal symbiosis (AMS). A previous study showed that MtNF-YC6 and MtNF-YC11 are activated in cortical cells of mycorrhizal roots, but the gene functions were unknown. Herein, we identified both MtNF-YB17 and MtNF-YB12 as the interacting partners of MtNF-YC6 and MtNF-YC11 in yeast and plants. MtNF-YB17 was highly induced by AMS and activated in cortical cells only in mycorrhizal roots but MtNF-YB12 was not affected. The formation of B/C heterodimers led the protein complexes to transfer from the cytoplasm to the nucleus. Silencing MtNF-YC6 and C11 by RNA interference (RNAi) resulted in decreased colonization efficiency and arbuscule richness. Coincidently, genes associated with arbuscule development and degeneration in RNAi roots were also downregulated. In silico analysis showed CCAAT-binding motifs in the promoter regions of downregulated genes, further supporting the involvement of NF-Y complexes in transcriptional regulation of symbiosis. Taken together, this study identifies MtNF-YC6- or MtNF-YC11-containing protein complexes as novel transcriptional regulators of symbiotic program and provides a list of potential downstream target genes. These data will help to further dissect the AMS regulatory network.
Colonization characteristics of fungi in Polygonum hydropipe L. and Polygonum lapathifolium L. and its effect on the content of active ingredients
Authors: Zhang Xiaorui , Lv Hongyang , Tian Maoying , Dong Zhaowei , Fu Qinwen , Sun Jilin , Huang Qinwan , Wang Jin
Published: September 2022

Polygonum hydropiper, is a plant of the Persicaria genus, which is commonly used to treat various diseases, including gastrointestinal disorders, neurological disorders, inflammation, and diarrhea. However, because of different local standards of P. hydropiper, people often confuse it with Polygonum lapathifolium L. and other closely related plants. This poses a serious threat to the safety and efficacy of the clinical use of P. hydropiper. This study aims to determine the six active ingredients of P. hydropiper and P. lapathifolium. Then the endophytic fungi and rhizosphere soil of the two species were sequenced by Illumina Miseq PE300. The results show significant differences between the community composition of the leaves, stems, and roots of the P. hydropiper and the P. lapathifolium in the same soil environment. Of the six secondary metabolites detected, five had significant differences between P. hydropiper and P. lapathifolium. Then, we evaluated the composition of the significantly different communities between P. hydropiper and P. lapathifolium. In the P. hydropiper, the relative abundance of differential communities in the leaves was highest, of which Cercospora dominated the differential communities in the leaves and stem; in the P. lapathifolium, the relative abundance of differential community in the stem was highest, and Cladosporium dominated the differential communities in the three compartments. By constructing the interaction network of P. hydropiper and P. lapathifolium and analyzing the network nodes, we found that the core community in P. hydropiper accounted for 87.59% of the total community, dominated by Cercospora; the core community of P. lapathifolium accounted for 19.81% of the total community, dominated by Sarocladium. Of these core communities, 23 were significantly associated with active ingredient content. Therefore, we believe that the community from Cercospora significantly interferes with recruiting fungal communities in P. hydropiper and affects the accumulation of secondary metabolites in the host plant. These results provide an essential foundation for the large-scale production of P. hydropiper. They indicate that by colonizing specific fungal communities, secondary metabolic characteristics of host plants can be helped to be shaped, which is an essential means for developing new medicinal plants.
Melatonin enhanced low-temperature combined with low-light tolerance of pepper (Capsicum annuum L.) seedlings by regulating root growth, antioxidant defense system, and osmotic adjustment
Authors: Li Jing , Xie Jianming , Yu Jihua , Lyv Jian , Zhang Junfeng , Ding Dongxia , Li Nenghui , Zhang Jing , Bakpa Emily Patience , Yang Yan , Niu Tianhang , Gao Feng
Published: September 2022

Melatonin (MT) is an important biologically active hormone that plays a vital role in plant growth and development. In particular, it has been investigated for its roles in abiotic stress management. In this study, pepper seedlings were subjected to low-temperature combined with low-light stress (LL) (15/5°C, 100 μmol m-2s-1) prior to a foliar spray of 200mM MT for 168h to investigate the protective role of MT in pepper seedlings. Our results demonstrated that LL stress negatively affected root growth, and accelerated the accumulation of reactive oxygen species (ROS), including H2O2 and O2−, changed the osmolytes contents, and antioxidative system. However, these were reversed by exogenous MT application. MT effectively promoted the root growth as indicated by significant increase in root length, surface area, root volume, tips, forks, and crossings. In addition, MT reduced the burst of ROS and MDA contents induced by LL, enhanced the activities of SOD, CAT, POD, APX, DHAR, and MDHAR resulted by upregulated expressions of CaSOD, CaPOD, CaCAT, CaAPX, CaDHAR, and CaMDHAR, and elevated the contents of AsA and GSH, declined DHA and GSSH contents, which prevented membrane lipid peroxidation and protected plants from oxidative damages under LL stress. Furthermore, seedlings treated with MT released high contents of soluble sugar and soluble protein in leave, which might enhance LL tolerance by maintaining substance biosynthesis and maintaining cellular homeostasis resulted by high levels of osmolytes and carbohydrate in the cytosol. Our current findings confirmed the mitigating potential of MT application for LL stress by promoting pepper root growth, improving antioxidative defense system, ascorbate-glutathione cycle, and osmotic adjustment.
Systematic analysis of the pectin methylesterase gene family in Nicotiana tabacum and reveal their multiple roles in plant development and abiotic stresses
Authors: Sun Jinhao , Tian Zhen , Li Xiaoxu , Li Shaopeng , Li Zhiyuan , Wang Jinling , Hu Zongyu , Chen Haiqing , Guo Cun , Xie Minmin , Xu Ruyan
Published: September 2022

The pectin methylesterases (PMEs) play multiple roles in regulating plant development and responses to various stresses. In our study, a total of 121 PME genes were identified in the tobacco genome, which were clustered into two groups based on phylogenetic analysis together with Arabidopsis members. The investigations of gene structure and conserved motif indicated that exon/intron and motif organizations were relatively conserved in each group. Additionally, several stress-related elements were identified in the promoter region of these genes. The survey of duplication events revealed that segmental duplications were critical to the expansion of the PME gene family in tobacco. The expression profiles analysis revealed that these genes were expressed in various tissues and could be induced by diverse abiotic stresses. Notably, NtPME029 and NtPME043, were identified as homologues with AtPME3 and AtPME31, respectively. Furthermore, NtPME029 was highly expressed in roots and the over-expression of the NtPME029 gene could promote the development of roots. While NtPME043 could be induced by salt and ABA treatments, and the over-expression of the NtPME043 gene could significantly enhance the salt-stress tolerance in tobacco. Overall, these findings may shed light on the biological and functional characterization of NtPME genes in tobacco.
The role of women’s resources in the prediction of intimate partner violence revictimization by the same or different aggressors
Authors: Bellot Ana , Izal María , Montorio Ignacio
Published: September 2022

The literature studying the characteristics associated with revictimization in Intimate Partner Violence (IPV) is heterogeneous and inconclusive. The absence of studies on the role of the emotional variables of the victims and the failure to distinguish revictimization by the same or different aggressors are two of the main limitations in this area of research. The aim of this work was to study the relative contribution of the material, social, and emotional resources available to IPV victims in predicting revictimization by the same or different perpetrators. The sample consisted of 290 women registered in the city of Madrid who had filed at least one police report for intimate partner violence. The material resources of the victims were evaluated through their level of monthly income and employability status, the social resources through perceived social support, and the emotional resources through emotional regulation and coping strategies. Hierarchical multinomial logistic regression models were estimated to predict single-offender victimization (SRV), same-offender revictimization (VSRSA), and multiple-offender revictimization (VSRDA). The results revealed that: (1) differentiating between revictimization by the same and different aggressors improved the fit of the model by 50.8% compared to when only differentiating between victimized and revictimized women; (2) material resources had no significant weight in the prediction of any type of revictimization; (3) SRV women had more social support than VSRDA women (ExpB = 1.027; p < 0.011); (4), those victims who had made several reports to the authorities of violence by different aggressors (VSRDA), had worse emotional regulation than those victims who had made a single report to the authorities (VSRs; ExpB = 2.934; p < 0.026); and (5) VSRDA obtained the worst mental health indexes and they used more coping strategies based on positive reappraisal than the VSR women (ExpB = 0.863; p < 0.009) and those victims with several reports by the same aggressor (VSRSA; ExpB = 0.891; p < 0.028). These results show that being a victim of several episodes of intimate partner violence by different aggressors should be understood as a form of revictimization of great severity associated with worse emotional regulation and less social support.
Digital health and modern technologies applied in patients with heart failure: Can we support patients’ psychosocial well-being?
Authors: Uchmanowicz Izabella , Wleklik Marta , Foster Marva , Olchowska-Kotala Agnieszka , Vellone Ercole , Kaluzna-Oleksy Marta , Szczepanowski Remigiusz , Uchmanowicz Bartosz , Reczuch Krzysztof , Jankowska Ewa Anita
Published: September 2022

Despite advances in the treatment of heart failure (HF), the physical symptoms and stress of the disease continue to negatively impact patients’ health outcomes. Technology now offers promising ways to integrate personalized support from health care professionals via a variety of platforms. Digital health technology solutions using mobile devices or those that allow remote patient monitoring are potentially more cost effective and may replace in-person interaction. Notably, digital health methods may not only improve clinical outcomes but may also improve the psycho-social status of HF patients. Using digital health to address biopsychosocial variables, including elements of the person and their context is valuable when considering chronic illness and HF in particular, given the multiple, cross-level factors affecting chronic illness clinical management needed for HF self-care.
Exploring the role of COVID-19 pandemic-related changes in social interactions on preschoolers' emotion labeling
Authors: Wermelinger Stephanie , Moersdorf Lea , Ammann Simona , Daum Moritz M.
Published: September 2022

During the COVID-19 pandemic people were increasingly obliged to wear facial masks and to reduce the number of people they met in person. In this study, we asked how these changes in social interactions are associated with young children's emotional development, specifically their emotion recognition via the labeling of emotions. Preschoolers labeled emotional facial expressions of adults (Adult Faces Task) and children (Child Faces Task) in fully visible faces. In addition, we assessed children's COVID-19-related experiences (i.e., time spent with people wearing masks, number of contacts without masks) and recorded children's gaze behavior during emotion labeling. We compared different samples of preschoolers (4.00–5.75 years): The data for the no-COVID-19-experience sample were taken from studies conducted before the pandemic (Adult Faces Task: N = 40; Child Faces Task: N = 30). The data for the with-COVID-19-experience sample (N = 99) were collected during the COVID-19 pandemic in Switzerland between June and November 2021. The results did not indicate differences in children's labeling behavior between the two samples except for fearful adult faces. Children with COVID-19-experience more often labeled fearful faces correctly compared to children with no COVID-19 experience. Furthermore, we found no relations between children's labeling behavior, their individual COVID-19-related experiences, and their gaze behavior. These results suggest that, even though the children had experienced differences in the amount and variability of facial input due to the pandemic, they still received enough input from visible faces to be able to recognize and label different emotions.