Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of the jasmonate ligands and their biosynthetic pathways

Jasmonates are phytohormones that regulate multiple aspects of plant development and responses to stress, activating a conserved signaling pathway in land plants. The characterization of jasmonates biosynthetic and signaling pathways revealed that (+)-7-iso-JA-Ile (JA-Ile) is the ligand for the COI1/JAZ receptor in angiosperms, where jasmonates are synthesized through the OPR3-dependent or OPR3-independent pathways. More recently, studies on different model species identified dn-cis-OPDA, dn-iso-OPDA and Δ4-dn-iso-OPDA as the ligands of the COI1/JAZ receptor in the liverwort Marchantia polymorpha, and a receptor-independent role for several jasmonates in streptophytes. To understand the distribution of bioactive jasmonates in the green lineage and how their biosynthetic pathways evolved, we combined phylogenetic analyses and jasmonates metabolomics in representative species from different lineages. We found that both OPDA and dn-cis-OPDA are ubiquitous in land plants and present also in charophyte algae, underscoring their importance as ancestral signalling molecules. In contrast, JA-Ile biosynthesis emerged within lycophytes coincident with the evolutionary appearance of JAR1 function. We show that JA biosynthesis mediated by OPR1/OPR2 appeared in charophytes most likely as a degradation pathway of OPDA/dn-cis-OPDA before OPR3 emergence. Therefore, our results demonstrate that the OPR3-independent JA biosynthesis pathway is ancient and predates the evolutionary appearance of the OPR3-dependent pathway. Moreover, we identified a negative correlation between dn-iso-OPDA and JA-Ile in land plants which supports that dn-iso-OPDA is the relevant form of the hormone perceived by COI1/JAZ in bryophytes and lycophytes.
Imaging microglia surveillance during sleep-wake cycles in freely behaving mice

Microglia surveillance manifests itself as dynamic changes in cell morphology and functional remodeling. Whether and how microglia surveillance is coupled to brain state switches during natural sleep-wake cycles remain unclear. To address this question, we used miniature two-photon microscopy (mTPM) to acquire time-lapse high-resolution microglia images of the somatosensory cortex, along with EEG/EMG recordings and behavioral video, in freely-behaving mice. We uncovered fast and robust brain state-dependent changes in microglia surveillance, occurring in parallel with sleep dynamics and early-onset phagocytic microglial contraction during sleep deprivation stress. We also detected local norepinephrine fluctuation occurring in a sleep state-dependent manner. We showed that the locus coeruleus-norepinephrine system, which is crucial to sleep homeostasis, is required for both sleep state-dependent and stress-induced microglial responses and β2-adrenergic receptor signaling plays a significant role in this process. These results provide direct evidence that microglial surveillance is exquisitely tuned to signals and stressors that regulate sleep dynamics and homeostasis so as to adjust its varied roles to complement those of neurons in the brain. In vivo imaging with mTPM in freely behaving animals, as demonstrated here, opens a new avenue for future investigation of microglia dynamics and sleep biology in freely behaving animals.
Physiological adaptation in flagellar architecture improves Vibrio alginolyticus chemotaxis in complex environments

Bacteria navigate natural habitats with a wide range of mechanical properties, from the ocean to the digestive tract and soil, by rotating helical flagella like propellers. Species differ in the number, position, and shape of their flagella, but the adaptive value of these flagellar architectures is unclear. Many species traverse multiple types of environments, such as pathogens inside and outside a host. We investigate the hypothesis that flagellar architectures mediate environment-specific benefits in the marine pathogen Vibrio alginolyticus which exhibits physiological adaptation to the mechanical environment. In addition to its single polar flagellum, the bacterium produces lateral flagella in environments that differ mechanically from water. These are known to facilitate surface motility and attachment. We use high-throughput 3D bacterial tracking to quantify chemotactic performance of both flagellar architectures in three archetypes of mechanical environments relevant to the bacterium’s native habitats: water, polymer solutions, and hydrogels. We reveal that lateral flagella impede chemotaxis in water by lowering the swimming speed but improve chemotaxis in both types of complex environments. Statistical trajectory analysis reveals two distinct underlying behavioral mechanisms: In viscous solutions of the polymer PVP K90, lateral flagella increase the swimming speed. In agar hydrogels, despite lowering the swimming speed, lateral flagella improve overall chemotactic performance by preventing trapping in pores. Our findings show that lateral flagella are multi-purpose tools with a wide range of applications beyond surfaces. They implicate flagellar architecture as a mediator of environment-specific benefits and point to a rich space of bacterial navigation behaviors in complex environments.
he pph ] 3 0 A ug 2 01 8 “ Spin-dependent ” μ → e Conversion on Light Nuclei

The experimental sensitivity to μ → e conversion will improve by four or more orders of magnitude in coming years, making it interesting to consider the “spin-dependent” (SD) contribution to the rate. This process does not benefit from the atomic-number-squared enhancement of the spin-independent (SI) contribution, but probes different operators. We give details of our recent estimate of the spin dependent rate, expressed as a function of operator coefficients at the experimental scale. Then we explore the prospects for distinguishing coefficients or models by using different targets, both in an EFT perspective, where a geometric representation of different targets as vectors in coefficient space is introduced, and also in three leptoquark models. It is found that comparing the rate on isotopes with and without spin could allow to detect spin dependent coefficients that are at least a factor of few larger than the spin independent ones. Distinguishing among the axial, tensor and pseudoscalar operators that induce the SD rate would require calculating the nuclear matrix elements for the second two. Comparing the SD rate on nuclei with an odd proton vs odd neutron could allow to distinguish operators involving u quarks from those involving d quarks; this is interesting because the distinction is difficult to make for SI operators.
Knowledge mining for the differentiation pattern with respect to the productivity and trophic status of some selected lakes of Western Himalayas

The present study deals with an account of the primary productivity and trophic status of Rewalsar, Kuntbhyog, and Prashar lakes of Western Himalayas. Seasonal variations in gross primary productivity (GPP) (g C m–2 day–1), net primary productivity (NPP, respiration (R), and the NPP/R ratio have been studied and compared with hydrobiological factors. Among various factors, temperature, light, nutrients, and chlorophyll a were accountable for high productivity. Nygaard’s trophic state indices were calculated. GPP showed a positive relationship with water temperature, penetration of light, nitrate, and with phosphate. The extensive range of the compound index observed in Rewalsar (12.00–20.00) and Kuntbhyog lakes (12.50–18.00) confirmed their eutrophic nature. Based on the trophic classification of waters and on the basis of productivity, Nygaard’s trophic state indices, and richness of nutrients, Rewalsar and Kuntbhyog lakes could be categorized as eutrophic, whereas Prashar Lake, as oligo-eutrophic. Based on the presence, absence, frequency of appearance, and abundance of different organisms recorded during the present investigation, bioindicators of trophic status have been determined.
Psychological mechanisms and interventions directed at vaccination attitudes

Attitudes about vaccination impact not only the individual but also society. Therefore, understanding the underlying psychological processes of those who disagree with vaccination is critical for creating compassion through understanding and change through promoting autonomy. The current review aimed to fill a gap in the literature, outlining the state of the recent research on vaccination attitudes, specifically on the underlying mechanisms driving anti-vaccination movements and individuals' thoughts and behaviors. In addition, we aimed to evaluate current research on the effectiveness of interventions targeting these mechanisms. Overall, results indicated that those declining vaccines had beliefs related to distrust in the scientific community and pharmaceutical companies and moral preferences for purity and liberty. In addition, our review identified the potential for utilizing motivational interviewing techniques as an intervention. This literature review provides a platform for further research and enhances the current understanding of vaccination attitudes.
Immunity of turbot Induced by inactivated vaccine of Aeromonas salmonicida from the perspective of DNA methylation

Introduction DNA methylation was one of the most important modification in epigenetics and played an important role in immune response. Since the introduction of Scophthalmus maximus, the scale of breeding has continued to expand, during which diseases caused by various bacteria, viruses and parasites have become increasingly serious. Therefore, the inactivated vaccines have been widely researched and used in the field of aquatic products with its unique advantages. However, the immune mechanism that occurred in turbot after immunization with inactivated vaccine of Aeromonas salmonicida was not clear. Methods In this study, differentially methylated regions (DMRs) were screened by Whole Genome Bisulfite Sequencing (WGBS) and significantly differentially expressed genes (DEGs) were screened by Transcriptome sequencing. Double luciferase report assay and DNA pull-down assay were further verified the DNA methylation state of the gene promoter region affected genes transcriptional activity after immunization with inactivated vaccine of Aeromonas salmonicida. Results A total of 8149 differentially methylated regions (DMRs) were screened, in which there were many immune-related genes with altered DNA methylation status. Meanwhile, 386 significantly differentially expressed genes (DEGs) were identified, many of which were significantly enriched in Toll-like receptor signaling pathway, NOD-like receptor signaling pathway and C-type lectin receptor signaling pathway. Combined analysis of WGBS results and RNA-seq results, a total of 9 DMRs of negatively regulated genes are located in the promoter region, including 2 hypermethylated genes with lower expression and 7 hypomethylated genes with higher expression. Then, two immune-related genes C5a anaphylatoxin chemotactic receptor 1-like (C5ar1-Like) and Eosinophil peroxidase-like (EPX-Like), were screened to explore the regulation mechanism of DNA methylation modification on their expression level. Moreover, the DNA methylation state of the gene promoter region affected genes transcriptional activity by inhibiting the binding of transcription factors, which lead to changes in the expression level of the gene. Discussion We jointly analyzed WGBS and RNA-seq results and revealed the immune mechanism that occurred in turbot after immunized with inactivated vaccine of A. salmonicida from the perspective of DNA methylation.
Incidence and predictors of HBV functional cure in patients with HIV/HBV coinfection: A retrospective cohort study

Background This study was the first to examine the association of baseline clinical factors with the rate of HBsAg clearance in a large retrospective cohort of Chinese patients with HIV/HBV coinfection treated with combination antiretroviral therapy (ART). Methods Our retrospective cohort included 431 patients with HIV/HBV coinfection treated with TDF-containing ART. The median follow-up was 6.26 years. Logistic regression was used to investigate the association of baseline variables with HBsAg clearance, and Cox regression was used to investigate the association of baseline variables with time to HBsAg clearance. Results The clearance rate of HBsAg in our study was 0.072 (95% CI 0.049~0.101). In the multivariate logistic regression, advanced age (OR=1.1, P=0.007), high CD4 cell count (OR=2.06, P=0.05), and HBeAg positivity (OR=8.00, P=0.009) were significantly associated with the rate of HBsAg clearance. The AUC of the model integrating the above three predictors was 0.811. Similar results were found in the multivariate Cox regression (HR = 1.09, P = 0.038 for age, HR = 1.05, P = 0.012 for CD4 count and HR = 7.00, P = 0.007 for HBeAg). Conclusions Long-term TDF-containing ART can lead to HBsAg clearance of 7.2% in Chinese patients with HIV/HBV coinfection. Advanced age, high CD4 cell count, and positive HBeAg at baseline could be regarded as potential predictors and biological markers for HBsAg clearance in patients with HIV/HBV coinfection.
Biomechanical evaluation of a novel intervertebral disc repair technique for large box-shaped ruptures

Objective: The purpose of this study was to analyze the feasibility of repairing a ruptured intervertebral disc using a patch secured to the inner surface of the annulus fibrosus (AF). Different material properties and geometries for the patch were evaluated. Methods: Using finite element analysis, this study created a large box-shaped rupture in the posterior-lateral region of the AF and then repaired it with a circular and square inner patch. The elastic modulus of the patches ranged from 1 to 50 MPa to determine the effect on the nucleus pulposus (NP) pressure, vertical displacement, disc bulge, AF stress, segmental range of motion (ROM), patch stress, and suture stress. The results were compared against the intact spine to determine the most suitable shape and properties for the repair patch. Results: The intervertebral height and ROM of the repaired lumbar spine was similar to the intact spine and was independent of the patch material properties and geometry. The patches with a modulus of 2–3 MPa resulted in an NP pressure and AF stresses closest to the healthy disc, and produced minimal contact pressure on the cleft surfaces and minimal stress on the suture and patch of all models. Circular patches caused lower NP pressure, AF stress and patch stress than the square patch, but also caused greater stress on the suture. Conclusion: A circular patch with an elastic modulus of 2–3 MPa secured to the inner region of the ruptured annulus fibrosus was able to immediately close the rupture and maintain an NP pressure and AF stress similar to the intact intervertebral disc. This patch had the lowest risk of complications and produced the greatest restorative effect of all patches simulated in this study.
Read the clonotype: Next-generation sequencing-based lymphocyte clonality analysis and perspectives for application in pathology

Clonality assessment using the unique rearrangements of immunoglobulin (IG) and T-cell receptor (TR) genes in lymphocytes is a widely applied supplementary test for the diagnosis of B-cell and T-cell lymphoma. To enable a more sensitive detection and a more precise comparison of clones compared with conventional clonality analysis based on fragment analysis, the EuroClonality NGS Working Group developed and validated a next-generation sequencing (NGS)-based clonality assay for detection of the IG heavy and kappa light chain and TR gene rearrangements for formalin-fixed and paraffin-embedded tissues. We outline the features and advantages of NGS-based clonality detection and discuss potential applications for NGS-based clonality testing in pathology, including site specific lymphoproliferations, immunodeficiency and autoimmune disease and primary and relapsed lymphomas. Also, we briefly discuss the role of T-cell repertoire of reactive lymphocytic infiltrations in solid tumors and B-lymphoma.
Well-being and quality of life in people with disabilities practicing sports, athletes with disabilities, and para-athletes: Insights from a critical review of the literature

Global well-being (GWB) is a complex, multi-dimensional, and multi-faceted construct that can be explored from two different, but often overlapping, complementary perspectives: the subjective and the objective ones. The subjective perspective, in turn, is comprised of two dimensions: namely, the hedonic and the eudaimonic standpoints. Within the former dimension, researchers have developed the concept of subjective hedonic well-being (SHWB), whereas, within the latter, they have built the framework of psychological and social well-being (PSWB). Disabled people have poorer well-being due to their pathology and may more frequently suffer from anxiety and depressive disorders than their able-bodied counterparts. Sports participation is an essential way to cope with disability. On the other hand, compared with their able-bodied peers, athletes with disabilities and para-athletes undergo a unique series of stressors. Little is known in terms of hedonic and eudaimonic well-being and quality of life in this specific population. Here, we review the literature, with an emphasis on the current state-of-art and gaps in knowledge that need to be addressed by future research. High-quality, large-scale investigations are needed to have a better understanding of the self-perceived (hedonic) and objective (eudaimonic) well-being and quality of life of disabled people practicing sports, athletes with disabilities, and para-athletes.
Gray matter reduction is associated with cognitive dysfunction in depressed patients comorbid with subclinical hypothyroidism

Introduction To explore the association between regional gray matter volume (GMV) and cognitive impairments and ascertain whether the regional brain alterations related to cognitive impairments occur in major depressive disorder (MDD) patients with comorbid subclinical hypothyroidism (SHypo). Methods We enrolled 32 MDD patients, 32 MDD patients with comorbid SHypo, and 32 normal controls and subjected them to thyroid function tests, neurocognitive tests, and magnetic resonance imaging (MRI). Using voxel-based morphometry (VBM) analysis, we examined the pattern of gray matter (GM) in these participants. We also used ANOVA to detect group differences and partial correlation to explore the potential association between GMV alterations and cognitive tests in comorbid patients. Results The comorbid patients exhibited significantly smaller GMV in the right middle frontal gyrus (MFG) than the non-comorbid group. Furthermore, the partial correlation analysis showed that GMV of the right MFG was associated with poor executive function (EF) performance in comorbid patients. Conclusion These findings provide valuable insight into the relationship between the alteration of GMV and cognitive dysfunction of MDD patients with comorbid SHypo.
The Usher syndrome 1C protein harmonin regulates canonical Wnt signaling

Human Usher syndrome (USH) is the most common form of hereditary combined deaf-blindness. USH is a complex genetic disorder, and the pathomechanisms underlying the disease are far from being understood, especially in the eye and retina. The USH1C gene encodes the scaffold protein harmonin which organizes protein networks due to binary interactions with other proteins, such as all USH proteins. Interestingly, only the retina and inner ear show a disease-related phenotype, although USH1C/harmonin is almost ubiquitously expressed in the human body and upregulated in colorectal cancer. We show that harmonin binds to β-catenin, the key effector of the canonical Wnt (cWnt) signaling pathway. We also demonstrate the interaction of the scaffold protein USH1C/harmonin with the stabilized acetylated β-catenin, especially in nuclei. In HEK293T cells, overexpression of USH1C/harmonin significantly reduced cWnt signaling, but a USH1C-R31* mutated form did not. Concordantly, we observed an increase in cWnt signaling in dermal fibroblasts derived from an USH1C R31*/R80Pfs*69 patient compared with healthy donor cells. RNAseq analysis reveals that both the expression of genes related to the cWnt signaling pathway and cWnt target genes were significantly altered in USH1C patient-derived fibroblasts compared to healthy donor cells. Finally, we show that the altered cWnt signaling was reverted in USH1C patient fibroblast cells by the application of Ataluren, a small molecule suitable to induce translational read-through of nonsense mutations, hereby restoring some USH1C expression. Our results demonstrate a cWnt signaling phenotype in USH establishing USH1C/harmonin as a suppressor of the cWnt/β-catenin pathway.
A NONLINEAR RETURN-TO-ISOTROPY MODEL WITH REYNOLDS NUMBER AND ANISOTROPY DEPENDENCY

A new computational model for the return to isotropy is presented. In order to reproduce the significant role of the third invariant IIIb(=bijbjkbki) of the Reynolds stress anisotropy bij[=uiuj/(2k)−(1/3)δij] in the return‐to‐isotropy process, a nonlinear return‐to‐isotropy model is formulated by a Taylor series expansion up to fifth power of bij. Then the strong realizability condition for non‐negativity of the component energies is utilized to reduce the number of model constants produced. Correction for the low Reynolds number effect is then included by investigating an energy‐weighted average time scale of eddies over the three‐dimensional energy spectrum. Superiority of the proposed model performance is exemplified by a number of test computations of homogeneous relaxing turbulence in a wide range of turbulence Reynolds number and IIIb.
Important role of precipitation in controlling a more uniform spring phenology in the Qinba Mountains, China

Under global warming, the gradual pattern of spring phenology along elevation gradients (EG) has significantly changed. However, current knowledge on the phenomenon of a more uniform spring phenology is mainly focused on the effect of temperature and neglected precipitation. This study aimed to determine whether a more uniform spring phenology occurs along EG in the Qinba Mountains (QB) and explore the effect of precipitation on this pattern. We used Savitzky-Golay (S-G) filtering to extract the start of season (SOS) of the forest from the MODIS Enhanced Vegetation Index (EVI) during 2001-2018 and determined the main drivers of the SOS patterns along EG by partial correlation analyses. The SOS showed a more uniform trend along EG in the QB with a rate of 0.26 ± 0.01 days 100 m-1 per decade during 2001-2018, but there were differences around 2011. A delayed SOS at low elevations was possibly due to the reduced spring precipitation (SP) and spring temperature (ST) between 2001 and 2011. Additionally, an advanced SOS at high elevations may have been caused by the increased SP and reduced winter temperature (WT). These divergent trends contributed to a significant uniform trend of SOS with a rate of 0.85 ± 0.02 days 100 m-1 per decade. Since 2011, significantly higher SP (especially at low elevations) and rising ST advanced the SOS, and the SOS at lower altitudes was more advanced than at higher altitudes, resulting in greater SOS differences along EG (0.54 ± 0.02 days 100 m-1 per decade). The SP determined the direction of the uniform trend in SOS by controlling the SOS patterns at low elevations. A more uniform SOS may have important effects on local ecosystem stability. Our findings could provide a theoretical basis for establishing ecological restoration measures in areas experiencing similar trends.