Miracle-dz/UniFAR-FTUs huggingface dataset:
Interplay between Candida albicans and Lactic Acid Bacteria in the Gastrointestinal Tract: Impact on Colonization Resistance, Microbial Carriage, Opportunistic Infection, and Host Immunity

Emerging studies have highlighted the disproportionate role of Candida albicans in influencing both early community assembly of the bacterial microbiome and dysbiosis during allergic diseases and intestinal inflammation. Nonpathogenic colonization of the human gastrointestinal (GI) tract by C. albicans is common, and the role of this single fungal species in modulating bacterial community reassembly after broad-spectrum antibiotics can be readily recapitulated in mouse studies. SUMMARY Emerging studies have highlighted the disproportionate role of Candida albicans in influencing both early community assembly of the bacterial microbiome and dysbiosis during allergic diseases and intestinal inflammation. Nonpathogenic colonization of the human gastrointestinal (GI) tract by C. albicans is common, and the role of this single fungal species in modulating bacterial community reassembly after broad-spectrum antibiotics can be readily recapitulated in mouse studies. One of the most notable features of C. albicans-associated dysbiotic states is a marked change in the levels of lactic acid bacteria (LAB). C. albicans and LAB share metabolic niches throughout the GI tract, and in vitro studies have identified various interactions between these microbes. The two predominant LAB affected are Lactobacillus species and Enterococcus species. Lactobacilli can antagonize enterococci and C. albicans, while Enterococcus faecalis and C. albicans have been reported to exhibit a mutualistic relationship. E. faecalis and C. albicans are also causative agents of a variety of life-threatening infections, are frequently isolated together from mixed-species infections, and share certain similarities in clinical presentation—most notably their emergence as opportunistic pathogens following disruption of the microbiota. In this review, we discuss and model the mechanisms used by Lactobacillus species, E. faecalis, and C. albicans to modulate each other’s growth and virulence in the GI tract. With multidrug-resistant E. faecalis and C. albicans strains becoming increasingly common in hospital settings, examining the interplay between these three microbes may provide novel insights for enhancing the efficacy of existing antimicrobial therapies.
Inhibition of mTOR signaling and clinical activity of metformin in oral premalignant lesions

BACKGROUND The aberrant activation of the PI3K/mTOR signaling circuitry is one of the most frequently dysregulated signaling events in head and neck squamous cell carcinoma (HNSCC). Here, we conducted a single-arm, open-label phase IIa clinical trial in individuals with oral premalignant lesions (OPLs) to explore the potential of metformin to target PI3K/mTOR signaling for HNSCC prevention. METHODS Individuals with OPLs, but who were otherwise healthy and without diabetes, underwent pretreatment and posttreatment clinical exam and biopsy. Participants received metformin for 12 weeks (week 1, 500 mg; week 2, 1000 mg; weeks 3–12, 2000 mg daily). Pretreatment and posttreatment biopsies, saliva, and blood were obtained for biomarker analysis, including IHC assessment of mTOR signaling and exome sequencing. RESULTS Twenty-three participants were evaluable for response. The clinical response rate (defined as a ≥50% reduction in lesion size) was 17%. Although lower than the proposed threshold for favorable clinical response, the histological response rate (improvement in histological grade) was 60%, including 17% complete responses and 43% partial responses. Logistic regression analysis revealed that when compared with never smokers, current and former smokers had statistically significantly increased histological responses (P = 0.016). Remarkably, a significant correlation existed between decreased mTOR activity (pS6 IHC staining) in the basal epithelial layers of OPLs and the histological (P = 0.04) and clinical (P = 0.01) responses. CONCLUSION To our knowledge this is the first phase II trial of metformin in individuals with OPLs, providing evidence that metformin administration results in encouraging histological responses and mTOR pathway modulation, thus supporting its further investigation as a chemopreventive agent. TRIAL REGISTRATION NCT02581137 FUNDING NIH contract HHSN261201200031I, grants R01DE026644 and R01DE026870
Three-well, resonant-phonon depopulation, quantum cascade lasers with thinned active regions and surface-plasmon waveguides

We report, for the first time, high performance three-well, resonant-phonon depopulation, terahertz quantum cascade lasers with thinned active regions. Lasers operated at 3.1 THz in a surface plasmon waveguide. The variation of output power, maximum operating temperature, and threshold current density is presented for active regions of 10 µm, 7,5 µm, 6 µm, and 5 µm thickness, and in each case results are presented as a function of duty cycle.
Global Geographic Diversity and Distribution of the Myxobacteria

The diversity and distribution of bacteria are crucial for our understanding of their ecological importance and application potential. Myxobacteria are fascinating prokaryotes with multicellular behaviors and a potent capacity for producing secondary metabolites, and have a wide range of potential applications. ABSTRACT Bacteria are globally distributed in various environments on earth, but a global view of the geographic diversity and distribution of a single taxon is lacking. The Earth Microbiome Project (EMP) has established a global collection of microbial communities, providing the possibility for such a survey. Myxococcales is a bacterial order with a potent ability to produce diverse natural products and have wide application potential in agriculture, biomedicine, and environmental protection. In this study, through a comparative analysis of the EMP data and public information, we determined that myxobacteria account for 2.34% of the total bacterial operational taxonomic units (OTUs), and are one of the most diverse bacterial groups on Earth. Myxococcales OTUs are globally distributed and prefer nonsaline soil and sediments, followed by saline environments, but rarely appear in host-associated environments. Myxobacteria are among the least-investigated bacterial groups. The presently cultured and genome-sequenced myxobacteria are most likely environmentally widespread and abundant taxa, and account for approximately 10% and 7% of the myxobacterial community (>97% similarity), respectively. This global panoramic view of the geographic distribution and diversity of myxobacteria, as well as their cultured and genome-sequenced information, will enable us to explore these important bioresources more reasonably and efficiently. The diversity and distribution of myxobacteria beyond the EMP data are further discussed. IMPORTANCE The diversity and distribution of bacteria are crucial for our understanding of their ecological importance and application potential. Myxobacteria are fascinating prokaryotes with multicellular behaviors and a potent capacity for producing secondary metabolites, and have a wide range of potential applications. The ecological importance of myxobacteria in major ecosystems is becoming established, but the global geographic diversity and distribution remain unclear. From a global survey we revealed that Myxococcales OTUs are globally distributed and prefer nonsaline soil and sediments, followed by saline environments, but rarely appear in host-associated environments. The global panoramic view of the geographic distribution and diversity of myxobacteria, as well as their cultured and genome-sequenced information, will enable us to explore these important bioresources more reasonably and efficiently.
HieRFIT: a hierarchical cell type classification tool for projections from complex single-cell atlas datasets

MOTIVATION The emergence of single-cell RNA sequencing (scRNA-seq) has led to an explosion in novel methods to study biological variation among individual cells, and to classify cells into functional and biologically meaningful categories. RESULTS Here, we present a new cell type projection tool, HieRFIT (Hierarchical Random Forest for Information Transfer), based on hierarchical random forests. HieRFIT uses a priori information about cell type relationships to improve classification accuracy, taking as input a hierarchical tree structure representing the class relationships, along with the reference data. We use an ensemble approach combining multiple random forest models, organized in a hierarchical decision tree structure. We show that our hierarchical classification approach improves accuracy and reduces incorrect predictions especially for inter-dataset tasks which reflect real life applications. We use a scoring scheme that adjusts probability distributions for candidate class labels and resolves uncertainties while avoiding the assignment of cells to incorrect types by labeling cells at internal nodes of the hierarchy when necessary. AVAILABILITY HieRFIT is implemented as an R package, and it is available at (https://github.com/yasinkaymaz/HieRFIT/releases/tag/v1.0.0). t. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Supportive Accountability and Mobile App Use in a Tobacco Control Intervention Targeting Low-Income Minority Mothers Who Smoke: Observational Study

Background Smartphone mobile apps are frequently used in standalone or multimodal smoking cessation interventions. However, factors that impede or improve app usage are poorly understood. Objective This study used the supportive accountability model to investigate factors that influence app usage in the context of a trial designed to reduce maternal smoking in low-income and predominantly minority communities. Methods We conducted a secondary analysis of data (N=181) from a randomized controlled trial that included a smoking cessation app (QuitPal-m). Supportive accountability was measured by the number of times a participant was advised by their cessation counselor to use QuitPal-m. Participants reported app use helpfulness and barriers. Investigators tracked reported phone and technical problems that impeded app use. Results Most participants rated the app as very helpful (103/155, 66.5%), but daily use declined rapidly over time. App use was positively related to the level of perceived app helpfulness (P=.02) and education (P=.002) and inversely related to perceived barriers (P=.003), phone technical problems (P<.001), and cigarettes smoked per day at the end of treatment (P<.001). Participants used the app a greater proportion of the days following app advice than those preceding app advice (0.45 versus 0.34; P<.001). The positive relation between counselor app advice and app usage 24 hours after receiving advice was stronger among smokers with no plan to quit than in those planning to quit (P=.03), independent of education and phone or app problems. Conclusions Findings show the utility of supportive accountability for increasing smoking cessation app use in a predominantly low-income, minority population, particularly if quit motivation is low. Results also highlight the importance of addressing personal and phone/technical barriers in addition to adding supportive accountability. Trial Registration ClinicalTrials.gov NCT02602288; https://clinicaltrials.gov/ct2/show/NCT02602288
Controlling Aggregation in Highly Emissive Pt(II) Complexes Bearing Tridentate Dianionic N∧N∧N Ligands. Synthesis, Photophysics, and Electroluminescence

Neutral Pt(II) complexes bearing tridentate dianionic 2,6-bis(1H-1,2,4-triazol-5-yl)pyridine and ancillary alkyl-substituted pyridine ligands have been synthesized and characterized. They show bright green emission, reaching 73% photoluminescence quantum yield in deareated chloroform solution, which can be assigned to a predominantly metal-perturbed ligand-centered phosphorescence. We have followed two strategies to preserve the spectral purity of the monomeric species by varying the substituents on the chromophoric or on the ancillary ligands. However, variations in the substitution patterns only modestly affected the radiative and radiationless deactivation rate constants of the monomers. Photophysical and electrochemical properties have been measured for all the complexes and correlated with calculations using time-dependent density functional theory. The electroluminescence spectra of the brightest, nonaggregating derivative showed a better color purity than that of iridium(III) tris(phenylpyridine), .
Circulating white blood cells and lung function impairment: the observational studies and Mendelian randomization analysis

Abstract Background Circulating white blood cell (WBC) counts have been related to lung function impairment, but causal relationship was not established. We aimed to evaluate independent effects and causal relationships of WBC subtypes with lung function. Methods The 19,159 participants from NHANES 2011–2012 (n = 3570), coke-oven workers (COW, n = 1762) and Dongfeng-Tongji (DFTJ, n = 13,827) cohorts were included in the observational studies. The associations between circulating counts of WBC subtypes and prebronchodilator lung function were evaluated by linear regression models and LASSO regression was used to select effective WBC subtypes. Summary statistics for WBC-associated SNPs were extracted from literature, and Mendelian randomization (MR) analysis with inverse-variance weighted (IVW) method was applied to estimate the causal effects of total WBC and subtypes on lung function among 4012 subjects from COW (n = 1126) and DFTJ cohorts (n = 2886). Results Total WBC counts were negatively associated with lung function among three populations and their pooled analysis indicated that per 1 × 109 cells/L increase in total WBC was associated with 36.13 (95% CI: 30.35, 41.91) mL and 25.23 (95% CI: 19.97, 30.50) mL decrease in FVC and FEV1, respectively. Independent associations with lung function were found for neutrophils, monocytes, eosinophils and basophils (all p < .05), except lymphocytes. Besides, IVW MR analysis showed that genetically predicted total WBC and neutrophil counts were associated with reduced FVC (p = .017 and .021, respectively) and FEV1 (p = .048 and .043, respectively). Conclusions WBC subtypes were independently associated with lower lung function except lymphocytes. Our findings suggest that circulating neutrophils may be causal factors in lung function impairment. KEY MESSAGES White blood cell (WBC) subtypes were negatively associated with lung function level except lymphocytes in the observational studies. Associations of WBC subtypes with lung function may be modified by sex and smoking. Mendelian randomization analysis shows that neutrophils may be causal factors in lung function impairment.
Cognitive outcomes at ages seven and nine years in South African children from the children with HIV early antiretroviral (CHER) trial: a longitudinal investigation

Many children living with HIV (CLWH) display impaired cognition. Although early combination antiretroviral therapy (ART) produces improved cognitive outcomes, more long‐term outcome data are needed. After concluding the Children with HIV Early antiRetroviral (CHER) trial in 2011, we investigated cognitive performance, at seven and nine years of age. Participants had been randomized to deferred ART (ART‐Def; n = 22); immediate time‐limited ART for 40 weeks (ART‐40W; n = 30) and immediate time‐limited ART for 96 weeks (ART‐96W; n = 18). We also recruited HIV‐exposed uninfected (CHEU; n = 28) and HIV‐unexposed (CHU; n = 35) children.
Efficient bipedal locomotion on rough terrain via compliant ankle actuation with energy regulation

Legged locomotion enables robotic platforms to traverse on rough terrain, which is quite challenging for other locomotion types, such as in wheeled and tracked systems. However, this benefit—moving robustly on rough terrain—comes with an inherent drawback due to the higher cost of transport in legged robots. The ultimate need for energy efficiency motivated the utilization of passive dynamics in legged locomotion. Nevertheless, a handicap in passive dynamic walking is the fragile basin of attraction that limits the locomotion capabilities of such systems. There have been various extensions to overcome such limitations by incorporating additional actuators and active control approaches at the expense of compromising the benefits of passivity. Here, we present a novel actuation and control framework, enabling efficient and sustained bipedal locomotion on significantly rough terrain. The proposed approach reinforces the passive dynamics by intermittent active feedback control within a bio-inspired compliant ankle actuation framework. Specifically, we use once-per-step energy regulation to adjust the spring precompression of the compliant ankle based on the liftoff instants—when the toe liftoffs from the ground—of the locomotion. Our results show that the proposed approach achieves highly efficient (with a cost of transport of 0.086) sustained locomotion on rough terrain, withstanding height variations up to 15% of the leg length. We provide theoretical and numerical analysis to demonstrate the performance of our approach, including systematic comparisons with the recent and state-of-the-art techniques in the literature.
A self-supervised deep neural network for image completion resembles early visual cortex fMRI activity patterns for occluded scenes

Abstract The promise of artificial intelligence in understanding biological vision relies on the comparison of computational models with brain data with the goal of capturing functional principles of visual information processing. Convolutional neural networks (CNN) have successfully matched the transformations in hierarchical processing occurring along the brain's feedforward visual pathway, extending into ventral temporal cortex. However, we are still to learn if CNNs can successfully describe feedback processes in early visual cortex. Here, we investigated similarities between human early visual cortex and a CNN with encoder/decoder architecture, trained with self-supervised learning to fill occlusions and reconstruct an unseen image. Using representational similarity analysis (RSA), we compared 3T functional magnetic resonance imaging (fMRI) data from a nonstimulated patch of early visual cortex in human participants viewing partially occluded images, with the different CNN layer activations from the same images. Results show that our self-supervised image-completion network outperforms a classical object-recognition supervised network (VGG16) in terms of similarity to fMRI data. This work provides additional evidence that optimal models of the visual system might come from less feedforward architectures trained with less supervision. We also find that CNN decoder pathway activations are more similar to brain processing compared to encoder activations, suggesting an integration of mid- and low/middle-level features in early visual cortex. Challenging an artificial intelligence model to learn natural image representations via self-supervised learning and comparing them with brain data can help us to constrain our understanding of information processing, such as neuronal predictive coding.
Web-Based Health Information Seeking Among African American and Hispanic Men Living With Chronic Conditions: Cross-sectional Survey Study

Background Previous research has identified disparities in seeking and using web-based health information to inform health-related behaviors. Relatively few studies however have examined the correlations between web-based health information seeking and use based on race, gender, age, and the presence of chronic health conditions. Objective In this study, we identify factors associated with seeking and using web-based health information among a uniquely vulnerable and intersectional population—middle-aged and older (40 years and older) African American and Hispanic men living with one or more chronic conditions. Methods Survey responses were collected from a purposive sample of African American and Hispanic men using Qualtrics web-based survey management software. To qualify for inclusion in the study, respondents had to identify as African American or Hispanic men, report having at least one chronic condition, and be aged 40 years and older. A series of binary logistic regression models was created using backward elimination. Statistical significance was determined at P<. 05 for all analyses. Results Web-based health information seeking among African American and Hispanic men is a function of education, the presence of multiple chronic conditions, frustration with health care providers, internet use, and the perceived reliability of web-based health information. The use of web-based health information to inform interactions with health care providers was more common among African American and Hispanic men, who rated their health as relatively good, perceived barriers to care, used technology regularly, and took more daily medications. Conclusions Understanding the factors that influence African American and Hispanic men seeking web-based health information may help improve the care and treatment of chronic conditions. African American and Hispanic men seek web-based health information as a substitute for routine care and to inform their discussions with health care providers.
Prognostic value of fatty acid metabolism-related genes in patients with hepatocellular carcinoma

The deregulation of fatty acid metabolism plays a crucial role in cancer. However, the prognostic value of genes involved in the metabolism in hepatocellular carcinoma (HCC) remains largely unknown. We first constructed a multi-fatty acid metabolic gene prognostic model of HCC based on The Cancer Genome Atlas (TCGA) and further validated it using the International Cancer Genome Consortium (ICGC) database. The model was integrated with the clinical parameters, and a nomogram was built and weighted. Moreover, immune cell infiltration of the tumor microenvironment was investigated. A prognostic model was constructed using 6 selected fatty acid metabolism-related genes, and HCC patients were divided into high- and low-risk groups. Receiver operating characteristic curve (ROC) analysis, principal component analysis (PCA), and t-distributed stochastic neighbor embedding (t-SNE) analysis showed the optimal performance of the model. The concordance index (C-index), ROC curve, calibration plot and decision curve analysis (DCA) all confirmed the satisfactory predictive capacity of the nomogram. The analysis of immune cell infiltration in HCC patients revealed a correlation with different risk levels. Our findings indicate that a prognostic model based on fatty acid metabolism-related genes has superior predictive capacities, which provides the possibility for further improving the individualized treatment of patients with HCC.