Miracle-dz/UniFAR-FTUs huggingface dataset:
DeepTracer ID: De Novo Protein Identification from Cryo-EM Maps

The recent revolution in cryo-electron microscopy has made it possible to determine macromolecular structures directly from cell extracts. However, identifying the correct protein from the cryo-EM map is still challenging and often needs additional sequence information from other techniques, such as tandem mass spectrometry and/or bioinformatics. Here, we present DeepTracer-ID, a server-based approach to identify the candidate protein in a user-provided organism de novo from a cryo-EM map, without the need for additional information. Our method first uses DeepTracer to generate a protein backbone model that best represents the cryo-EM map, and this model is then searched against the library of AlphaFold2 predictions for all proteins in the given organism. This method is highly accurate and robust: in all 13 experimental maps tested blindly, DeepTracer-ID identified the correct proteins as the top candidates. Eight of the maps were of known structures, while the other five unpublished maps were validated by prior protein annotation and careful inspection of the model refined into the map. The program also showed promising results for both homomeric and heteromeric protein complexes. This platform is possible because of the recent breakthroughs in large-scale protein 3D structure prediction. Statement of Significance While it has now become routine for cryo-EM maps of proteins to reach a near-atomic resolution, potentially allowing for reliable atomic models to be built, there are a growing number of instances where the protein identity may not be known. Without knowing the protein sequence, it is impossible to build an atomic model. DeepTracer-ID is a server-based approach to surmount this problem by identifying the proteins in a given organism that are found in the cryo-EM map. A free web service for global academic access is provided.
Proximal Linearized Iteratively Reweighted Algorithms for Nonconvex and Nonsmooth Optimization Problem

The nonconvex and nonsmooth optimization problem has been attracting increasing attention in recent years in image processing and machine learning research. The algorithm-based reweighted step has been widely used in many applications. In this paper, we propose a new, extended version of the iterative convex majorization–minimization method (ICMM) for solving a nonconvex and nonsmooth minimization problem, which involves famous iterative reweighted methods. To prove the convergence of the proposed algorithm, we adopt the general unified framework based on the Kurdyka–Łojasiewicz inequality. Numerical experiments validate the effectiveness of the proposed algorithm compared to the existing methods.
The ubiquitin-ligase Smurf1 functions in selective autophagy of M. tuberculosis and anti-tuberculous host defense

SUMMARY During antibacterial autophagy, ubiquitination of intracellular bacteria recruits proteins that mediate bacterial delivery to the lysosome for degradation. Smurf1 is an E3 ubiquitin-ligase whose role in selective bacterial autophagy is unknown. We show that Smurf1 facilitates selective autophagy of the human pathogen Mycobacterium tuberculosis (Mtb). Smurf1 −/− macrophages are defective in recruiting polyubiquitin, the proteasome, the ubiquitin-binding autophagy adaptor NBR1, the autophagy protein LC3, and the lysosomal marker LAMP1 to Mtb-associated structures, and are more permissive for Mtb growth. This function of Smurf1 requires both its ubiquitin-ligase and C2 phospholipid-binding domains, and involves K48-rather than K63-linked ubiquitination. Chronically infected Smurf1 −/− mice have increased bacterial load, increased lung inflammation, and accelerated mortality. SMURF1 controls Mtb replication in human macrophages and associates with bacteria in lungs of patients with pulmonary tuberculosis. Thus, Smurf1 is required for selective autophagy of Mtb and host defense against tuberculosis infection. Franco et al. describe a role for the ubiquitin ligase Smurf1 in selective autophagy of intracellular bacteria including M. tuberculosis (Mtb) and L. monocytogenes. Smurf1 mediates K48-ubiquitination of Mtb and recruitment of the proteasome and autophagy machinery components. Smurf1 helps restrict Mtb replication in macrophages and in mice.
Antimicrobial Terpenes Suppressed the Infection Process of Phytophthora in Fennel-Pepper Intercropping System

The interactions between non-host roots and pathogens may be key to the inhibition of soilborne pathogens in intercropping systems. Fennel (Foeniculum vulgare) can be intercropped with a wide range of other plants to inhibit soilborne pathogens in biodiversity cultivation. However, the key compounds of fennel root exudates involved in the interactions between fennel roots and pathogens are still unknown. Here, a greenhouse experiment confirmed that intercropping with fennel suppressed pepper (Capsicum annuum) blight disease caused by Phytophthora capsici. Experimentally, the roots and root exudates of fennel can effectively interfere with the infection process of P. capsici at rhizosphere soil concentrations by attracting zoospores and inhibiting the motility of the zoospores and germination of the cystospores. Five terpene compounds (D-limonene, estragole, anethole, gamma-terpenes, and beta-myrcene) that were identified in the fennel rhizosphere soil and root exudates were found to interfere with P. capsica infection. D-limonene was associated with positive chemotaxis with zoospores, and a mixture of the five terpene compounds showed a strong synergistic effect on the infection process of P. capsici, especially for zoospore rupture. Furthermore, the five terpene compounds can induce the accumulation of reactive oxygen species (ROS), especially anethole, in hyphae. ROS accumulation may be one of the antimicrobial mechanisms of terpene compounds. Above all, we proposed that terpene compounds secreted from fennel root play a key role in Phytophthora disease suppression in this intercropping system.
Interpersonal Emotion Regulation: Consequences for Brands in Customer Service Interactions

This research demonstrates that interpersonal emotion regulation—attempts to manage others’ feelings—influences consumer perceptions during sales and service interactions impacting brand trust and loyalty. Building on previous research linking interpersonal emotion regulation to improved outcomes between people, across five experiments, we demonstrate that antecedent-focused interpersonal emotion regulation strategies result in enhanced brand loyalty and brand trust compared to response-focused interpersonal emotion regulation strategies. Analysis of mediation models reveals this effect is explained by changes in the consumer’s emotions, which in turn influence evaluations of the service interaction and subsequently impacts brand outcomes. We identify reactance as a moderator of this effect, such that customers with low (high) reactance to interpersonal regulation attempts exhibit more (less) favorable brand trust and loyalty evaluations. Further, we demonstrate that the visibility of interpersonal emotion regulation represents an important boundary condition. These findings support the process model of interpersonal emotion regulation and generate important insights for both theory and practice.
Asymmetric Interaction Between Two Mycorrhizal Fungal Guilds and Consequences for the Establishment of Their Host Plants

Arbuscular mycorrhiza (AM) and ectomycorrhiza (EcM) are the most abundant and widespread types of mycorrhizal symbiosis, but there is little and sometimes conflicting information regarding the interaction between AM fungi (AMF) and EcM fungi (EcMF) in soils. Their competition for resources can be particularly relevant in successional ecosystems, which usually present a transition from AM-forming herbaceous vegetation to EcM-forming woody species. The aims of this study were to describe the interaction between mycorrhizal fungal communities associated with AM and EcM hosts naturally coexisting during primary succession on spoil banks and to evaluate how this interaction affects growth and mycorrhizal colonization of seedlings of both species. We conducted a greenhouse microcosm experiment with Betula pendula and Hieracium caespitosum as EcM and AM hosts, respectively. They were cultivated in three-compartment rhizoboxes. Two lateral compartments contained different combinations of both host plants as sources of fungal mycelia colonizing the middle compartment, where fungal biomass, diversity, and community composition as well as the growth of each host plant species’ seedlings were analyzed. The study’s main finding was an asymmetric outcome of the interaction between the two plant species: while H. caespitosum and associated AMF reduced the abundance of EcMF in soil, modified the composition of EcMF communities, and also tended to decrease growth and mycorrhizal colonization of B. pendula seedlings, the EcM host did not have such effects on AM plants and associated AMF. In the context of primary succession, these findings suggest that ruderal AM hosts could hinder the development of EcM tree seedlings, thus slowing the transition from AM-dominated to EcM-dominated vegetation in early successional stages.
The Impact of Entrepreneurial Spirituality on Business Performance: Based on the Survey of Private Enterprise Executives in Fujian China

Entrepreneurship is the main engine of economic development. This paper aims to explore the impact of high executives’ entrepreneurial spirituality (ES) on the business performance in China under the background of “mass entrepreneurship and innovation. ” By analyzing the relevant literature of entrepreneurship, the connotation and elements of ES are determined. According to the relevant research, we design the questionnaire of ES and business performance. The questionnaire was distributed to 100 private enterprise entrepreneurs by equidistant sampling, and 74 valid questionnaires were recovered. According to the questionnaire, responsibility has the highest score, followed by innovation, proactiveness, and risk-taking. The ES of women is slightly higher than that of men. The entrepreneurs with higher education also have higher score in ES. After analyzing the impact of different elements of ES on enterprise performance using structural equation modeling (SEM) and regression equation model, it is found that: (1) ES has a positive impact on enterprise performance. (2) Different factors of ES have different effects on business performance, and innovation and proactiveness play the greatest role. (3) There is an inverted U-shaped relationship between innovation, risk-taking, and business performance.
Emotions Modulate Affordances-Related Motor Responses: A Priming Experiment

Traditionally, research on affordances and emotions follows two separate routes. For the first time, this article explicitly links the two phenomena by investigating whether, in a discrimination task (artifact vs. natural object), the motivational states induced by emotional images can modulate affordances-related motor response elicited by dangerous and neutral graspable objects. The results show faster RTs: (i) for both neutral and dangerous objects with neutral images; (ii) for dangerous objects with pleasant images; (iii) for neutral objects with unpleasant images. Overall, these data support a significant effect of emotions on affordances. The article also proposes a brain neural network underlying emotions and affordance interplay.
Red Blood Cell Distribution Width Is Associated With Adverse Kidney Outcomes in Patients With Chronic Kidney Disease

Background Chronic kidney disease (CKD) is a global public health issue. Red blood cell distribution width (RDW) is a recently recognized potential inflammatory marker, which mirrors the variability in erythrocyte volume. Studies indicate that elevated RDW is associated with increased risk of mortality in CKD patients, while evidence regarding the impact of RDW on kidney outcome is limited. Methods Altogether 523 patients with CKD stage 1–4 from a single center were enrolled. We identified the cutoff point for RDW level using maximally selected log-rank statistics. The time-averaged estimated glomerular filtration rate (eGFR) slope was determined using linear mixed effects models. Rapid CKD progression was defined by an eGFR decline >5 ml/min/1.73 m2/year. The composite endpoints were defined as doubling of serum creatinine, a 30% decline in initial eGFR or incidence of eGFR < 15 ml/min/1.73 m2, whichever occurred first. Multivariable logistic regression or Cox proportional hazards regression was performed, as appropriate. Results During a median follow-up of 26 [interquartile range (IQR): 12, 36] months, 65 (12.43%) patients suffered a rapid CKD progression and 172 (32.89%) composite kidney events occurred at a rate of 32.3/100 patient-years in the high RDW group, compared with 14.7/100 patient-years of the remainder. The annual eGFR change was clearly steeper in high RDW group {−3.48 [95% confidence interval (CI): −4.84, −2.12] ml/min/1.73 m2/year vs. −1.86 [95% CI: −2.27, −1.45] ml/min/1.73 m2/year among those with RDW of >14.5% and ≤14.5%, respectively, P for between-group difference <0.05}. So was the risk of rapid renal function loss (odds ratio = 6.79, 95% CI: 3.08–14.97) and composite kidney outcomes (hazards ratio = 1.51, 95% CI: 1.02–2.23). The significant association remained consistent in the sensitivity analysis. Conclusion Increased RDW value is independently associated with accelerated CKD deterioration. Findings of this study suggest RDW be a potential indicator for risk of CKD progression.
Suffer or Survive: Decoding Salt-Sensitivity of Lemongrass and Its Implication on Essential Oil Productivity

The cultivation of lemongrass (Cymbopogon flexuosus) crop is dominated by its medicinal, food preservative, and cosmetic demands. The growing economy of the lemongrass market suggests the immense commercial potential of lemongrass and its essential oil. Nevertheless, the continuous increase of the saline regime threatens the growth and productivity of most of the plant life worldwide. In this regard, the present experiment explores the salt sensitiveness of the lemongrass crop against five different levels of salt stress. Metabolomic analyses suggest that lemongrass plants can effectively tolerate a salt concentration of up to 80 mM and retain most of their growth and productivity. However, extreme NaCl concentrations (≥160 mM) inflicted significant (α = 0.05) damage to the plant physiology and exhausted the lemongrass antioxidative defence system. Therefore, the highest NaCl concentration (240 mM) minimised plant height, chlorophyll fluorescence, and essential oil production by up to 50, 27, and 45%. The overall data along with the salt implications on photosynthetic machinery and ROS metabolism suggest that lemongrass can be considered a moderately sensitive crop to salt stress. The study, sensu lato, can be used in reclaiming moderately saline lands with lemongrass cultivation converting such lands from economic liability to economic asset.
Lingonberry (Vaccinium vitis-idaea L.) Interact With Lachnum pygmaeum to Mitigate Drought and Promote Growth

The application of Ericoid mycorrhizal (ErM) fungi is considered to be an important strategy for increasing plant yield and drought resistance. In this study, we isolated and identified two ErM fungi that can promote the growth of lingonberry. We tried to understand the potential of these two ErM fungi to promote the growth of lingonberry and the strategies to help plants cope with water shortage. The use value of ErM fungi was evaluated by inoculating Oidiodendron maius FC (OmFC) or Lachnum pygmaeum ZL6 (LpZL6), well-watered (WW) and severe drought stress (SDS). The results showed that the mycelium of LpZL6 was denser than that of OmFC, and both ErM fungi significantly increased the biomass of lingonberry stems and roots. They also significantly increased the chlorophyll content by 65.6 and 97.8%, respectively. In addition, inoculation with LpZL6 fungi can improve drought resistance, promote root growth and increase root wet weight by 1157.6%. Drought reduced the chlorophyll content and soluble sugar content of lingonberry but increased significantly after inoculation with LpZL6. Inoculation with LpZL6 decreased lingonberry’s malondialdehyde (MDA) content but increased the superoxide dismutase (SOD) activity. Overall, these results indicated that the successful coexistence of ErM fungi and lingonberry alleviated the adverse effects of drought stress through higher secondary metabolites and photosynthetic pigment synthesis.
Exposure of Keratinocytes to Candida Albicans in the Context of Atopic Milieu Induces Changes in the Surface Glycosylation Pattern of Small Extracellular Vesicles to Enhance Their Propensity to Interact With Inhibitory Siglec Receptors

Candida albicans (C. albicans) infection is a potential complication in the individuals with atopic dermatitis (AD) and can affect clinical course of the disease. Here, using primary keratinocytes we determined that atopic milieu promotes changes in the interaction of small extracellular vesicles (sEVs) with dendritic cells and that this is further enhanced by the presence of C. albicans. sEV uptake is largely dependent on the expression of glycans on their surface; modelling of the protein interactions indicated that recognition of this pathogen through C. albicans-relevant pattern recognition receptors (PRRs) is linked to several glycosylation enzymes which may in turn affect the expression of sEV glycans. Here, significant changes in the surface glycosylation pattern, as determined by lectin array, could be observed in sEVs upon a combined exposure of keratinocytes to AD cytokines and C. albicans. This included enhanced expression of multiple types of glycans, for which several dendritic cell receptors could be proposed as binding partners. Blocking experiments showed predominant involvement of the inhibitory Siglec-7 and -9 receptors in the sEV-cell interaction and the engagement of sialic acid-containing carbohydrate moieties on the surface of sEVs. This pointed on ST6 β-Galactoside α-2,6-Sialyltransferase 1 (ST6GAL1) and Core 1 β,3-Galactosyltransferase 1 (C1GALT1) as potential enzymes involved in the process of remodelling of the sEV surface glycans upon C. albicans exposure. Our results suggest that, in combination with atopic dermatitis milieu, C. albicans promotes alterations in the glycosylation pattern of keratinocyte-derived sEVs to interact with inhibitory Siglecs on antigen presenting cells. Hence, a strategy aiming at this pathway to enhance antifungal responses and restrict pathogen spread could offer novel therapeutic options for skin candidiasis in AD.
The Obsessive–Compulsive Symptoms in Tic Disorders and the Psychometric Properties of Children’s Yale–Brown Obsessive–Compulsive Scale: An Evidence-Based Survey in a Chinese Sample

Objective Patients with tic disorders (TDs) usually also have obsessive–compulsive disorder (OCD). The severity of obsessive–compulsive symptoms (OCSs) in TD is widely evaluated using the Children’s Yale–Brown Obsessive–Compulsive Scale (CY-BOCS). However, there is no survey on the severity of OCSs in patients with TD based on a Chinese sample, and the reliability and validity of the CY-BOCS in patients with TD have not been well established in China. This study examined the severity of OCSs in TDs and the psychometric properties of the CY-BOCS in Chinese pediatric patients with TD. Methods A total of 367 patients who were diagnosed with TD [152 with Tourette syndrome (TS)] were enrolled in the Department of Psychiatry at Beijing Children’s Hospital in China. The mean age of the patients was 9.21 ± 2.06 years (range: 5–16 years). The Yale Global Tic Severity Scale (YGTSS) and CY-BOCS were used as screening tools. The psychometric properties of the CY-BOCS were assessed using Cronbach’s alpha, test-retest reliability, and construct validity. Results The OCSs in TDs were 3.93 ± 5.15 based on the CY-BOCS in the whole sample. The older adolescent group showed higher scores than the young adolescent groups (Z = −3.37, p = 0.001). However, the young adolescent group showed a higher incidence rate of OCSs than the older adolescent group (p < 0.01). Men with TDs also showed a higher incidence rate of OCSs than women (p = 0.03). The reliability and validity analyses of the CY-BOCS showed Cronbach’s alpha and test-retest reliability values of 0.81 and 0.82, respectively. The CY-BOCS showed an acceptable level in the two-factor structure (obsession and compulsive) in patients with TD. The comparative fit index (CFI) was 0.84 for TD, 0.86 for Tourette, 0.94 for the younger adolescent group, and 0.74 for the older adolescent group. Conclusion More OCSs were identified in the TS group and the older adolescent group with TDs. The CY-BOCS showed good psychometric properties in children and adolescents with TD, especially in younger patients with TD. OCSs might be associated with age and functional impairment of TD.
Age, Motivation, and Emotion Regulation Skills Predict Treatment Outcome in an Internet-Based Self-Help Intervention for COVID-19 Related Psychological Distress

Introduction First evidence suggests that internet-based self-help interventions effectively reduce COVID-19 related psychological distress. However, it is yet unclear which participant characteristics are associated with better treatment outcomes. Therefore, we conducted secondary analyses on data from a randomized controlled trial investigating the efficacy of a 3-week internet-based self-help intervention for COVID-19 related psychological distress. In this exploratory analysis, we examined several predictors ranging from sociodemographic variables to psychological distress, resource-related, and treatment-related variables. This includes, for example, age, motivation, and emotion regulation skills. Treatment outcomes were defined as post-treatment depressive symptoms and post-treatment resilience. Methods In a total of 107 participants with at least mild depressive symptoms, possible predictor variables and treatment outcomes were assessed using self-report measures. For example, emotion regulation skills were assessed by the Self-report measure for the assessment of emotion regulation skills. In a first step, we performed a separate linear regression analysis for each potential predictor. In a second step, predictors meeting a significant threshold of p < 0.05 were entered in linear multiple regression models. Baseline scores of the respective outcome measure were controlled for. Results The mean age of the participants was 40.36 years (SD = 14.59, range = 18–81 years) with the majority being female (n = 87, 81.3%). Younger age predicted lower post-treatment depressive symptoms. Additionally, higher motivation to use the intervention and better pre-treatment emotion regulation skills predicted higher post-treatment resilience. Conclusion The current study provides preliminary evidence regarding the relationship between participant characteristics and treatment outcome in internet-based self-help interventions for COVID-19 related distress. Our results suggest that under the circumstances surrounding COVID-19 such interventions might be particularly beneficial for young adults regarding depressive symptoms. Moreover, focusing on participants' existing strengths might be a promising approach to promote resilience through internet-based self-help interventions. However, since this was an exploratory analysis in an uncontrolled setting, further studies are needed to draw firm conclusions about the relationship of participant characteristics and treatment outcome in internet-based self-help interventions for COVID-19 related psychological distress.