Miracle-dz/UniFAR-FTUs huggingface dataset:
Switching Between Methanol Accumulation and Cell Growth by Expression Control of Methanol Dehydrogenase in Methylosinus trichosporium OB3b Mutant

Methanotrophs have been used to convert methane to methanol at ambient temperature and pressure. In order to accumulate methanol using methanotrophs, methanol dehydrogenase (MDH) must be downregulated as it consumes methanol. Here, we describe a methanol production system wherein MDH expression is controlled by using methanotroph mutants. We used the MxaF knockout mutant of Methylosinus trichosporium OB3b. It could only grow with MDH (XoxF) which has a cerium ion in its active site and is only expressed by bacteria in media containing cerium ions. In the presence of 0 μM copper ion and 25 μM cerium ion, the mutant grew normally. Under conditions conducive to methanol production (10 μM copper ion and 0 μM cerium ion), cell growth was inhibited and methanol accumulated (2.6 μmol·mg−1 dry cell weight·h−1). The conversion efficiency of the accumulated methanol to the total amount of methane added to the reaction system was ~0.3%. The aforementioned conditions were repeatedly alternated by modulating the metal ion composition of the bacterial growth medium.
A New Platinum-Based Prodrug Candidate for Chemotherapy and Its Synergistic Effect With Hadrontherapy: Novel Strategy to Treat Glioblastoma

Glioblastoma (GBM) is the most common tumor of the central nervous system. Current therapies, often associated with severe side effects, are inefficacious to contrast the GBM relapsing forms. In trying to overcome these drawbacks, (OC-6-44)-acetatodiamminedichlorido(2-(2-propynyl)octanoato)platinum(IV), also called Pt(IV)Ac-POA, has been recently synthesized. This new prodrug bearing as axial ligand (2-propynyl)octanoic acid (POA), a histone deacetylase inhibitor, has a higher activity due to (i) its high cellular accumulation by virtue of its high lipophilicity and (ii) the inhibition of histone deacetylase, which leads to the increased exposure of nuclear DNA, permitting higher platination and promoting cancer cell death. In the present study, we investigated the effects induced by Pt(IV)Ac-POA and its potential antitumor activity in human U251 glioblastoma cell line using a battery of complementary techniques, i.e., flow cytometry, immunocytochemistry, TEM, and Western blotting analyses. In addition, the synergistic effect of Pt(IV)Ac-POA associated with the innovative oncological hadrontherapy with carbon ions was investigated, with the aim to identify the most efficient anticancer treatment combination. Our in vitro data demonstrated that Pt(IV)Ac-POA is able to induce cell death, through different pathways, at concentrations lower than those tested for other platinum analogs. In particular, an enduring Pt(IV)Ac-POA antitumor effect, persisting in long-term treatment, was demonstrated. Interestingly, this effect was further amplified by the combined exposure to carbon ion radiation. In conclusion, Pt(IV)Ac-POA represents a promising prodrug to be incorporated into the treatment regimen for GBM. Moreover, the synergistic efficacy of the combined protocol using chemotherapeutic Pt(IV)Ac-POA followed by carbon ion radiation may represent a promising approach, which may overcome some typical limitations of conventional therapeutic protocols for GBM treatment.
Why Do They Enroll in This Course? Undergraduates’ Course Choice From a Motivational Perspective

Why do students pick various courses? Interdisciplinary research has highlighted the role of structural constraints, normative expectations, and individual motivation as the joint influences of agency and structure in the service of life goals. Here, we examined undergraduates’ reasons for course choices for their most difficult and most important courses. We compared the reasons for non-major vs. major courses, for freshman vs. juniors, and across different disciplines. College students selected courses that fulfilled their major or breadth requirements, particularly in their freshman year. STEM courses were taken more for career development reasons than other disciplines, particularly humanities courses; social sciences courses were taken more for interest than STEM courses; and humanities courses were taken more for intellectual broadening than STEM courses.
The Realm of Microbial Pigments in the Food Color Market

Colors are added to food items to make them more attractive and appealing. Food colorants therefore, have an impressive market due to the requirements of food industries. A variety of synthetic coloring agents approved as food additives are available and being used in different types of food prepared or manufactured worldwide. However, there is a growing concern that the use of synthetic colors may exert a negative impact on human health and environment in the long run. The natural pigments obtained from animals, plants, and microorganisms are a promising alternative to synthetic food colorants. Compared to animal and plant sources, microorganisms offer many advantages such as no seasonal impact on the quality and quantity of the pigment, ease of handling and genetic manipulation, amenability to large scale production with little or no impact on biodiversity etc. Among the microorganisms algae, fungi and bacteria are being used to produce pigments as food colorants. This review describes the types of microbial food pigments in use, their benefits, production strategies, and associated challenges.
Diffusion Tensor Imaging Group Analysis Using Tract Profiling and Directional Statistics

Group analysis in diffusion tensor imaging is challenging. Comparisons of tensor morphology across groups have typically been performed on scalar measures of diffusivity, such as fractional anisotropy (FA), disregarding the complex three-dimensional morphologies of diffusion tensors. Scalar measures consider only the magnitude of the diffusion but not directions. In the present study, we have introduced a new approach based on directional statistics to use directional information of diffusion tensors in statistical group analysis based on Bingham distribution. We have investigated different directional statistical models to find the best fit. During the experiments, we confirmed that carrying out directional statistical analysis along the tract is much more effective than voxel- or skeleton-guided directional statistics. Hence, we propose a new method called tract profiling and directional statistics (TPDS) applicable to fiber bundles. As a case study, the method has been applied to identify connectivity differences of patients with major depressive disorder. The results obtained with the directional statistic-based analysis are consistent with those of NBS, but additionally, we found significant changes in the right hemisphere striatum, ACC, and prefrontal, parietal, temporal, and occipital connections as well as left hemispheric differences in the limbic areas such as the thalamus, amygdala, and hippocampus. The results are also evaluated with respect to fiber lengths. Comparison with the output of the network-based statistical toolbox indicated that the benefit of the proposed method becomes much more distinctive as the tract length increases. The likelihood of finding clusters of voxels that differ in long tracts is higher in TPDS, while that relationship is not clearly established in NBS.
3D Classification of Cold-Water Coral Reefs: A Comparison of Classification Techniques for 3D Reconstructions of Cold-Water Coral Reefs and Seabed

Cold-water coral (CWC) reefs are complex structural habitats that are considered biodiversity “hotspots” in deep-sea environments and are subject to several climate and anthropogenic threats. As three-dimensional structural habitats, there is a need for robust and accessible technologies to enable more accurate reef assessments. Photogrammetry derived from remotely operated vehicle video data is an effective and non-destructive method that creates high-resolution reconstructions of CWC habitats. Here, three classification workflows [Multiscale Geometrical Classification (MGC), Colour and Geometrical Classification (CGC) and Object-Based Image Classification(OBIA)] are presented and applied to photogrammetric reconstructions of CWC habitats in the Porcupine Bank Canyon, NE Atlantic. In total, six point clouds, orthomosaics, and digital elevation models, generated from structure-from-motion photogrammetry, are used to evaluate each classification workflow. Our results show that 3D Multiscale Geometrical Classification outperforms the Colour and Geometrical Classification method. However, each method has advantages for specific applications pertinent to the wider marine scientific community. Results suggest that advancing from commonly employed 2D image analysis techniques to 3D photogrammetric classification methods is advantageous and provides a more realistic representation of CWC habitat composition.
M2 Macrophage Co-Expression Factors Correlate With Immune Phenotype and Predict Prognosis of Bladder Cancer

Purpose Therapeutic targets of tumor-associated macrophages have been discovered and used clinically as immunotherapy. M2 macrophages are tumor-associated macrophages that promote cancer progression. This article explores the related factors and the effects of type M2 macrophages. Method We obtained bladder cancer (BC) sequencing data from TCGA and GSE31189. We used the CIBERSORT algorithm calculate M2 macrophage proportions among 22 type immune cells. The Estimate package was used to measure BC purity. M2 macrophage-related genes were selected using WGCNA. Receiver operating characteristic curves and Kaplan–Meier analyses were performed to determine the risk score, conducted for M2 macrophage-related factors. The Pearson test was used to determine the correlation among M2 macrophage-related genes, clinical phenotype, immune phenotype and tumor mutation burden (TMB). The TIMER database was used to calculate correlations among M2 macrophages and other cancers. Results Expression of four M2 macrophages co-expressed genes (CD163, CD209, CSF1, MMD) positively correlated with infiltration of M2 macrophages, which were enriched in the negative regulation of immune system process and the positive regulation of tumor necrosis factor production. M2 macrophage-related factors are robust biomarkers for predicting the BC and immune phenotypes. The Cox regression model built on these four co-expression factors showed a close correlation with outcome (AUC = 0.64). The four co-expression factors negatively correlated outcome and TMB. Conclusion Four co-expressed genes promote high levels of infiltration of type M2 macrophages in the negative regulation of immune system processes and the positive regulation of tumor necrosis factor production processes. These co-expressed genes and the biological process they involve might suggest new strategies for regulation of chemotaxis in M2 macrophages.
Critical Dynamics in Spontaneous Resting-State Oscillations Are Associated With the Attention-Related P300 ERP in a Go/Nogo Task

Sustained attention is the ability to continually concentrate on task-relevant information, even in the presence of distraction. Understanding the neural mechanisms underlying this ability is critical for comprehending attentional processes as well as neuropsychiatric disorders characterized by attentional deficits, such as attention deficit hyperactivity disorder (ADHD). In this study, we aimed to investigate how trait-like critical oscillations during rest relate to the P300 evoked potential—a biomarker commonly used to assess attentional deficits. We measured long−range temporal correlations (LRTC) in resting-state EEG oscillations as index for criticality of the signal. In addition, the attentional performance of the subjects was assessed as reaction time variability (RTV) in a continuous performance task following an oddball paradigm. P300 amplitude and latencies were obtained from EEG recordings during this task. We found that, after controlling for individual variability in task performance, LRTC were positively associated with P300 amplitudes but not latencies. In line with previous findings, good performance in the sustained attention task was related to higher P300 amplitudes and earlier peak latencies. Unexpectedly, we observed a positive relationship between LRTC in ongoing oscillations during rest and RTV, indicating that greater criticality in brain oscillations during rest relates to worse task performance. In summary, our results show that resting-state neuronal activity, which operates near a critical state, relates to the generation of higher P300 amplitudes. Brain dynamics close to criticality potentially foster a computationally advantageous state which promotes the ability to generate higher event-related potential (ERP) amplitudes.
A Self-Compassion and Mindfulness-Based Cognitive Mobile Intervention (Serene) for Depression, Anxiety, and Stress: Promoting Adaptive Emotional Regulation and Wisdom

Introduction: Many individuals and families are currently experiencing a high level of COVID-19-related stress and are struggling to find helpful coping mechanisms. Mindfulness-based interventions are becoming an increasingly popular treatment for individuals experiencing depression and chronic levels of stress. The app (Serene) draws from scholarly evidence on the efficacy of mindfulness meditations and builds on the pre-existing apps by incorporating techniques that are used in some therapies such as cognitive behavioral therapy and mindfulness-based cognitive therapy. Methods: Participants were randomly assigned to a 4-week mindfulness and self-compassion-based cognitive smartphone intervention (Serene) or a wait-list control group. They were instructed to engage in self-compassion and mindfulness practices and a cognitive restructuring task. They also completed measures that evaluated their levels of depression, stress, anxiety, self-compassion, wisdom, psychological well-being, and subjective well-being. The intervention group was also instructed to track their weekly engagement with the app. Standardized effect sizes for between-group differences were calculated using Cohen's d for complete case analyses. Results: Complete case analyses from baseline to the end of this randomized controlled trial demonstrated significant moderate between-group differences for depressive symptoms (d = −0.43) and decisiveness (d = 0.34). Moderate between-group differences were also found for self-compassion (d = 0.6) such that significant improvements in self-kindness, common humanity, mindfulness and decreases in self-judgement, isolation, and overidentification were observed. A small between-group difference was found for emotional regulation (d = 0.28). Moreover, a significant moderate within-group decrease in stress (d = −0.52) and anxiety symptoms (d = −0.47) was also observed in the intervention group. Conclusions: Serene is an effective intervention that promotes increased levels of self-compassion and emotional regulation. Engaging with Serene may help reduce depressive symptoms through mindfulness, self-compassion, and cognitive restructuring which help reduce overidentification with one's negative emotions. As individuals rebalance their thinking through cognitive restructuring, they can identify the varying stressors in their life, develop action plans and engage in adaptive coping strategies to address them. Serene may promote greater self-understanding which may provide one with a more balanced perspective on their current upsetting situations to positively transform their challenges during the pandemic.
Prognostic Implication of the Expression Level of PECAM-1 in Non-small Cell Lung Cancer

Background: Lung cancer is a malignant disease that threatens human health. Hence, it is crucial to identify effective prognostic factors and treatment targets. Single-cell RNA sequencing can quantify the expression profiles of transcripts in individual cells. Methods: GSE117570 profiles were downloaded from the Gene Expression Omnibus database. Key ligand-receptor genes in the tumor and the normal groups were screened to identify integrated differentially expressed genes (DEGs) from the GSE118370 and The Cancer Genome Atlas Lung Adenocarcinoma databases. DEGs associated with more ligand-receptor pairs were selected as candidate DEGs for Gene Ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and survival analysis. In addition, we conducted validation immunohistochemical experiments on postoperative specimens of 30 patients with lung cancer. Results: A total of 18 candidate DEGs were identified from the tumor and the normal groups. The analysis of the GO biological process revealed that these DEGs were mainly enriched in wound healing, in response to wounding, cell migration, cell motility, and regulation of cell motility, while the KEGG pathway analysis found that these DEGs were mainly enriched in proteoglycans in cancer, bladder cancer, malaria, tyrosine kinase inhibitor resistance in Epidermal Growth Factor Receptor (EGFR), and the ERBB signaling pathway. Survival analysis showed that a high, rather than a low, expression of platelet endothelial cell adhesion molecule-1 (PECAM-1) was associated with improved survival. Similarly, in postoperative patients with lung cancer, we found that the overall survival of the PECAM-1 high-expression group shows a better trend than the PECAM-1 low-expression group (p = 0.172). Conclusions: The candidate DEGs identified in this study may play some important roles in the occurrence and development of lung cancer, especially PECAM-1, which may present potential prognostic biomarkers for the outcome.
Inhibition of Shear-Induced Platelet Aggregation by Xueshuantong via Targeting Piezo1 Channel-Mediated Ca2+ Signaling Pathway

XueShuanTong (XST) comprising therapeutically active ginsenosides, a lyophilized extract of Panax notoginseng roots, is extensively used in traditional Chinese medicine to treat ischemic heart and cerebrovascular diseases. Our recent study shows that treatment with XST inhibits shear-induced thrombosis formation but the underlying mechanism remained unclear. This study aimed to investigate the hypothesis that XST inhibited shear-induced platelet aggregation via targeting the mechanosensitive Ca2+-permeable Piezo1 channel by performing platelet aggregation assay, Ca2+ imaging and Western blotting analysis. Exposure to shear at physiologically (1,000–2000 s−1) and pathologically related rates (4,000–6,000 s−1) induced platelet aggregation that was inhibited by treatment with GsMTx-4. Exposure to shear evoked robust Ca2+ responses in platelets that were inhibited by treatment with GsMTx-4 and conversely enhanced by treatment with Yoda1. Treatment with XST at a clinically relevant concentration (0.15 g L−1) potently inhibited shear-induced Ca2+ responses and platelet aggregation, without altering vWF-mediated platelet adhesion and rolling. Exposure to shear, while resulting in no effect on the calpain-2 expression in platelets, induced calpain-2-mediated cleavage of talin1 protein, which is known to be critical for platelet activation. Shear-induced activation of calpain-2 and cleavage of talin1 were attenuated by treatment with XST. Taken together, our results suggest that XST inhibits shear-induced platelet aggregation via targeting the Piezo1 channel to prevent Piezo1-mediated Ca2+ signaling and downstream calpain-2 and talin1 signal pathway, thus providing novel insights into the mechanism of the therapeutic action of XST on platelet aggregation and thrombosis formation.
Characterization of CRN-Like Genes From Plasmopara viticola: Searching for the Most Virulent Ones

Grapevine downy mildew is an insurmountable disease that endangers grapevine production and the wine industry worldwide. The causal agent of the disease is the obligate biotrophic oomycete Plasmopara viticola, for which the pathogenic mechanism remains largely unknown. Crinkling and necrosis proteins (CRN) are an ancient class of effectors utilized by pathogens, including oomycetes, that interfere with host plant defense reactions. In this study, 27 CRN-like genes were cloned from the P. viticola isolate YL genome, hereafter referred to as PvCRN genes, and characterized in silico and in planta. PvCRN genes in ‘YL’ share high sequence identities with their ortholog genes in the other three previously sequenced P. viticola isolates. Sequence divergence among the genes in the PvCRN family indicates that different PvCRN genes have different roles. Phylogenetic analysis of the PvCRN and the CRN proteins encoded by genes in the P. halstedii genome suggests that various functions might have been acquired by the CRN superfamily through independent evolution of Plasmopara species. When transiently expressed in plant cells, the PvCRN protein family shows multiple subcellular localizations. None of the cloned PvCRN proteins induced hypersensitive response (HR)-like cell death on the downy mildew-resistant grapevine Vitis riparia. This was in accordance with the result that most PvCRN proteins, except PvCRN11, failed to induce necrosis in Nicotiana benthamiana. Pattern-triggered immunity (PTI) induced by INF1 was hampered by several PvCRN proteins. In addition, 15 PvCRN proteins prevented Bax-induced plant programmed cell death. Among the cell death-suppressing members, PvCRN17, PvCRN20, and PvCRN23 were found to promote the susceptibility of N. benthamiana to Phytophthora capsici, which is a semi-biotrophic oomycete. Moreover, the nucleus-targeting member, PvCRN19, promoted the susceptibility of N. benthamiana to P. capsici. Therefore, these PvCRN proteins were estimated to be virulent effectors involved in the pathogenicity of P. viticola YL. Collectively, this study provides comprehensive insight into the CRN effector repertoire of P. viticola YL, which will help further elucidate the molecular mechanisms of the pathogenesis of grapevine downy mildew.
Similar Is Not the Same – Mate Recognition in a Parasitoid Wasp

Finding and recognizing a suitable mate is a key prerequisite to reproductive success. Insects often recognize prospective mates using chemical cues and signals. Among these, cuticular lipids commonly serve for mate recognition at close range. The lipid layer on the surface of insects is comprised predominantly of cuticular hydrocarbons (CHCs), though more polar compounds may also be present. While the composition of the cuticular profile is typically species specific, many species additionally show differentiation between the sexes by sex specific compounds and/or compound ratios. It is often assumed that a clear sexual dimorphism of cuticular lipid profiles is a prerequisite for a potential function as sex pheromones. Both, sex specific single compounds or the profiles as a whole have been shown to serve as sex pheromones in parasitoid wasps. Here, we studied parasitoid wasps of the species Tachinaephagus zealandicus (Encyrtidae, Hymenoptera). Chemical analyses revealed that this species presents a case where males and females produce the same set of CHCs in similar relative amounts. To test whether these wasps nonetheless can use the cuticular lipids for close range mate recognition, we tested the reaction of males toward freeze-killed conspecifics. Males showed copulation behavior exclusively toward dead females, but not toward dead males. Dead females from which the cuticular lipids had been removed did not elicit copulation behavior by tested males. Reapplication of female whole body extracts restored bioactivity, and males reacted with copulation attempts as often as toward the freeze-killed females. Bioassays with lipid fractions revealed that only the CHC fraction was bioactive on its own. Here, again, males reacted to female, but not to male CHCs. Our results indicate that these wasps are capable of using CHCs for close range sex recognition despite the similarity of male and female profiles.