Miracle-dz/UniFAR-FTUs huggingface dataset:
Surface Properties of LaNi5 and TiFe—Future Opportunities of Theoretical Research in Hydrides

Hydrogen in the solid state compounds is still considered as a safe method of energy storage. The ultimate metal hydrides or other materials that can be used for this purpose remain unknown. Such metal hydrides shall have favorable thermodynamics and kinetics of hydrogen ad/desorption, and it shall be resistant to contamination of H2 and should not constitute any environmental hazards. Theoretical investigations, based on quantum mechanics approach, have a well-established position in modern materials research; however, their application for design of new alloys with tailored properties for reversible hydrogen storage is rarely present in the literature. The mainstream research deals with accurate prediction of thermodynamic and structural properties of hydrides as a function of composition or external parameters. On the other hand, the kinetic effects related to hydrogen transport or interaction between solid and pure or contaminated H2 are more demanding. They cannot be easily automated. We present calculations of the equilibrium crystal shapes for LaNi5 and TiFe—two important materials that show reversible hydrogen cycling near ambient conditions. Understanding of the surface properties is crucial for development of materials with better cyclability or resistance to hydrogen impurities. Indeed, the calculated adsorption energy of carbon oxides or water is stronger than hydrogen. These molecules block the active sites for H2 dissociation, leading to formation of surface oxides. Particularly strong adsorption of CO/CO2 on TiFe explains large degradation of hydrogen storage capacity of this compound by carbon oxides. Over-representation of La on exposed facets of LaNi5 is related to formation of La2O3 and La(OH)3. Such examples show that the present development of computational methods allows reliable studies of intermetallic properties related to their surface or novel catalytic applications.
Academic Burnout and Problematic Smartphone Use During the COVID-19 Pandemic: The Effects of Anxiety and Resilience

Background: Academic burnout has been associated with problematic smartphone use. However, the mechanism underlying this relation has been inadequately explored during the COVID-19 pandemic. Materials and Methods: A total of 748 Chinese undergraduate students were recruited in the study who were measured with their levels of academic burnout, anxiety, resilience, and problematic smartphone use. Results: Our study showed that academic burnout significantly predicted problematic smartphone use both directly and indirectly via anxiety. By constructing a moderated mediation model, our study found that resilience moderated the direct impact and the second half of the indirect path (between anxiety and problematic smartphone use); however, with the moderation effects of resilience, both the indirect impact of academic burnout on problematic smartphone use via anxiety became insignificant. Conclusions: Our findings brought additional evidence on the association between academic burnout and problematic smartphone use and significantly suggested the potential solution to alleviate the influences.
CdgC, a Cyclic-di-GMP Diguanylate Cyclase of Azospirillum baldaniorum Is Involved in Internalization to Wheat Roots

Azospirillum baldaniorum is a plant growth-promoting rhizobacterium (PGPR) capable of fixing nitrogen, the synthesis of several phytohormones including indole-acetic acid, and induction of plant defenses against phytopathogens. To establish a successful and prolonged bacteria-plant interaction, A. baldaniorum can form biofilms, bacterial communities embedded in a self-made matrix formed by extracellular polymeric substances which provide favorable conditions for survival. A key modulator of biofilm formation is the second messenger bis-(3′–5′)-cyclic-dimeric-GMP (c-di-GMP), which is synthesized by diguanylate cyclases (DGC) and degraded by specific phosphodiesterases. In this study, we analyzed the contribution of a previously uncharacterized diguanylate cyclase designated CdgC, to biofilm formation and bacterial-plant interaction dynamics. We showed that CdgC is capable of altering c-di-GMP levels in a heterologous host, strongly supporting its function as a DGC. The deletion of cdgC resulted in alterations in the three-dimensional structure of biofilms in a nitrogen-source dependent manner. CdgC was required for optimal colonization of wheat roots. Since we also observed that CdgC played an important role in exopolysaccharide production, we propose that this signaling protein activates a physiological response that results in the strong attachment of bacteria to the roots, ultimately contributing to an optimal bacterium-plant interaction. Our results demonstrate that the ubiquitous second messenger c-di-GMP is a key factor in promoting plant colonization by the PGPR A. baldaniorum by allowing proficient internalization in wheat roots. Understanding the molecular basis of PGPR-plant interactions will enable the design of better biotechnological strategies of agro-industrial interest.
Correlating Biodegradation Kinetics of 2,4-Dichlorophenoxyacetic Acid (2,4-D) and 2,4,5-Trichlorophenoxyacetic Acid (2,4,5-T) to the Dynamics of Microbial Communities Originating From Soil in Vietnam Contaminated With Herbicides

We determined the degradation rates of the herbicides 2,4-D and 2,4,5-T by two different bacterial communities. One of these originated from soil heavily contaminated with herbicides from Bien Hoa airbase, the other from the same soil but amended with additional carbon and Gibbs energy sources. The community from the contaminated, but untreated, soil degraded both 2,4-D and 2,4,5-T within 5 days of cultivation. The one from the amended soil, however, hardly showed any degradation of the compounds throughout 23 days of cultivation. After refreshment of the medium and prolonged culturing, however, this community degraded both herbicides within 25 days with progressively increasing rates. nMDS analysis revealed a highly significant differentiation pattern of the two communities. Cultures inoculated with amended soil showed a significant increase of Bacillus and Paenibacillus upon prolonged exposure to the herbicides. The succession in the culture from untreated soil, on the other hand, was dominated by species from the Proteobacteria. We were able to isolate two of them and they were shown to be related to Bordetella petrii and Sphingomonas histidinilytica, successively. Subsequent PCR analyses of their DNA revealed the presence of key genes involved in the degradation of the herbicides. This study provides a more fundamental understanding of the biodegradation of 2,4-D and 2,4,5-T by displaying part of the bacterial community succession during their breakdown allowing a comprehensive view on potential key degraders.
Gain-of-Function Properties of a Dynamin 2 Mutant Implicated in Charcot-Marie-Tooth Disease

Mutations in the gene encoding dynamin 2 (DNM2), a GTPase that catalyzes membrane constriction and fission, are associated with two autosomal-dominant motor disorders, Charcot-Marie-Tooth disease (CMT) and centronuclear myopathy (CNM), which affect nerve and muscle, respectively. Many of these mutations affect the pleckstrin homology domain of DNM2, yet there is almost no overlap between the sets of mutations that cause CMT or CNM. A subset of CMT-linked mutations inhibit the interaction of DNM2 with phosphatidylinositol (4,5) bisphosphate, which is essential for DNM2 function in endocytosis. In contrast, CNM-linked mutations inhibit intramolecular interactions that normally suppress dynamin self-assembly and GTPase activation. Hence, CNM-linked DNM2 mutants form abnormally stable polymers and express enhanced assembly-dependent GTPase activation. These distinct effects of CMT and CNM mutations are consistent with current findings that DNM2-dependent CMT and CNM are loss-of-function and gain-of-function diseases, respectively. In this study, we present evidence that at least one CMT-causing DNM2 mutant (ΔDEE; lacking residues 555DEE557) forms polymers that, like the CNM mutants, are resistant to disassembly and display enhanced GTPase activation. We further show that the ΔDEE mutant undergoes 2-3-fold higher levels of tyrosine phosphorylation than wild-type DNM2. These results suggest that molecular mechanisms underlying the absence of pathogenic overlap between DNM2-dependent CMT and CNM should be re-examined.
Comparison of the IOLMaster 700 and the Pentacam in the Analysis of the Lens Nuclear Density Before the Cataract Surgery

Purpose: To evaluate the difference of the lens nuclear density measured before and after mydriasis by using the IOLMaster 700 (Carl Zeiss Meditec AG, Jena, Germany) and the Pentacam Scheimpflug imaging (Pentacam HR, Oculus Incorporation, Wetzlar, Germany) and investigate the relationship between the measurement data and the phacoemulsification parameters. Methods: Patients with age-related nuclear cataracts diagnosed on the slit-lamp examination were enrolled in the age range of 53–76 years. No patient had a history of ocular surgery, laser treatment, or general disorders affecting vision. The mean optical density (OD) was measured by the IOLMaster 700 by using the Image-Pro® Plus software before and after mydriasis. The Pentacam nucleus densitometry (PND) was obtained automatically from the Pentacam Scheimpflug imaging and compared with OD. The correlation between OD and effective phacoemulsification time (EPT), PND, and EPT were analyzed, respectively. Results: In this study, 53 eyes of 52 patients were evaluated. Before and after mydriasis, the mean OD values were 64.34 ± 23.31 and 63.81 ± 23.21 pixel units, respectively; the mean PND values were 28.51 ± 11.42 and 25.41 ± 11.31, respectively; and the mean EPT value was 6.24 ± 3.49. The Bland–Altman analysis showed that the lens nuclear densities of the two devices were highly consistent. There was no significant difference in the OD values (t = 0.455, p > 0.05) before and after mydriasis, but the difference has existed in the PND values (t = 2.509, p < 0.05). The OD and PND values were positively correlated with EPT before and after mydriasis (rOD−Before = 0.604, rOD−After = 0.593, rPND−Before = 0.701, and rPND−After = 0.891, p < 0.01). Conclusion: The combination of the IOLMaster 700 and the Image-Pro® Plus software can quantitatively evaluate the degree of the cataract lens opacification. It has good consistency with the Pentacam and is positively correlated with the phacoemulsification parameters. It is expected to become a new method to predict the phacoemulsification parameters before and during cataract surgery.
Three-Dimensional Subject-Specific Knee Shape Reconstruction with Asynchronous Fluoroscopy Images Using Statistical Shape Modeling

Background and objectives: Statistical shape modeling (SSM) based on computerized tomography (CT) datasets has enabled reasonably accurate reconstructions of subject-specific 3D bone morphology from one or two synchronous radiographs for clinical applications. Increasing the number of radiographic images may increase the reconstruction accuracy, but errors related to the temporal and spatial asynchronization of clinical alternating bi-plane fluoroscopy may also increase. The current study aimed to develop a new approach for subject-specific 3D knee shape reconstruction from multiple asynchronous fluoroscopy images from 2, 4, and 6 X-ray detector views using a CT-based SSM model; and to determine the optimum number of planar images for best accuracy via computer simulations and in vivo experiments. Methods: A CT-based SSM model of the knee was established from 60 training models in a healthy young Chinese male population. A new two-phase optimization approach for 3D subject-specific model reconstruction from multiple asynchronous clinical fluoroscopy images using the SSM was developed, and its performance was evaluated via computer simulation and in vivo experiments using one, two and three image pairs from an alternating bi-plane fluoroscope. Results: The computer simulation showed that subject-specific 3D shape reconstruction using three image pairs had the best accuracy with RMSE of 0.52 ± 0.09 and 0.63 ± 0.085 mm for the femur and tibia, respectively. The corresponding values for the in vivo study were 0.64 ± 0.084 and 0.69 ± 0.069 mm, respectively, which was significantly better than those using one image pair (0.81 ± 0.126 and 0.83 ± 0.108 mm). No significant differences existed between using two and three image pairs. Conclusion: A new two-phase optimization approach was developed for SSM-based 3D subject-specific knee model reconstructions using more than one asynchronous fluoroscopy image pair from widely available alternating bi-plane fluoroscopy systems in clinical settings. A CT-based SSM model of the knee was also developed for a healthy young Chinese male population. The new approach was found to have high mode reconstruction accuracy, and those for both two and three image pairs were much better than for a single image pair. Thus, two image pairs may be used when considering computational costs and radiation dosage. The new approach will be useful for generating patient-specific knee models for clinical applications using multiple asynchronous images from alternating bi-plane fluoroscopy widely available in clinical settings. The current SSM model will serve as a basis for further inclusion of training models with a wider range of sizes and morphological features for broader applications.
The Efficacy and Safety of Fecal Microbiota Transplantation Combined With Biofeedback for Mixed Constipation: A Retrospective Cohort Study

This study aims to assess the effectiveness and safety of fecal microbiota transplantation (FMT) combined with biofeedback for patients with mixed constipation. Patients who received biofeedback (biofeedback group, n = 40) and those who received FMT combined with biofeedback (FMT combination group, n = 45) were enrolled. Spontaneous bowel movements (SBMs) frequency, Bristol Stool Form Scale (BSFS), and Patient Assessment of Constipation Symptoms (PAC-SYM) score were analyzed to evaluate the effect of treatment. Gastrointestinal Quality of Life Index (GIQLI) scores of patients were used to assess the quality of life, and the safety of FMT combination therapy was evaluated by the presence of adverse events. The 16S rRNA gene sequencing was performed on the fecal samples of 12 donors, feces of 31 patients before and after receiving FMT combination treatment. Comparing the biofeedback group and the FMT combination group 1 month after the treatment, significant differences were observed in the mean value of SBM frequency, BSFS, and PAC-SYM scores, which were 2.15 ± 1.05 vs. 3.61 ± 0.89 (p = 0.0031), 2.1 ± 0.9 vs. 2.5 ± 1.2 (p = 0.008), and 2.4 ± 0.5 vs. 2.2 ± 0.6 (p = 0.0021), respectively. Meanwhile, FMT combination therapy had long-term beneficial effects according to the data collected at six months and 12 months after the treatment. With respect to the quality of life, GIQLI scores were higher in the FMT combination group (103.6 ± 15.1) compared with that in the biofeedback group (88.7 ± 10.1) one month after administration (p = 0.0042). In addition, there were no significant differences between the two groups in adverse events, including abdominal pain, diarrhea, dizziness, nausea, vomiting, and other side effects. Results of 16S rRNA gene sequencing showing some well-known probiotics had significantly increased after FMT combination treatment compared with pre-FMT samples, such as Prevotella and Bifidobacterium. Findings of this study suggested that FMT combined with biofeedback could be effective and safe for patients with mixed constipation.
Bitbow Enables Highly Efficient Neuronal Lineage Tracing and Morphology Reconstruction in Single Drosophila Brains

Identifying the cellular origins and mapping the dendritic and axonal arbors of neurons have been century old quests to understand the heterogeneity among these brain cells. Current Brainbow based transgenic animals take the advantage of multispectral labeling to differentiate neighboring cells or lineages, however, their applications are limited by the color capacity. To improve the analysis throughput, we designed Bitbow, a digital format of Brainbow which exponentially expands the color palette to provide tens of thousands of spectrally resolved unique labels. We generated transgenic Bitbow Drosophila lines, established statistical tools, and streamlined sample preparation, image processing, and data analysis pipelines to conveniently mapping neural lineages, studying neuronal morphology and revealing neural network patterns with unprecedented speed, scale, and resolution.
Gene Signatures Detect Damaged Liver Sinusoidal Endothelial Cells in Chronic Liver Diseases

Liver sinusoidal endothelial cells have a gatekeeper function in liver homeostasis by permitting substrates from the bloodstream into the space of Disse and regulating hepatic stellate cell activation status. Maintenance of LSEC's highly specialized phenotype is crucial for liver homeostasis. During liver fibrosis and cirrhosis, LSEC phenotype and functions are lost by processes known as capillarization and LSEC dysfunction. LSEC capillarization can be demonstrated by the loss of fenestrae (cytoplasmic pores) and the manifestation of a basement membrane. Currently, no protein or genetic markers can clearly distinguish healthy from damaged LSECs in acute or chronic liver disease. Single cell (sc)RNA sequencing efforts have identified several LSEC populations in mouse models for liver disease and in human cirrhotic livers. Still, there are no clearly defined genesets that can identify LSECs or dysfunctional LSEC populations in transcriptome data. Here, we developed genesets that are enriched in healthy and damaged LSECs which correlated very strongly with healthy and early stage- vs. advanced human liver diseases. A damaged LSEC signature comprised of Fabp4/5 and Vwf/a1 was established which could efficiently identify damaged endothelial cells in single cell RNAseq data sets. In LSECs from an acute CCl4 liver injury mouse model, Fabp4/5 and Vwf/a1 expression is induced within 1–3 days while in cirrhotic human livers these 4 genes are highly enriched in damaged LSECs. In conclusion, our newly developed gene signature of damaged LSECs can be applicable to a wide range of liver disease etiologies, implicating a common transcriptional alteration mechanism in LSEC damage.
Optimization of the Heterologous Expression of the Cannabinoid Type-1 (CB1) Receptor

The G protein-coupled type 1 cannabinoid receptor (CB1R) mediates virtually all classic cannabinoid effects, and both its agonists and antagonists hold major therapeutic potential. Heterologous expression of receptors is vital for pharmacological research, however, overexpression of these proteins may fundamentally alter their localization pattern, change the signalling partner preference and may also spark artificial clustering. Additionally, recombinant CB1Rs are prone to intense proteasomal degradation, which may necessitate substantial modifications, such as N-terminal truncation or signal sequence insertion, for acceptable cell surface expression. We report here that tuning down the expression intensity of the full-length CB1R reduces proteasomal degradation and offers receptor levels that are comparable to those of endogenous CB1 receptors. As opposed to high-efficiency expression with conventional promoters, weak promoter-driven CB1R expression provides ERK 1/2 and p38 MAPK signalling that closely resemble the activity of endogenous CB1Rs. Moreover, weakly expressed CB1R variants exhibit plasma membrane localization, preserve canonical Gi-signalling but prevent CB1R-Gs coupling observed with high-expression variants. Based on these findings, we propose that lowering the expression level of G protein-coupled receptors should always be considered in heterologous expression systems in order to reduce the pressure on the proteasomal machinery and to avoid potential signalling artefacts.
Statistical Modeling for the Effects of Vegetative Growth on Power Distribution System Reliability

The purpose of this paper is to examine the effects of vegetative growth on the reliability of electric power distribution system under normal (storm exclusion) operating conditions, and to determine an effective vegetation maintenance schedule. Generalized statistical linear regression models, including Poisson, Negative Binomial, Zero-Inflated, and their mixed model variants are developed and are applied into a 5-years outage data along with vegetation maintenance history from a power company in Midwestern United States. From the methodological point of view, advanced statistical models such as zero-inflated models and mixed models are utilized the first time on outage data and provided good fit to the occurrence of outages. In practice, numerical results from this study suggest that an optimal cycle length of every 6 years could be greatly helpful for power companies in devising a cost-effective schedule, improving system reliability, and maintaining customer satisfaction.
Mycobacterium tuberculosis Exploits Focal Adhesion Kinase to Induce Necrotic Cell Death and Inhibit Reactive Oxygen Species Production

Tuberculosis is a deadly, contagious respiratory disease that is caused by the pathogenic bacterium Mycobacterium tuberculosis (Mtb). Mtb is adept at manipulating and evading host immunity by hijacking alveolar macrophages, the first line of defense against inhaled pathogens, by regulating the mode and timing of host cell death. It is established that Mtb infection actively blocks apoptosis and instead induces necrotic-like modes of cell death to promote disease progression. This survival strategy shields the bacteria from destruction by the immune system and antibiotics while allowing for the spread of bacteria at opportunistic times. As such, it is critical to understand how Mtb interacts with host macrophages to manipulate the mode of cell death. Herein, we demonstrate that Mtb infection triggers a time-dependent reduction in the expression of focal adhesion kinase (FAK) in human macrophages. Using pharmacological perturbations, we show that inhibition of FAK (FAKi) triggers an increase in a necrotic form of cell death during Mtb infection. In contrast, genetic overexpression of FAK (FAK+) completely blocked macrophage cell death during Mtb infection. Using specific inhibitors of necrotic cell death, we show that FAK-mediated cell death during Mtb infection occurs in a RIPK1-depedent, and to a lesser extent, RIPK3-MLKL-dependent mechanism. Consistent with these findings, FAKi results in uncontrolled replication of Mtb, whereas FAK+ reduces the intracellular survival of Mtb in macrophages. In addition, we demonstrate that enhanced control of intracellular Mtb replication by FAK+ macrophages is a result of increased production of antibacterial reactive oxygen species (ROS) as inhibitors of ROS production restored Mtb burden in FAK+ macrophages to same levels as in wild-type cells. Collectively, our data establishes FAK as an important host protective response during Mtb infection to block necrotic cell death and induce ROS production, which are required to restrict the survival of Mtb.