Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolomics Reveal Induction of ROS Production and Glycosylation Events in Wheat Upon Exposure to the Green Leaf Volatile Z-3-Hexenyl Acetate

The activation and priming of plant defense upon perception of green leaf volatiles (GLVs) have often been reported. However, information as to which metabolic pathways in plants are affected by GLVs remains elusive. We report the production of reactive oxygen species in the tip of young wheat leaves followed by activation of antioxidant-related enzyme activity. In this study, we aimed to uncover metabolic signatures upon exposure to the GLV Z-3-hexenyl acetate (Z-3-HAC). By using an untargeted metabolomics approach, we observed changes in the phenylpropanoid pathways which yield metabolites that are involved in many anti-oxidative processes. Furthermore, exposure to GLV, followed by infection with Fusarium graminearum (Fg), induced significantly greater changes in the phenylpropanoid pathway compared to a sole Z-3-HAC treatment. Fragmentation of a selection of metabolites, which are significantly more upregulated in the Z-3-HAC + Fg treatment, showed D-glucose to be present as a substructure. This suggests that Z-3-HAC induces early glycosylation processes in plants. Additionally, we identified the presence of hexenyl diglycosides, which indicates that aerial Z-3-HAC is metabolized in the leaves by glycosyltransferases. Together these data indicate that GLV Z-3-HAC is taken up by leaves and incites oxidative stress. This subsequently results in the modulation of the phenylpropanoid pathway and an induction of glycosylation processes.
Imaging Neurochemistry and Brain Structure Tracks Clinical Decline and Mechanisms of ALS in Patients

Background: Oxidative stress and protein aggregation are key mechanisms in amyotrophic lateral sclerosis (ALS) disease. Reduced glutathione (GSH) is the most important intracellular antioxidant that protects neurons from reactive oxygen species. We hypothesized that levels of GSH measured by MR spectroscopic imaging (MRSI) in the motor cortex and corticospinal tract are linked to clinical trajectory of ALS patients. Objectives: Investigate the value of GSH imaging to probe clinical decline of ALS patients in combination with other neurochemical and structural parameters. Methods: Twenty-four ALS patients were imaged at 3 T with an advanced MR protocol. Mapping GSH levels in the brain is challenging, and for this purpose, we used an optimized spectral-edited 3D MRSI sequence with real-time motion and field correction to image glutathione and other brain metabolites. In addition, our imaging protocol included (i) an adiabatic T1ρ sequence to image macromolecular fraction of brain parenchyma, (ii) diffusion tensor imaging (DTI) for white matter tractography, and (iii) high-resolution anatomical imaging. Results: We found GSH in motor cortex (r = −0.431, p = 0.04) and corticospinal tract (r = −0.497, p = 0.016) inversely correlated with time between diagnosis and imaging. N-Acetyl-aspartate (NAA) in motor cortex inversely correlated (r = −0.416, p = 0.049), while mean water diffusivity (r = 0.437, p = 0.033) and T1ρ (r = 0.482, p = 0.019) positively correlated with disease progression measured by imputed change in revised ALS Functional Rating Scale. There is more decrease in the motor cortex than in the white matter for GSH compared to NAA, glutamate, and glutamine. Conclusions: Our study suggests that a panel of biochemical and structural imaging biomarkers defines a brain endophenotype, which can be used to time biological events and clinical progression in ALS patients. Such a quantitative brain endophenotype may stratify ALS patients into more homogeneous groups for therapeutic interventions compared to clinical criteria.
Hydrogenotrophic Methanogenesis Under Alkaline Conditions

A cement-based geological disposal facility (GDF) is one potential option for the disposal of intermediate level radioactive wastes. The presence of both organic and metallic materials within a GDF provides the opportunity for both acetoclastic and hydrogenotrophic methanogenesis. However, for these processes to proceed, they need to adapt to the alkaline environment generated by the cementitious materials employed in backfilling and construction. Within the present study, a range of alkaline and neutral pH sediments were investigated to determine the upper pH limit and the preferred route of methane generation. In all cases, the acetoclastic route did not proceed above pH 9.0, and the hydrogenotrophic route dominated methane generation under alkaline conditions. In some alkaline sediments, acetate metabolism was coupled to hydrogenotrophic methanogenesis via syntrophic acetate oxidation, which was confirmed through inhibition studies employing fluoromethane. The absence of acetoclastic methanogenesis at alkaline pH values (>pH 9.0) is attributed to the dominance of the acetate anion over the uncharged, undissociated acid. Under these conditions, acetoclastic methanogens require an active transport system to access their substrate. The data indicate that hydrogenotrophic methanogenesis is the dominant methanogenic pathway under alkaline conditions (>pH 9.0).
Detecting Citrus in Orchard Environment by Using Improved YOLOv4

Real-time detection of fruits in orchard environments is one of crucial techniques for many precision agriculture applications, including yield estimation and automatic harvesting. Due to the complex conditions, such as different growth periods and occlusion among leaves and fruits, detecting fruits in natural environments is a considerable challenge. A rapid citrus recognition method by improving the state-of-the-art You Only Look Once version 4 (YOLOv4) detector is proposed in this paper. Kinect V2 camera was used to collect RGB images of citrus trees. The Canopy algorithm and the K-Means++ algorithm were then used to automatically select the number and size of the prior frames from these RGB images. An improved YOLOv4 network structure was proposed to better detect smaller citrus under complex backgrounds. Finally, the trained network model was used for sparse training, pruning unimportant channels or network layers in the network, and fine-tuning the parameters of the pruned model to restore some of the recognition accuracy. The experimental results show that the improved YOLOv4 detector works well for detecting different growth periods of citrus in a natural environment, with an average increase in accuracy of 3.15% (from 92.89% to 96.04%). This result is superior to the original YOLOv4, YOLOv3, and Faster R-CNN. The average detection time of this model is 0.06 s per frame at 1920 × 1080 resolution. The proposed method is suitable for the rapid detection of the type and location of citrus in natural environments and can be applied to the application of citrus picking and yield evaluation in actual orchards.
Trust-Based Missing Link Prediction in Signed Social Networks with Privacy Preservation

With the development of mobile Internet, more and more individuals and institutions tend to express their views on certain things (such as software and music) on social platforms. In some online social network services, users are allowed to label users with similar interests as “trust” to get the information they want and use “distrust” to label users with opposite interests to avoid browsing content they do not want to see. The networks containing such trust relationships and distrust relationships are named signed social networks (SSNs), and some real-world complex systems can be also modeled with signed networks. However, the sparse social relationships seriously hinder the expansion of users’ social circle in social networks. In order to solve this problem, researchers have done a lot of research on link prediction. Although these studies have been proved to be effective in the unsigned social network, the prediction of trust and distrust in SSN has not achieved good results. In addition, the existing link prediction research does not consider the needs of user privacy protection, so most of them do not add privacy protection measures. To solve these problems, we propose a trust-based missing link prediction method (TMLP). First, we use the simhash method to create a hash index for each user. Then, we calculate the Hamming distance between the two users to determine whether they can establish a new social relationship. Finally, we use the fuzzy computing model to determine the type of their new social relationship (e.g., trust or distrust). In the paper, we gradually explain our method through a case study and prove our method’s feasibility.
Effect of unbleached pulp Kappa number on the kinetics of chlorine dioxide delignification

Chlorine dioxide delignification of different unbleached kraft pulps from Eucalyptus globulus, having Kappa numbers of 12 to 18, was studied in the temperature range of 285 K to 358 K. The effect of the unbleached pulp Kappa number on the initial fast phase of delignification was investigated with respect to the depletion factors for Kappa number and chlorine dioxide concentration, as proposed by Barroca et al. Furthermore, the behaviour of the floor lignin content of the pulp, or the floor Kappa number, was analysed within this range. The results show that all pulps exhibit a similar pattern, with respect to temperature, in depletion factors for Kappa number and chlorine dioxide concentration. The degree of normalised delignification and chlorine dioxide consumption is very similar and independent of the Kappa number of the unbleached pulps. Moreover, the results reveal that there is a strong correlation between the floor lignin content and the temperature, and that this correlation is applicable to a wide range of unbleached pulp Kappa numbers, since the residual Kappa number is independent of its initial value. The results enable the general application of a kinetic model to kraft pulps with different unbleached Kappa numbers.
How Resilience Promotes Mental Health of Patients With DSM-5 Substance Use Disorder? The Mediation Roles of Positive Affect, Self-Esteem, and Perceived Social Support

Objectives: The existing studies found that resilience is a salient trait that can significantly affect people's psychological well-being with substance use disorders (SUDs). However, few studies examined how the mechanisms are connected between resilience and mental health among patients with Diagnostic and Statistical Manual of Mental Disorders—fifth edition SUD. This study investigated the mediation effects of positive affect, perceived social support, and self-esteem on the effect of resilience on perceived stress and life satisfaction in SUD patients. Design: A total of 415 patients diagnosed with Diagnostic and Statistical Manual of Mental Disorders—fifth edition SUD from the south of China joined the research. Outcome Measures: The study applied Connor–Davidson Resilience Scale, Positive and Negative Affect Scale, Multidimensional Scale of Perceived Social Support, Rosenberg Self-Esteem Scale, and Satisfaction with Life Scale to measure patients' resilience, positive affect, self-esteem, perceived social support, perceived stress, and life satisfaction. Results: Structural equation model analysis revealed that positive affect and self-esteem partially mediate the relationship between resilience and perceived stress. In contrast, positive affect and perceived social support partially mediate the relationship between resilience and life satisfaction. Conclusion: The findings provide insights for evidence-based substance abuse intervention that positive affect, self-esteem, and perceived social support can conditional the effects of resilience on promoting the mental health of SUD patients.
Temporal Progression of Excitotoxic Calcium Following Distal Middle Cerebral Artery Occlusion in Freely Moving Mice

Ischemic stroke is recognized as one of the leading causes of adult disability, morbidity, and death worldwide. Following stroke, acute neuronal excitotoxicity can lead to many deleterious consequences, one of which is the dysregulation of intracellular calcium ultimately culminating in cell death. However, to develop neuroprotective treatments that target neuronal excitotoxicity, it is essential to know the therapeutic time window for intervention following an ischemic event. To address this question, the current study aimed to characterize the magnitude and temporal progression of neuronal intracellular calcium observed following distal middle cerebral artery occlusion (dMCAO) in mice. Using the calcium fluorescence indicator, GCaMP, we tracked neuronal population response in freely moving animals immediately following dMCAO in both the core infarct and peri-infarct regions. Our results demonstrate that calcium excitotoxicity following artery occlusion can be generally characterized by two phases: a transient increase in activity that lasts tens of minutes, followed by a long, slow sustained increase in fluorescence signal. The first phase is primarily thought to represent neuronal hyperexcitability, defining our therapeutic window, while the second may represent gradual cell death. Importantly, we show that the level of intracellular calcium following artery occlusion correlated with the infarct size at 24 h demonstrating a direct connection between excitotoxicity and cell death in our stroke model. In addition, we show that administration of the NMDA antagonist MK-801 resulted in both a decrease in calcium signal and a subsequent reduction in the infarct size. Altogether, this study represents the first demonstration in freely moving animals characterizing the temporal progression of toxic calcium signaling following artery occlusion. In addition, these results define a critical time window for neuroprotective therapeutic intervention in mice.
Dopaminergic System Alteration in Anxiety and Compulsive Disorders: A Systematic Review of Neuroimaging Studies

Objective: The dopaminergic system is involved in many psychiatric disorders as a GABAergic, serotonergic, and glutamatergic system. A systematic review and meta-analysis was performed to elucidate the alteration of the dopaminergic system in anxiety and compulsive disorders. Methods: The databases of Pubmed, Embase, and ScienceDirect were searched and articles reporting the involvement of the dopaminergic system in patients with anxiety disorder and obsessive compulsive disorder (OCD) were recognized. The key research data were extracted from the included articles and standardized mean differences were calculated using meta-analyses if there were more than two studies with obtainable data. Sensitivity analyses were further performed to detect the stability of results, and the qualities of all the included studies were assessed using the Newcastle Ottawa scale. Results: Finally, we identified 8 and 11 studies associated with anxiety disorder and OCD for further analysis, respectively. Most consistently, the striatal dopamine D2 receptor (D2R) of OCD patients had decreased while no significant correlation was found between striatal D2R and disease severity. The striatal dopamine transporter (DAT) had not been significantly altered in both the anxiety disorder and OCD patients. The heterogeneity values from the meta-analyses were extremely high while those results remained stable after sensitivity analyses. Inconsistent data were found in the striatal D2R of patients with anxiety disorder. Limited data had suggested that dopamine synthesis increased in most regions of the cerebral cortex and cerebellum in OCD patients. Conclusions: The most convincing finding was that the D2 receptor decreased in patients with obsessive compulsive disorder. The dopamine transporter may have no relationship with anxiety and compulsive disorder.
Differential Skewing of Circulating MR1-Restricted and γδ T Cells in Human Psoriasis Vulgaris

Psoriasis vulgaris (PV) is a chronic, recurrent inflammatory dermatosis mediated by aberrantly activated immune cells. The role of the innate-like T cells, particularly gammadelta T (γδT) cells and MR1-restricted T lymphocytes, is incompletely explored, mainly through animal models, or by use of surrogate lineage markers, respectively. Here, we used case-control settings, multiparameter flow cytometry, 5-OP-RU-loaded MR1-tetramers, Luminex technology and targeted qRT-PCR to dissect the cellular and transcriptional landscape of γδ and MR1-restricted blood T cells in untreated PV cases (n=21, 22 matched controls). High interpersonal differences in cell composition were observed, fueling transcriptional variability at healthy baseline. A minor subset of canonical CD4+CD8+MR1-tet+TCRVα7. 2+ and CD4+CD8-MR1-tet+TCRVα7. 2+ T cells was the most significantly underrepresented community in male PV individuals, whereas Vδ2+ γδ T cells expressing high levels of TCR and Vδ1-δ2- γδ T cells expressing intermediate levels of TCR were selectively enriched in affected males, partly reflecting disease severity. Our findings highlight a formerly unappreciated skewing of human circulating MAIT and γδ cytomes during PV, and reveal their compositional changes in relation to sex, CMV exposure, serum cytokine content, BMI, and inflammatory burden. Complementing numerical alterations, we finally show that flow-sorted, MAIT and γδ populations exhibit divergent transcriptional changes in mild type I psoriasis, consisting of differential bulk expression for signatures of cytotoxicity/type-1 immunity (EOMES, RUNX3, IL18R), type-3 immunity (RORC, CCR6), and T cell innateness (ZBTB16).
Research and Application of Chondroitin Sulfate/Dermatan Sulfate-Degrading Enzymes

Chondroitin sulfate (CS) and dermatan sulfate (DS) are widely distributed on the cell surface and in the extracellular matrix in the form of proteoglycan, where they participate in various biological processes. The diverse functions of CS/DS can be mainly attributed to their high structural variability. However, their structural complexity creates a big challenge for structural and functional studies of CS/DS. CS/DS-degrading enzymes with different specific activities are irreplaceable tools that could be used to solve this problem. Depending on the site of action, CS/DS-degrading enzymes can be classified as glycosidic bond-cleaving enzymes and sulfatases from animals and microorganisms. As discussed in this review, a few of the identified enzymes, particularly those from bacteria, have wildly applied to the basic studies and applications of CS/DS, such as disaccharide composition analysis, the preparation of bioactive oligosaccharides, oligosaccharide sequencing, and potential medical application, but these do not fulfill all of the needs in terms of the structural complexity of CS/DS.
Quantification of oxide film thickness at the surface of aluminium using XPS

Oxide films grown anodically at the surface of superpure aluminium are used as standards to assess the accuracy of the thickness (dXPS) determined using the Beer–Lambert treatment of the Al 2p metal and oxide peak intensities. For the fitting conditions employed, the value of dXPS is found to be very close to the true film thickness for films <10 nm thick, beyond which imprecise values are obtained. A surface layer of hydration is identified from the curve fitting of the O 1s core level, which would qualitatively account for the slight underestimate of film thickness provided by the expression for dXPS. The validity of the Al 2p fit may be determined through this correlation of thickness but requires first a quantitative assessment of the thickness and composition of the hydroxide‐rich layer. Copyright © 2002 John Wiley & Sons, Ltd.
Deficiency of Mitochondrial Functions and Peroxidation of Frontoparietal Cortex Enhance Isoflurane Sensitivity in Aging Mice

Background: Hypersensitivity to general anesthetics may predict poor postoperative outcomes, especially among the older subjects. Therefore, it is essential to elucidate the mechanism underlying hypersensitivity to volatile anesthetics in the aging population. Given the fact that isoflurane sensitivity increases with aging, we hypothesized that deficiencies of mitochondrial function and elevated oxidative levels in the frontoparietal cortex may contribute to the enhanced sensitivity to isoflurane in aging mice. Methods: Isoflurane sensitivity in aging mice was determined by the concentration of isoflurane that is required for loss of righting reflex (LORR). Mitochondrial bioenergetics of the frontoparietal cortex was measured using a Seahorse XFp analyzer. Protein oxidation and lipid oxidation in the frontoparietal cortex were assessed using the Oxyblot protein oxidation detection kit and thiobarbituric acid reactive substance (TBARS) assay, respectively. Contributions of mitochondrial complex II inhibition by malonate and peroxidation by ozone to isoflurane sensitivity were tested in vivo. Besides, effects of antioxidative therapy on mitochondrial function and isoflurane sensitivity in mice were also measured. Results: The mean concentration of isoflurane that is required for LORR in aging mice (14–16 months old) was 0.83% ± 0.13% (mean ± SD, n = 80). Then, the mice were divided into three groups as sensitive group (S group, mean − SD), medium group (M group), and resistant group (R group, mean + SD) based on individual concentrations of isoflurane required for LORR. Activities of mitochondrial complex II and complex IV in mice of the S group were significantly lower than those of the R group, while frontoparietal cortical malondialdehyde (MDA) levels were higher in the mice of S group. Both inhibition of mitochondrial complexes and peroxidation significantly decreased the concentration of isoflurane that is required for LORR in vivo. After treatment with idebenone, the levels of lipid oxidation were alleviated and mitochondrial function was restored in aging mice. The concentration of isoflurane that required for LORR was also elevated after idebenone treatment. Conclusions: Decreased mitochondrial functions and higher oxidative stress levels in the frontoparietal cortex may contribute to the hypersensitivity to isoflurane in aging mice.
Hybridization Slows Rate of Evolution in Crop-Wild Compared to Wild Populations of Weedy Raphanus Across a Moisture Gradient

Hybrid offspring of crops and their wild relatives commonly possess non-adaptive phenotypes and diminished fitness. Regularly, diminished success in early-generation hybrid populations is interpreted to suggest reduced biosafety risk regarding the unintended escape of novel traits from crop populations. Yet hybrid populations have been known to evolve to recover fitness relative to wild progenitors and can do so more rapidly than wild populations, although rates of evolution (for both hybrid populations and their wild progenitors) are sensitive to environmental context. In this research, we asked whether hybrid populations evolved more rapidly than wild populations in the context of soil moisture. We estimated evolutionary rates for 40 Raphanus populations that varied in their history of hybridization and environmental context (imposed by an experimental moisture cline) in two common gardens. After five generations of growing wild and crop-wild hybrid populations across a soil-moisture gradient, hybrid populations exhibited increased seedling emergence frequencies (~6% more), earlier emergence (~1 day), later flowering (~3 days), and larger body size (15–35%)—traits correlated with fitness—relative to wild populations. Hybrid populations, however, exhibited slower evolutionary rates than wild populations. Moreover, the rate of evolution in hybrid populations was consistent across evolutionary watering environments, but varied across watering environments in wild populations. These consistent evolutionary rates exhibited in hybrid populations suggests the evolution of robust traits that perform equally across soil moisture environments—a survival strategy characterized as “jack of all trades. ” Although, diverse integrated weed management practices must be applied to wild and hybrid genotypes to diversify selection on these populations, evaluating the evolutionary rates of weeds in diverse environments will support the development of multi-faceted weed control strategies and effective integrated weed management policies.