Miracle-dz/UniFAR-FTUs huggingface dataset:
Abdominal Adiposity and Total Body Fat as Predictors of Cardiometabolic Health in Children and Adolescents With Obesity

Objective: We aimed to assess the role of adipose tissue distribution in cardiometabolic risk (in particular insulin sensitivity) in a population of children and adolescents with obesity. Methods: In this cross-sectional study, participants were 479 children and adolescents with obesity (322 boys and 157 girls) aged 3 to 18 years attending the Children's Hospital at Zhejiang University School of Medicine (Hangzhou, China). Clinical assessments included anthropometry, body composition (DXA scans), carotid artery ultrasounds, and OGTT. Insulin sensitivity was assessed using the Matsuda index. Participants were stratified into groups by sex and pubertal stage. Key predictors were DXA-derived android-to-gynoid-fat ratio (A/G) and total body fat percentage (TBF%). Results: Irrespective of sex and pubertal stage, there was a strong association between increasing A/G (i.e., greater abdominal adiposity) and lower insulin sensitivity. In multivariable models, every 0.1 increase in A/G was associated with a reduction in insulin sensitivity in prepubertal boys [−29% (95% CI −36%, −20%); p < 0.0001], pubertal boys [−13% (95% CI −21%, −6%); p = 0.001], and pubertal girls [−16% (95% CI −24%, −6%); p = 0.002]. In contrast, TBF% was not associated with insulin sensitivity when A/G was adjusted for, irrespective of pubertal stage or sex. In addition, every 0.1 increase in A/G was associated with increased likelihood of dyslipidemia in prepubertal boys [adjusted odds ratio (aOR) 1.62 (95% CI 1.05, 2.49)], impaired glucose tolerance in pubertal boys [aOR 1.64 (95% CI 1.07, 2.51)] and pubertal girls [aOR 1.81 (95% CI 1.10, 2.98)], and odds of NAFLD in both prepubertal [aOR 2.57 (95% CI 1.56, 4.21)] and pubertal [aOR 1.69 (95% CI 1.18, 2.40)] boys. In contrast, higher TBF% was only associated with higher fasting insulin and ALT in pubertal boys, being also predictive of NAFLD in this group [aOR 1.15 per percentage point (95% CI 1.06, 1.26)], but was not associated with the likelihood of other cardiometabolic outcomes assessed in any group. Conclusions: A/G is a much stronger independent predictor of cardiometabolic risk factors in children and adolescents with obesity in China, particularly glucose metabolism.
Transport Properties of Gramicidin A Ion Channel in a Free-Standing Lipid Bilayer Filled With Oil Inclusions

Ion channels are key proteins in mammalian cell membranes. They have a central role in the physiology of excitable cells such as neurons, muscle, and heart cells. They also play a crucial role in kidney physiology. The gramicidin ion channel is one of the most studied ion channels, in particular it was intensively employed to investigate the lipid–protein interactions in model cell membranes. For example, even though the sequence of gramicidin is extremely hydrophobic, its motion is impaired in membrane bilayer, i.e., it does not rapidly flip to the other membrane leaflet, and low channel activity were observed when gramicidin is added asymmetrically to only one leaflet of a model cell membrane. In this article, we study the transport properties of gramicidin channel in a heterogeneous model membrane. Using microfluidics, we are forming freestanding bilayers as model cell membranes including heterogeneous domains that are created by oil inclusions. The presence of oil inclusions is then demonstrated by measuring the bilayer capacity via a patch-clamp amplifier and fluorescent confocal inspection. Based on electrophysiological and optical measurements Gramicidin A (gA) ion channels are dispersed into the buffer phases on both side of the formed lipid bilayer and insert spontaneously into the bilayer upon formation. The presence of functional Gramicidin A is then demonstrated by measuring conductivity signals. Based on electrophysiological and optical measurements, we explore the consequence of the presence of these oil inclusions on the functionality of incorporated gA ion channels. For low oil concentration, we measure a decrease of gA transport properties due to the reduction of the bilayer tension. For large oil concentration, we measure a saturation of gA transport properties due to an increase of the bilayer thickness.
Machine Learning Methods for Fluorescence Lifetime Imaging (FLIM) Based Label-Free Detection of Microglia

Automated computational analysis techniques utilizing machine learning have been demonstrated to be able to extract more data from different imaging modalities compared to traditional analysis techniques. One new approach is to use machine learning techniques to existing multiphoton imaging modalities to better interpret intrinsically fluorescent cellular signals to characterize different cell types. Fluorescence Lifetime Imaging Microscopy (FLIM) is a high-resolution quantitative imaging tool that can detect metabolic cellular signatures based on the lifetime variations of intrinsically fluorescent metabolic co-factors such as nicotinamide adenine dinucleotide [NAD(P)H]. NAD(P)H lifetime-based discrimination techniques have previously been used to develop metabolic cell signatures for diverse cell types including immune cells such as macrophages. However, FLIM could be even more effective in characterizing cell types if machine learning was used to classify cells by utilizing FLIM parameters for classification. Here, we demonstrate the potential for FLIM-based, label-free NAD(P)H imaging to distinguish different cell types using Artificial Neural Network (ANN)-based machine learning. For our biological use case, we used the challenge of differentiating microglia from other glia cell types in the brain. Microglia are the resident macrophages of the brain and spinal cord and play a critical role in maintaining the neural environment and responding to injury. Microglia are challenging to identify as most fluorescent labeling approaches cross-react with other immune cell types, are often insensitive to activation state, and require the use of multiple specialized antibody labels. Furthermore, the use of these extrinsic antibody labels prevents application in in vivo animal models and possible future clinical adaptations such as neurodegenerative pathologies. With the ANN-based NAD(P)H FLIM analysis approach, we found that microglia in cell culture mixed with other glial cells can be identified with more than 0.9 True Positive Rate (TPR). We also extended our approach to identify microglia in fixed brain tissue with a TPR of 0.79. In both cases the False Discovery Rate was around 30%. This method can be further extended to potentially study and better understand microglia’s role in neurodegenerative disease with improved detection accuracy.
Carbon-Deficient Titanium Carbide With Highly Enhanced Hardness

We report the synthesis of a polycrystalline specimen of TiC1−x under high-pressure and high-temperature (HPHT) conditions. The carbon vacancy, crystal structure, Vicker hardness, elastic constants, and bond features of the synthesized specimen were investigated. Though the specimens were synthesized with stoichiometric ratio at high pressure, a robust carbon vacancy was observed using energy dispersive and X-ray photoelectron spectrum. TiC1−x exhibits almost the highest asymptotic Vickers hardness in transition-metal light-element (TMLE) compounds. In this study, using Vickers hardness characterization, the asymptotic hardness was found to be 27.1 GPa. This exceeds the hardness of most transition metal borides with high boron concentrations. Based on the first-principles calculation of the Mulliken population of Ti-C bonds, the intrinsic high Vickers hardness of TiC1−x is attributed to the combination of covalent Ti-C bonds and the optimized eight-valence-electron structure, while the extrinsic contribution comes from the harden effect of carbon defects. This work demonstrates that a higher concentration of light elements or a higher-dimensional light element framework is not the critical factor for higher hardness, and carbon vacancy is another way to strengthen the crystal structure.
Intracellular Competitions Reveal Determinants of Plasmid Evolutionary Success

Plasmids are autonomously replicating genetic elements that are ubiquitous in all taxa and habitats where they constitute an integral part of microbial genomes. The stable inheritance of plasmids depends on their segregation during cell division and their long-term persistence in a host population is thought to largely depend on their impact on the host fitness. Nonetheless, many plasmids found in nature are lacking a clear trait that is advantageous to their host; the determinants of plasmid evolutionary success in the absence of plasmid benefit to the host remain understudied. Here we show that stable plasmid inheritance is an important determinant of plasmid evolutionary success. Borrowing terminology from evolutionary biology of cellular living forms, we hypothesize that Darwinian fitness is key for the plasmid evolutionary success. Performing intracellular plasmid competitions between non-mobile plasmids enables us to compare the evolutionary success of plasmid genotypes within the host, i.e., the plasmid fitness. Intracellular head-to-head competitions between stable and unstable variants of the same model plasmid revealed that the stable plasmid variant has a higher fitness in comparison to the unstable plasmid. Preemptive plasmid competitions reveal that plasmid fitness may depend on the order of plasmid arrival in the host. Competitions between plasmids characterized by similar stability of inheritance reveal plasmid fitness differences depending on the plasmid-encoded trait. Our results further reveal that competing plasmids can be maintained in coexistence following plasmid fusions that maintain unstable plasmid variants over time. Plasmids are not only useful accessory genetic elements to their host but they are also evolving and replicating entities, similarly to cellular living forms. There is a clear link between plasmid genetics and plasmid evolutionary success – hence plasmids are evolving entities whose fitness is quantifiable.
Overexpression of GmUBC9 Gene Enhances Plant Drought Resistance and Affects Flowering Time via Histone H2B Monoubiquitination

Ubiquitylation is a form of post-translational modification of proteins that can alter localization, functionality, degradation, or transcriptional activity within a cell. E2 ubiquitin-conjugating enzyme (UBC) and E3 ubiquitin ligases are the primary determinants of substrate specificity in the context of ubiquitin conjugation. Multiubiquitination modifies target proteins for 26S proteasome degradation, while monoubiquitination controls protein activation and localization. At present, research on the monoubiquitination, especially histone monoubiquitination, has mostly focused on model plants with relatively few on crop species. In this study, we identified 91 UBC-like genes in soybean. The chromosomal localization, phylogenetic relationships, gene structures, and putative cis-acting elements were evaluated. Furthermore, the tissue-specific expression patterns of UBC Class I genes under drought stress were also investigated. Among Class I genes, GmUBC9 induction in response to drought stress was evident, and so this gene was selected for further analysis. GmUBC9 localized to the nucleus and endoplasmic reticulum. The overexpression of GmUBC9 in Arabidopsis led to enhanced tolerance for drought conditions across a range of stages of development, while overexpression in soybean hairy roots similarly led to improvements in tolerance for drought conditions, increased proline content, and reduced MDA content in soybean seedlings compared to wild type plants. HISTONE MONOUBIQUITINATION 2 (HUB2), an E3-like protein involved in histone H2B ubiquitylation (H2Bub1), was found to interact with GmUBC9 through Y2H analysis and BiFC assays in Arabidopsis and soybean. Under drought conditions, the level of H2Bub1 increased, and transcription of drought response genes was activated in GmUBC9 transgenic Arabidopsis and soybean. In addition, GmUBC9 transgenic Arabidopsis and soybean showed a late-flowering phenotype and had increased expression levels of the flowering related genes FLC and MAF4. These findings indicate that GmUBC9 is important for drought stress response and regulation of flowering time in soybean.
Prenatal Stress Impairs Postnatal Learning and Memory Development via Disturbance of the cGMP–PKG Pathway and Oxidative Phosphorylation in the Hippocampus of Rats

Clinical and animal studies have found that prenatal stress can lead to pathological changes in embryos and fetuses. However, the mechanisms through which this occurs have not been made clear. In the present study, pregnant rats were subjected to chronic psychological stress during gestational days using an improved communication box system, and the changes in behavioral performance and proteins in the hippocampus of offspring were analyzed. It was found that prenatal stress caused postnatal growth retardation and impairment in spatial learning and memory. Furthermore, in isobaric tags for relative and absolute quantitation-based proteomics analyses, 158 significantly differentially expressed proteins (DEPs) were found between the two groups. Further analyses showed that these DEPs are involved in different molecular function categories and participate in several biological processes, such as energy metabolism, learning or memory, and synaptic plasticity. Moreover, the enrichment of pathways showed that the learning and memory impairment was primarily connected with the cyclic guanosine monophosphate–protein kinase G (cGMP–PKG) pathway and oxidative phosphorylation. At the same time, the cGMP level and the expression of PKG protein were significantly decreased, and the neuronal mitochondria appeared to have a swollen and irregular shape in the hippocampus of offspring of stressed rats. These results suggest that the chronic psychological stress that pregnant rats were subjected to during gestational days may have impaired the spatial learning and memory of offspring. This affected the hippocampal oxidative phosphorylation and inhibited the cGMP–PKG pathway.
Psychopathological Burden and Quality of Life in Substance Users During the COVID-19 Lockdown Period in Italy

Background Following the development of the COVID-19 pandemic, a rigid public health strategy of reduced social contact and shelter-in-place has been adopted by the Italian Government to reduce the spread of the virus. In this paper, we aim at evaluating the impact that the COVID-19 pandemic, and the relative containment measures, have had on a real-life sample of patients suffering from substance use disorders (SUDs) and/or behavioral addictions. Methods An anonymous questionnaire was filled out by 153 addicted patients, both outpatients and residential inpatients, recruited across Italy and highly representative of the current Italian population suffering from addictions. Psychopathological burden (anxiety and depressive symptomatology, somatization, irritability, and post-traumatic symptoms), quality of life, and craving changes in daily habits were assessed. Results In our sample, we found moderate rates of depression (22.9%), anxiety (30.1%), irritability (31.6%), and post-traumatic stress (5.4%) symptoms. Psychopathological burden was globally higher among residential patients. Reported levels of craving were generally low. Discussion This study is the first attempt to collect Italian data regarding the effects of the rigid quarantine period, during the COVID-19 pandemic, on patients suffering from a SUD and/or behavioral addictions. The presence of a moderate psychopathological burden correlated to poor quality of life and low craving scores represented the main outcomes. Long-term studies, with follow-up after the end of the restrictive measures, should be considered to implement our findings.
Fungal Composition and Diversity of the Tobacco Leaf Phyllosphere During Curing of Leaves

Rhizopus oryzae causes tobacco pole rot in China during tobacco flue-curing. Flue-curing is a post-harvest process done to prepare tobacco leaves and involves three different stages: the yellowing stage has the lowest temperatures and highest humidity, then the color-fixing stage has higher temperatures and medium humidity, and finally the stem-drying stage has the highest temperatures and lowest humidity. In this study, fungal culturing and IonS5XL high-throughput sequencing techniques were used to reveal the fungal community of the petioles and lamina of tobacco leaves infected with pole rot during flue-curing. A total of 108 fungal isolates belonging to 6 genera were isolated on media. The most common fungal species isolated was the pathogen, R. oryzae, that was most often found equally on petioles and laminas in the color-fixing stage, followed by saprotrophs, mostly Aspergillus spp. High-throughput sequencing revealed saprotrophs with Alternaria being the most abundant genus, followed by Phoma, Cercospora, and Aspergillus, whereas Rhizopus was the tenth most abundant genus, which was mostly found on petioles at the yellowing stage. Both culturable fungal diversity and fungal sequence diversity was higher at stem-drying stage than the yellowing and color-fixing stages, and diversity was higher with leaf lamina than petioles revealing that the changes in fungal composition and diversity during the curing process were similar with both methods. This study demonstrates that the curing process affects the leaf microbiome of tobacco during the curing process, and future work could examine if any of these saprotrophic fungi detected during the curing of tobacco leaves may be potential biocontrol agents for with pole rot in curing chambers.
Masculinized Second-to-Fourth Digit Ratio (2D:4D Ratio) Is Associated With Lower Cortisol Response in Infant Female Rhesus Monkeys (Macaca mulatta)

The second-to-fourth digit ratio (2D:4D ratio) is considered a postnatal proxy measure for the degree of prenatal androgen exposure (PAE), which is the primary factor responsible for masculinizing the brain of a developing fetus. Some studies suggest that the organizational effects of PAE may extend to the hypothalamic-pituitary-adrenal (HPA) axis response to stress. This study investigates the relationship between 2D:4D ratio and HPA axis functioning using a rhesus monkey (Macaca mulatta) model. Subjects were N = 268 (180 females, 88 males) rhesus monkey infants (3–4 months of age). Plasma cortisol concentrations were assayed from two blood samples obtained during a 25-h experimental social separation stressor at 2- and 7-h post-separation. Subjects’ 2D:4D ratio was measured later in life (Mage = 6.70 years). It was hypothesized that infant rhesus monkeys that exhibited a more masculine-like 2D:4D ratio would show lower levels of circulating cortisol after a social separation and relocation stressor. The results showed that there was a sex difference in the left-hand 2D:4D ratio. The results also showed that there was an overall sex difference in cortisol concentrations and that female, but not male, monkeys that exhibited a more masculine-like right- and left-hand 2D:4D ratio exhibited lower mean stress-induced cortisol concentrations early in life. These findings suggest that higher levels of prenatal androgens in females, as measured by 2D:4D ratio, may be related to an attenuated HPA axis stress-response, as measured by plasma cortisol levels. To the extent that these findings generalize to humans, they suggest that the organizational effects of PAE extend to the infant HPA axis, modulating the HPA axis response, particularly in females.
Drought-Conditioning of Quaking Aspen (Populus tremuloides Michx.) Seedlings During Nursery Production Modifies Seedling Anatomy and Physiology

In the western US, quaking aspen (Populus tremuloides Michx.) regenerates primarily by root suckers after disturbances such as low to moderate severity fires. Planting aspen seedlings grown from seed may provide a mechanism to improve restoration success and genetic diversity on severely disturbed sites. However, few studies have examined the use of container-grown aspen seedlings for restoration purposes from both the outplanting and nursery production perspective. Thus, the purpose of this novel study was to examine how alterations in irrigation levels during nursery production across three seed sources would impact seedling performance attributes on harsh, dry outplanting sites. Irrigation treatments were based on three irrigation levels, determined gravimetrically: High = 90%, Medium = 80%, and Low = 70% of container capacity. The three seed sources represented a latitudinal gradient across the aspen range (New Mexico, Utah, and Alberta). Carbon isotope analysis indicated irrigation treatments were effective in creating higher levels of water stress for both the Low and Medium irrigation levels compared to seedlings under the High irrigation level. Seedlings subject to the Low irrigation level were found to induce greater height, higher photosynthetic rates, larger percentages of hydraulically active xylem, and faster xylem flow velocities compared to the High irrigation level. The lack of an interaction between irrigation treatments and seed source for nearly all response variables suggests that nursery conditioning via irrigation limitations may be effective for a range of aspen seed sources.
Co-infection of Malassezia sympodialis With Bacterial Pathobionts Pseudomonas aeruginosa or Staphylococcus aureus Leads to Distinct Sinonasal Inflammatory Responses in a Murine Acute Sinusitis Model

Host-associated bacteria and fungi, comprising the microbiota, are critical to host health. In the airways, the composition and diversity of the mucosal microbiota of patients are associated with airway health status. However, the relationship between airway microbiota and respiratory inflammation is not well-understood. Chronic rhinosinusitis (CRS) is a complex disease that affects up to 14% of the US population. Previous studies have shown decreased microbial diversity in CRS patients and enrichment of either Staphylococcus aureus or Pseudomonas aeruginosa. Although bacterial community composition is variable across CRS patients, Malassezia is a dominant fungal genus in the upper airways of the majority of healthy and CRS subjects. We hypothesize that distinct bacterial-fungal interactions differentially influence host mucosal immune response. Thus, we investigated in vitro and in vivo interactions between Malassezia sympodialis, P. aeruginosa, and S. aureus. The in vitro interactions were evaluated using the modified Kirby-Bauer Assay, Crystal Violet assay for biofilm, and FISH. A pilot murine model of acute sinusitis was used to investigate relationships with the host immune response. S. aureus and P. aeruginosa were intranasally instilled in the presence or absence of M. sympodialis (n = 66 total mice; 3–5/group). Changes in the microbiota were determined using 16S rRNA gene sequencing and host immune response was measured using quantitative real-time PCR (qRT-PCR). In vitro, only late stage planktonic P. aeruginosa and its biofilms inhibited M. sympodialis. Co-infection of mice with M. sympodialis and P. aeruginosa or S. aureus differently influenced the immune response. In co-infected mice, we demonstrate different expression of fungal sensing (Dectin-1), allergic responses (IL-5, and IL-13) and inflammation (IL-10, and IL-17) in murine sinus depending on the bacterial species that co-infected with M. sympodialis (p < 0.05). The pilot results suggest that species-specific interactions in airway-associated microbiota may be implicated driving immune responses. The understanding of the role of bacterial-fungal interactions in CRS will contribute to development of novel therapies toward manipulation of the airway microbiota.