Miracle-dz/UniFAR-FTUs huggingface dataset:
Aberration Corrector Tuning with Machine-Learning-Based Emittance Measurements and Bayesian Optimization

Aberration-corrected scanning transmission electron microscopes (STEM) use a series of multipole magnets to generate a sub-Ångstrom-sized electron beam for atomic resolution imaging and chemical composition mapping 1 . A new scheme for aberration corrector alignment is proposed, including both new ways of beam quality measurement and aberration corrector control. The new scheme targets fully automated corrector alignment to achieve microscope tuning with greater speed and less human bias. For beam quality measurements, we trained a convolutional neural network (CNN) to determine the beam emittance 2 ⁠ from a single Ronchigram, as shown in Figure 1(a). Beam emittance is a single variable that characterizes the volume occupied by the beam in the phase space. Emittance is convex against the aberration coefficients, and proportional to the root mean square of the phase error, as shown in Figure 1(b). Both indicate that beam emittance is a single robust objective for aberration correction, and avoids the cusp-like instabilities of the individual aberration coefficients 3 . The emittance would be a conserved quantity without the introduction of aberrations, and aberration correction can be guided by minimizing the emittance growth. We trained a CNN with a VGG16 architecture using simulated Ronchigram-emittance pairs to predict emittance from a single Ronchigram. The Ronchigrams are simulated using a random phase plate following ref 4 , with
Correlative Light and Electron Microscopy for the Study of the Structural Arrangement of Bacterial Microcrystalline Cellulose Microfibrils

Cellulose is an abundant polymer with a crystalline structure that represents a large section of the total biomass on Earth The mechanical properties, biodegradability and abundant availability of cellulose makes it an ideal starting material for the production of biofuels, biocomposites and bioenergetics products The generation of cellulose-based products often requires both physical, chemical and biochemical processing including hydrolysis reactions to hydrolyse cellulose into cellulosic nanomaterials To improve the efficiency of these processes, it is crucial to understand the structure of cellulose at the micro-and nanoscale. Cellulose microfibrils are postulated to have frequent disordered regions that disrupt their crystalline structure forming “dislocations” that affect the overall structure and could influence depolymerisation reactions This structural model has been recently supported by studies involving super-resolution (SR) fluorescence imaging that showed the presence of sites with alternating high and low labelling densities along the length of bacterial cellulose microfibrils. While these observations suggest the presence of pockets of accessibility within the crystalline cellulose, their structural origin and morphology remains elusive. Insight into this question can be gained through correlative techniques, such as correlative light and electron microscopy (CLEM), which
Cathodoluminescence of alkaline earth hexafluorometallate nanowires

Cathodoluminescence alkaline earth nanowires Hexafluorometallates with the general formula ABF6 (A=Ba, Sr, Ca etc. and B = Si, Ge, Sn, Ti etc.) are widely studied as potential red-emitting phosphors by doping with Mn4+ transition metal ions however the cathodoluminescence from Mn4+ doped phosphors are poor. The class of materials mentioned above is also identified as potential host lattices for rare-earth (RE3+) dopants In general, alkaline earth metal fluorides their consistent luminescence the dopant ions and they are promising candidates for inorganic scintillators, their chemical stability corner-sharing of
Topic-based Visual Text Summarization and Analysis 1

We are building an interactive, visual text analysis tool that aids users in analyzing a large collection of text. Unlike existing work in text analysis, which focuses either on developing sophisticated text analytic techniques or inventing novel visualization metaphors, ours is tightly integrating state-of-the-art text analytics with interactive visualization to maximize the value of both. In this paper, we focus on describing our work from two aspects. First, we present the design and development of a time-based, visual text summary that effectively conveys complex text summarization results produced by the Latent Dirichlet Allocation (LDA) model. Second, we describe a set of rich interaction tools that allow users to work with a created visual text summary to further interpret the summarization results in context and examine the text collection from multiple perspectives. As a result, our work offers two unique contributions. First, we provide an effective visual metaphor that transforms complex and even imperfect text summarization results into a comprehensible visual summary of texts. Second, we offer users a set of flexible visual interaction tools as the alternatives to compensate for the deficiencies of current text summarization techniques. We have applied our work to a number of text corpora and our evaluation shows the promise of the work, especially in support of complex text analyses.
Changes in Parents’ Home Learning Activities With Their Children During the COVID-19 Lockdown – The Role of Parental Stress, Parents’ Self-Efficacy and Social Support

As a result of the abrupt closures of daycare centers in Germany due to the COVID-19 pandemic, parents’ ability to provide learning opportunities at home became all the more important. Building on the family stress model, the study investigates how parental stress affected changes in parents’ provision of home learning activities (HLA) during the lockdown, compared to before the lockdown. In addition, the study considers parental self-efficacy and perceived social support as protective factors that may play important roles in disrupting the negative effects of stress. Data stems from a nation-wide survey of 7,837 German parents of children ages 1–6 years, which was conducted in Spring 2020 during the first wave of COVID-19 infections and at a time of strict restrictions in Germany. Results revealed that parental stress was negatively related to changes in the provision of HLA. Parental self-efficacy and an intact social support system were protective of parental stress during the lockdown. Additionally, parental self-efficacy and – to a larger extend – perceived social support interacted with parental stress in the relation to changes in the provision of HLA. Specifically, self-efficacy and perceived social support acted as protective factors that buffered the negative influence of stress on parents’ ability to provide educational activities for their children at home. These results have important implications for supporting families with young children during challenging times, such as the COVID-19 pandemic and the temporary closure of daycare centers.
Phytoplankton Drivers of Dissolved Organic Material Production in Colorado Reservoirs and the Formation of Disinfection By-Products

Previous studies have shown that algal-derived dissolved organic matter (DOM) has a strong influence on the formation of disinfection byproducts (DBPs) during the treatment of drinking water. In the summer of 2010, we evaluated the role of nitrogen and phosphorus loading and phytoplankton abundance as drivers of the concentrations and quality of DOM and the associated DBP formation in 30 reservoirs in the mountains and plains of the State of Colorado. Optical properties such as Specific Ultraviolet Absorbance at 254 nm (SUVA254) and fluorescence spectroscopy were used to characterize DOM quality. Nutrient concentrations such as total nitrogen were also assessed and were associated with high concentrations of chlorophyll a (Chl-a). In turn, high total organic carbon (TOC) concentrations were associated with high concentrations of Chl-a, and the DOM in these reservoirs had a fluorescence signature indicative of contributions from phytoplankton growth. The reservoirs with TOC concentrations above 4 mgC/L were predominantly located in the plains and many are impacted by agricultural runoff and wastewater discharges, rather than in the mountains and are characterized by warm water conditions and shallow depths. For a subset of fourteen reservoirs, we characterized the composition of the phytoplankton using a rapid imaging microscopy technique and observed a dominance by filamentous Cyanobacteria in reservoirs with TOC concentrations above 4 mgC/L. The combination of high TOC concentrations with microbial characteristics resulted in high potential for production of two major classes of regulated DBPs, trihalomethanes and haloacetic acids. While fluorescence spectroscopy was useful in confirming the contribution of phytoplankton growth to high TOC concentrations, evaluation of predictive models for DBP yields found that all equally predictive models included SUVA254 and some of these models also included fluorescence indices or logTOC. These findings provide a limnological context in support of the recent guidelines that have been implemented for protection of high-quality drinking water supplies in the State of Colorado.
Revisiting the Mechanisms of Immune Evasion Employed by Human Parasites

For the establishment of a successful infection, i.e., long-term parasitism and a complete life cycle, parasites use various diverse mechanisms and factors, which they may be inherently bestowed with, or may acquire from the natural vector biting the host at the infection prelude, or may take over from the infecting host, to outmaneuver, evade, overcome, and/or suppress the host immunity, both innately and adaptively. This narrative review summarizes the up-to-date strategies exploited by a number of representative human parasites (protozoa and helminths) to counteract the target host immune defense. The revisited information should be useful for designing diagnostics and therapeutics as well as vaccines against the respective parasitic infections.
CT-Based Pelvic T1-Weighted MR Image Synthesis Using UNet, UNet++ and Cycle-Consistent Generative Adversarial Network (Cycle-GAN)

Background Computed tomography (CT) and magnetic resonance imaging (MRI) are the mainstay imaging modalities in radiotherapy planning. In MR-Linac treatment, manual annotation of organs-at-risk (OARs) and clinical volumes requires a significant clinician interaction and is a major challenge. Currently, there is a lack of available pre-annotated MRI data for training supervised segmentation algorithms. This study aimed to develop a deep learning (DL)-based framework to synthesize pelvic T1-weighted MRI from a pre-existing repository of clinical planning CTs. Methods MRI synthesis was performed using UNet++ and cycle-consistent generative adversarial network (Cycle-GAN), and the predictions were compared qualitatively and quantitatively against a baseline UNet model using pixel-wise and perceptual loss functions. Additionally, the Cycle-GAN predictions were evaluated through qualitative expert testing (4 radiologists), and a pelvic bone segmentation routine based on a UNet architecture was trained on synthetic MRI using CT-propagated contours and subsequently tested on real pelvic T1 weighted MRI scans. Results In our experiments, Cycle-GAN generated sharp images for all pelvic slices whilst UNet and UNet++ predictions suffered from poorer spatial resolution within deformable soft-tissues (e.g. bladder, bowel). Qualitative radiologist assessment showed inter-expert variabilities in the test scores; each of the four radiologists correctly identified images as acquired/synthetic with 67%, 100%, 86% and 94% accuracy. Unsupervised segmentation of pelvic bone on T1-weighted images was successful in a number of test cases Conclusion Pelvic MRI synthesis is a challenging task due to the absence of soft-tissue contrast on CT. Our study showed the potential of deep learning models for synthesizing realistic MR images from CT, and transferring cross-domain knowledge which may help to expand training datasets for 21 development of MR-only segmentation models.
Protective Effects of Thyroid Hormone Deprivation on Progression of Maladaptive Cardiac Hypertrophy and Heart Failure

Purpose: Thyroid hormones (TH) play a central role for cardiac function. TH influence heart rate and cardiac contractility, and altered thyroid function is associated with increased cardiovascular morbidity and mortality. The precise role of TH in onset and progression of heart failure still requires clarification. Methods: Chronic left ventricular pressure overload was induced in mouse hearts by transverse aortic constriction (TAC). One week after TAC, alteration of TH status was induced and the impact on cardiac disease progression was studied longitudinally over 4 weeks in mice with hypo- or hyperthyroidism and was compared to euthyroid TAC controls. Serial assessment was performed for heart function (2D M-mode echocardiography), heart morphology (weight, fibrosis, and cardiomyocyte cross-sectional area), and molecular changes in heart tissues (TH target gene expression, apoptosis, and mTOR activation) at 2 and 4 weeks. Results: In diseased heart, subsequent TH restriction stopped progression of maladaptive cardiac hypertrophy and improved cardiac function. In contrast and compared to euthyroid TAC controls, increased TH availability after TAC propelled maladaptive cardiac growth and development of heart failure. This was accompanied by a rise in cardiomyocyte apoptosis and mTOR pathway activation. Conclusion: This study shows, for the first time, a protective effect of TH deprivation against progression of pathological cardiac hypertrophy and development of congestive heart failure in mice with left ventricular pressure overload. Whether this also applies to the human situation needs to be determined in clinical studies and would infer a critical re-thinking of management of TH status in patients with hypertensive heart disease.
NMN Maintains Intestinal Homeostasis by Regulating the Gut Microbiota

The aim of this study was to determine the effects of long-term Nicotinamide mononucleotide (NMN) treatment on modulating gut microbiota diversity and composition, as well as its association with intestinal barrier function. In this study, C57BL/6J mice were fed different concentrations of NMN, and their feces were collected for detection of 16S rDNA and non-targeted metabolites to explore the effects of NMN on intestinal microbiota and metabolites. The results revealed that NMN increased the abundance of butyric acid-producing bacteria (Ruminococcae_UCG-014 and Prevotellaceae_NK3B31_group) and other probiotics (Akkermansia muciniphila), while the abundance of several harmful bacteria (Bilophila and Oscillibacter) were decreased after NMN treatment. Meanwhile, the level of bile acid-related metabolites in feces from the G1 group (0.1 mg/ml) was significantly increased compared to the control group, including cholic acid, taurodeoxycholic acid, taurocholic acid, glycocholic acid, and tauro-β-muricholic acid. In addition, long-term NMN treatment affected the permeability of the intestinal mucosa. The number of goblet cells and mucus thickness increased, as well as expression of tight junction protein. These results demonstrate that NMN reduced intestinal mucosal permeability and exerts a protective effect on the intestinal tract. This study lays the foundation for exploring NMN's utility in clinical research.
Rhamnolipid Enhances the Nitrogen Fixation Activity of Azotobacter chroococcum by Influencing Lysine Succinylation

The enhancement of nitrogen fixation activity of diazotrophs is essential for safe crop production. Lysine succinylation (KSuc) is widely present in eukaryotes and prokaryotes and regulates various biological process. However, knowledge of the extent of KSuc in nitrogen fixation of Azotobacter chroococcum is scarce. In this study, we found that 250 mg/l of rhamnolipid (RL) significantly increased the nitrogen fixation activity of A. chroococcum by 39%, as compared with the control. Real-time quantitative reverse transcription PCR (qRT-PCR) confirmed that RL could remarkably increase the transcript levels of nifA and nifHDK genes. In addition, a global KSuc of A. chroococcum was profiled using a 4D label-free quantitative proteomic approach. In total, 5,008 KSuc sites were identified on 1,376 succinylated proteins. Bioinformatics analysis showed that the addition of RL influence on the KSuc level, and the succinylated proteins were involved in various metabolic processes, particularly enriched in oxidative phosphorylation, tricarboxylic acid cycle (TCA) cycle, and nitrogen metabolism. Meanwhile, multiple succinylation sites on MoFe protein (NifDK) may influence nitrogenase activity. These results would provide an experimental basis for the regulation of biological nitrogen fixation with KSuc and shed new light on the mechanistic study of nitrogen fixation.
Lactate-Dependent Regulation of Immune Responses by Dendritic Cells and Macrophages

For decades, lactate has been considered an innocuous bystander metabolite of cellular metabolism. However, emerging studies show that lactate acts as a complex immunomodulatory molecule that controls innate and adaptive immune cells’ effector functions. Thus, recent advances point to lactate as an essential and novel signaling molecule that shapes innate and adaptive immune responses in the intestine and systemic sites. Here, we review these recent advances in the context of the pleiotropic effects of lactate in regulating diverse functions of immune cells in the tissue microenvironment and under pathological conditions.
Development and Initial Validation of the Humor Climate in Sport Scale

In sport teams, humor is an essential element that influences communication processes, and plays an important role in group dynamics. Despite this, no current instrument is presented in the literature to measure humor climate in sport teams. Therefore, the current study presents the development and initial validation of the Humor Climate in Sport Scale (HCSS). The aim was to assess content, structural and concurrent validity of the developed instrument, and to examine differential item functioning (DIF) as a function of sex. Three different phases were completed in this study. The first phase involved focus groups (n = 5) that explored humor as communication in a team sport context. In phase 2, information from the focus groups was used to create a pool of potential items for the questionnaire. Two discussion groups with sport science students contributed to the development of 80 potential items, that two different expert groups then assessed for item quality. The final version of the instrument after this phase contained 14 items, representing three different humor dimensions. In phase 3, two independent samples with a total number of 776 participants were recruited for the psychometric evaluation of the instrument. EFA, ICM-CFA, and ESEM analysis were performed, supporting a three-factor structure with positive humor, negative humor in-group, and negative humor out-group. In addition, partial DIF as a function of sex on the negative humor dimensions was found, indicating differences in how male and female interpret the negative humor items. The findings in the current study expand our understanding of humor in sport teams and may be a starting point for further research on humor climate in sport teams and its role in group function.
Production, Storage Stability, and Susceptibility Testing of Reuterin and Its Impact on the Murine Fecal Microbiome and Volatile Organic Compound Profile

Background: Probiotics are generally considered as safe, but infections may rarely occur in vulnerable patients. Alternatives to live microorganisms to manage dysbiosis may be of interest in these patients. Reuterin is a complex component system exhibiting broad spectrum antimicrobial activity and a possible candidate substance in these cases. Methods: Reuterin supernatant was cultured from Lentilactobacillus diolivorans in a bioreactor in a two-step process. Storage stability at −20°C and effect of repeated freeze-thaw cycles were assessed by high performance liquid chromatography (HPLC). Antimicrobial activity was tested against Clostridium difficile, Listeria monocytogenes, Escherichia coli, Enterococcus faecium, Staphylococcus (S.) aureus, Staphylococcus epidermidis, Streptococcus (S.) agalactiae, Propionibacterium acnes, and Pseudomonas aeruginosae. Male BALBc mice were gavage fed with reuterin supernatant (n = 10) or culture medium (n = 10). Fecal volatile organic compounds (VOC) were assessed by gas chromatography mass spectroscopy; the microbiome was examined by 16S rRNA gene sequencing. Results: The supernatant contained 13.4 g/L reuterin (3-hydroxypropionaldehyde; 3-HPA). 3-HPA content remained stable at −20°C for 35 days followed by a slow decrease of its concentration. Repeated freezing/thawing caused a slow 3-HPA decrease. Antimicrobial activity was encountered against S. aureus, S. epidermidis, and S. agalactiae. Microbiome analysis showed no differences in alpha and beta diversity markers. Linear discriminant effect size (LEfSe) analysis identified Lachnospiraceae_bacterium_COE1 and Ruminoclostridium_5_uncultured_Clostridiales_ bacterium (in the reuterin medium group) and Desulfovibrio_uncultured_ bacterium, Candidatus Arthromitus, Ruminococcae_NK4A214_group, and Eubacterium_xylanophilum_group (in the reuterin group) as markers for group differentiation. VOC analysis showed a significant decrease of heptane and increase of 3-methylbutanal in the reuterin group. Conclusion: The supernatant produced in this study contained acceptable amounts of 3-HPA remaining stable for 35 days at −20°C and exhibiting an antimicrobial effect against S. aureus, S. agalactiae, and S. epidermidis. Under in vivo conditions, the reuterin supernatant caused alterations of the fecal microbiome. In the fecal, VOC analysis decreased heptane and increased 3-methylbutanal were encountered. These findings suggest the high potential of the reuterin system to influence the intestinal microbiome in health and disease, which needs to be examined in detail in future projects.
Research on the Relationship Between Cross-Level Motivation, Integrated Emotion, and Virtual Knowledge Community Commitment

Community commitment is the key to the success of virtual communities. Under the background of virtual knowledge community, based on motivation hierarchy model and integrated emotion theory, this paper takes “motivation-emotion-community commitment” as the main framework, and introduces multiple mediation and regulation functions to establish the relationship model of motivation hierarchy, integrated emotions, and community commitment. The results show that the user motivation follows the hierarchical structure of the layer-by-layer influence from the situational level to the personality level, that is, knowledge-seeking motivation and entertainment-seeking motivation at a situational level will positively affect social- interaction motivation at the contextual level, thereby enhancing user self-efficacy at personality level. Users have abundant integrated emotions toward the virtual knowledge community, namely, satisfaction, attachment, and identity, and such multi-integrated emotional model is more conducive for promoting community commitment of users. At the same time, attachment, identity, and satisfaction have an interactive complement, that is, when satisfaction is low, attachment and identity will complement and strengthen community commitment.