Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbiota links to neural dynamics supporting threat processing

There is growing recognition that the composition of the gut microbiota influences behaviour, including responses to threat. The cognitive-interoceptive appraisal of threat-related stimuli relies on dynamic neural computations between the anterior insular (AIC) and the dorsal anterior cingulate (dACC) cortices. If, to what extent, and how microbial consortia influence the activity of this cortical threat processing circuitry is unclear. We addressed this question by combining a threat processing task, neuroimaging, 16S rRNA profiling, and computational modelling in healthy participants. Results showed interactions between high-level ecological indices with threat-related AIC-dACC neural dynamics. At finer taxonomic resolutions, the abundance of Ruminococcus was differentially linked to connectivity between, and activity within the AIC and dACC during threat updating. Functional inference analysis provides a strong rationale to motivate future investigations of microbiota-derived metabolites in the observed relationship with threat-related brain processes.
Phosphorylation of the M1 muscarinic acetylcholine receptor mediates protection in neurodegenerative disease

There are currently no treatments that can slow the progression of neurodegenerative diseases such as Alzheimer’s disease (AD). There is, however, a growing body of evidence that activation of the M1 muscarinic acetylcholine receptor (M1-receptor) can not only restore memory loss in AD patients, but in preclinical animal models can also slow neurodegenerative disease progression. The generation of an effective medicine targeting the M1-receptor has however been severely hampered by associated cholinergic adverse responses. By using genetically engineered mouse models that express a G protein-biased M1-receptor, we recently established that M1-receptor mediated adverse responses can be minimised by ensuring activating ligands maintain receptor phosphorylation/arrestin-dependent signalling. Here, we use these same genetic models in concert with murine prion disease, a terminal neurodegenerative disease showing key hallmarks of AD, to establish that phosphorylation/arrestin-dependent signalling delivers neuroprotection that both extends normal animal behaviour and prolongs the life span of prion diseased mice. Our data point to an important neuroprotective property inherent to the M1-receptor and indicate that next generation M1-receptor ligands designed to drive receptor phosphorylation/arrestin-dependent signalling would potentially show low adverse responses whilst delivering neuroprotection that will slow disease progression.
Concurrent assessment of motor unit firing properties and fascicle

28 Previous studies assessing relationships between muscle mechanics and neural activity have 29 concurrently assessed changes in fascicle length (FL) and neural activation with 30 electromyography (EMG) approaches with low spatial sampling from different muscle regions. 31 This project aimed to assess changes in FL and motor unit (MU) firing, simultaneously, on the 32 same region of interest, with high-density EMG electrodes transparent to ultrasound (HDEMG33 US). EMG signals and ultrasound images were recorded simultaneously from the tibialis anterior 34 of 10 participants, using a silicon matrix of 32 electrodes, while performing sustained-isometric 35 ankle-dorsiflexion contractions, at diverse joint positions (0 ̊ and 30 ̊ plantar flexion) and torques 36 (20% and 40% of maximum). EMG signals were decomposed into individual MUs and changes in 37 FL were assessed with a fascicle-tracking algorithm. MU firing data was converted into a 38 cumulative spike train (CST) that was cross-correlated with dorsiflexion torque (CST-torque) and 39 FL (CST-FL). On average, 7 (3) MUs were identified across contractions. Cross-correlations showed 40 that CST could explain on average 60% (range: 31-85%) and 71% (range: 0.31-0.88) of the 41 variance in FL and torque, respectively. Cross-correlation lags revealed that the delay between 42 CST-FL (~75ms) was smaller than CST-torque (~150ms, p<0.001). Finally, we could observe that 43 both delays increased by ~20ms at 30° of plantar flexion (p<0.05). This study is the first to 44 demonstrate the feasibility of recording single MU activity with HDEMG-US whilst simultaneously 45 evaluating changes in FL. The findings show a close relationship between dorsiflexion torque, FL 46 and CST, also allowing quantification of the delay between each of these signals. 47
Large-scale CRISPRi and transcriptomics of Staphylococcus epidermidis identify genetic factors implicated in commensal-pathogen lifestyle versatility

Staphylococcus (S.) epidermidis is a ubiquitous human commensal skin bacterium that is also one of the most prevalent nosocomial pathogens. The genetic factors underlying this remarkable lifestyle plasticity are incompletely understood, much due to the difficulties of genetic manipulation, precluding high-throughput functional profiling of this species. To probe S. epidermdis’ versatility to survive across a diversity of skin sites and infection niches, we developed a large-scale CRISPR interference (CRISPRi) screen complemented by transcriptional profiling (RNA-seq) across 24 diverse environmental conditions and piloted a droplet-based CRISPRi approach to enhance throughput and sensitivity. We identified putative essential genes, importantly, revealing amino acid metabolism as crucial to survival across diverse environments and demonstrated the importance of trace metal uptake for survival under multiple stress conditions. We identified pathways significantly enriched and repressed across our range of stress and nutrient limited conditions, demonstrating the considerable plasticity of S. epidermidis in responding to environmental stressors. We postulate a mechanism by which nitrogen metabolism is linked to lifestyle versatility in response to hyperosmotic challenges, such as those encountered on human skin. Finally, we examined S. epidermidis survival under acid stress and hypothesize a role for cell wall modification as a vital component of the survival response in acidic conditions. Taken together, this study integrates large scale CRISPRi and transcriptomics data across multiple environments to provide insights into a keystone member of the human skin microbiome. Our results additionally provide a valuable benchmarking analysis for CRISPRi screens and are rich resource for other staphylococcal researchers. Author summary Staphylococcus epidermidis is an important bacteria of the skin microbiome. While it has an important role in skin health, it can also be a major infectious agent, especially in bloodstream and catheter infections. Understanding the underlying genes and pathways that contribute to S. epidermidis’ ability to have both health and disease-associated abilities will be important to promoting the former and targeting the latter. Yet the function of many S. epidermidis genes, particularly in skin and infection environments, remains unknown. We developed a CRISPRi platform to knock down the function of S. epidermidis genes to better understand to what degree they are essential for growth in these environments. We complemented this gene essentiality data with gene expression data in the same environments to understand how regulation of these genes contribute to S. epidermidis’ survival. These large-scale data generated numerous hypotheses for new genetic links to S. epidermidis’ growth versatility.
The Second-Generation XPO1 Inhibitor Eltanexor Inhibits Human Cytomegalovirus (HCMV) Replication and Promotes Type I Interferon Response

Human cytomegalovirus (HCMV) is a ubiquitous opportunistic pathogen and can be life-threatening for immunocompromised individuals. There is currently no available vaccine for the prevention of HCMV- associated diseases and most of the available antiviral drugs that target viral DNA synthesis become ineffective in treating HCMV mutants that arise after long-term use in immunocompromised patients. Here, we examined the effects of Eltanexor, a second-generation selective inhibitor of nuclear export (SINE), on HCMV replication. Eltanexor effectively inhibits HCMV replication in human foreskin fibroblasts in a dose-dependent manner. Eltanexor does not significantly inhibit viral entry and nuclear import of viral genomic DNA, but rather suppress the transcript and protein levels of viral immediate-early (IE), early (E) and late (L) genes, and abolishes the production of infectious virions. We further found Eltanexor treatment promotes proteasome-mediated degradation of XPO1, which contributes to the nuclear retention of interferon regulatory factor 3 (IRF-3), resulting in increased expression of type I interferon as well as interferon stimulating genes ISG15 and ISG54. This study reveals a novel antiviral mechanism of Eltanexor which suggests it has potential to inhibit a broad spectrum of viral pathogens.
An Exploration of the Tumor Microenvironment Identified a Novel Five-Gene Model for Predicting Outcomes in Bladder Cancer

Bladder cancer (BC) is one of the top ten most common cancer types globally, accounting for approximately 7% of all male malignancies. In the last few decades, cancer research has focused on identifying oncogenes and tumor suppressors. Recent studies have revealed that the interplay between tumor cells and the tumor microenvironment (TME) plays an important role in the initiation and development of cancer. However, the current knowledge regarding its effect on BC is scarce. This study aims to explore how the TME influences the development of BC. We focused on immune and stromal components, which represent the major components of TME. We found that the proportion of immune and stromal components within the TME was associated with the prognosis of BC. Furthermore, based on the scores of immune and stromal components, 811 TME-related differentially expressed genes were identified. Three subclasses with distinct biological features were divided based on these TME-genes. Finally, five prognostic genes were identified and used to develop a prognostic prediction model for BC patients based on TME-related genes. Additionally, we validated the prognostic value of the five-gene model using three independent cohorts. By further analyzing features based on the five-gene signature, higher CD8+ T cells, higher tumor mutational burden, and higher chemosensitivity were found in the low-risk group, which presented a better prognosis. In conclusion, our exploration comprehensively analyzed the TME and identified TME-related prognostic genes for BC, providing new insights into potential therapeutic targets.
Efficacy of Feedforward and LSTM Neural Networks at Predicting and Gap Filling Coastal Ocean Timeseries: Oxygen, Nutrients, and Temperature

Ocean data timeseries are vital for a diverse range of stakeholders (ranging from government, to industry, to academia) to underpin research, support decision making, and identify environmental change. However, continuous monitoring and observation of ocean variables is difficult and expensive. Moreover, since oceans are vast, observations are typically sparse in spatial and temporal resolution. In addition, the hostile ocean environment creates challenges for collecting and maintaining data sets, such as instrument malfunctions and servicing, often resulting in temporal gaps of varying lengths. Neural networks (NN) have proven effective in many diverse big data applications, but few oceanographic applications have been tested using modern frameworks and architectures. Therefore, here we demonstrate a “proof of concept” neural network application using a popular “off-the-shelf” framework called “TensorFlow” to predict subsurface ocean variables including dissolved oxygen and nutrient (nitrate, phosphate, and silicate) concentrations, and temperature timeseries and show how these models can be used successfully for gap filling data products. We achieved a final prediction accuracy of over 96% for oxygen and temperature, and mean squared errors (MSE) of 2.63, 0.0099, and 0.78, for nitrates, phosphates, and silicates, respectively. The temperature gap-filling was done with an innovative contextual Long Short-Term Memory (LSTM) NN that uses data before and after the gap as separate feature variables. We also demonstrate the application of a novel dropout based approach to approximate the Bayesian uncertainty of these temperature predictions. This Bayesian uncertainty is represented in the form of 100 monte carlo dropout estimates of the two longest gaps in the temperature timeseries from a model with 25% dropout in the input and recurrent LSTM connections. Throughout the study, we present the NN training process including the tuning of the large number of NN hyperparameters which could pose as a barrier to uptake among researchers and other oceanographic data users. Our models can be scaled up and applied operationally to provide consistent, gap-free data to all data users, thus encouraging data uptake for data-based decision making.
Identification of Potential Binders of Mtb Universal Stress Protein (Rv1636) Through an in silico Approach and Insights Into Compound Selection for Experimental Validation

Millions of deaths caused by Mycobacterium tuberculosis (Mtb) are reported worldwide every year. Treatment of tuberculosis (TB) involves the use of multiple antibiotics over a prolonged period. However, the emergence of resistance leading to multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) is the most challenging aspect of TB treatment. Therefore, there is a constant need to search for novel therapeutic strategies that could tackle the growing problem of drug resistance. One such strategy could be perturbing the functions of novel targets in Mtb, such as universal stress protein (USP, Rv1636), which binds to cAMP with a higher affinity than ATP. Orthologs of these proteins are conserved in all mycobacteria and act as “sink” for cAMP, facilitating the availability of this second messenger for signaling when required. Here, we have used the cAMP-bound crystal structure of USP from Mycobacterium smegmatis, a closely related homolog of Mtb, to conduct a structure-guided hunt for potential binders of Rv1636, primarily employing molecular docking approach. A library of 1.9 million compounds was subjected to virtual screening to obtain an initial set of ~2,000 hits. An integrative strategy that uses the available experimental data and consensus indications from other computational analyses has been employed to prioritize 22 potential binders of Rv1636 for experimental validations. Binding affinities of a few compounds among the 22 prioritized compounds were tested through microscale thermophoresis assays, and two compounds of natural origin showed promising binding affinities with Rv1636. We believe that this study provides an important initial guidance to medicinal chemists and biochemists to synthesize and test an enriched set of compounds that have the potential to inhibit Mtb USP (Rv1636), thereby aiding the development of novel antitubercular lead candidates.
Association of Disinhibited Eating and Trait of Impulsivity With Insula and Amygdala Responses to Palatable Liquid Consumption

Eating behavior is not only influenced by the current energy balance, but also by the behavioral characteristics of eating. One of the recognized eating behavior constructs is ‘disinhibited eating,’ which refers to the tendency to overeat in response to negative emotional states or the presence of highly palatable foods. Food-related disinhibition is involved in binge eating, weight gain, and obesity and is also associated with the trait of impulsivity, which in turn, is linked to weight gain or maladaptive eating. However, the relationships among food-related disinhibition, the trait of impulsivity, and the neural substrates of eating behaviors in adolescence remain unclear. Therefore, we designed a functional magnetic resonance imaging (fMRI) study to examine the associations between brain responses to palatable liquid consumption and disinhibited eating behavior or impulsivity in healthy adolescents. Thirty-four adolescents (mean age ± standard deviation = 17.12 ± 1.91 years, age range = 14–19 years, boys = 15, girls = 19) participated in this study. Disinhibited eating was assessed with the disinhibition subscale of the Three-Factor Eating Questionnaire, while impulsivity was assessed using the Barratt impulsiveness scale. Participants received two fMRI sessions−a palatable liquid consumption fMRI and a resting-state fMRI. The fMRI experiment showed that increased disinhibited eating was positively associated with a greater insular response to palatable liquid consumption, while increased impulsivity was positively correlated with a greater amygdala response. The resting-state fMRI experiment showed that increased disinhibited eating was positively correlated with strengthened intrinsic functional connectivity between the insula and the amygdala, adjusting for sex (estimates of the beta coefficients = 0.146, standard error = 0.068, p = 0.040). Given that the amygdala and insular cortex are structurally and functionally connected and involved in trait impulsivity and ingestive behavior, our findings suggest that increased disinhibited eating would be associated with impulsivity via strengthened intrinsic functional connectivity between the insula and amygdala and linked to maladaptive eating.
Clozapine Regulates Microglia and Is Effective in Chronic Experimental Autoimmune Encephalomyelitis

Objective Progressive multiple sclerosis is characterized by chronic inflammation with microglial activation, oxidative stress, accumulation of iron and continuous neurodegeneration with inadequate effectiveness of medications used so far. We now investigated effects of iron on microglia and used the previously identified neuroprotective antipsychotic clozapine in vitro and in chronic experimental autoimmune encephalomyelitis (EAE). Methods Microglia were treated with iron and clozapine followed by analysis of cell death and response to oxidative stress, cytokine release and neuronal phagocytosis. Clozapine was investigated in chronic EAE regarding optimal dosing and therapeutic effectiveness in different treatment paradigms. Animals were scored clinically by blinded raters. Spinal cords were analyzed histologically for inflammation, demyelination, microglial activation and iron accumulation and for transcription changes of regulators of iron metabolism and inflammation. Effects on immune cells were analyzed using flow cytometry. Results Iron impaired microglial function in vitro regarding phagocytosis and markers of inflammation; this was regulated by clozapine, reflected in reduced release of IL-6 and normalization of neuronal phagocytosis. In chronic EAE, clozapine dose-dependently attenuated clinical signs and still had an effect if applied in a therapeutic setting. Early mild sedative effects habituated over time. Histologically, demyelination was reduced by clozapine and positive effects on inflammation strongly correlated with reduced iron deposition. This was accompanied by reduced expression of DMT-1, an iron transport protein. Conclusions Clozapine regulates microglial function and attenuates chronic EAE, even in a therapeutic treatment paradigm. This well-defined generic medication might therefore be considered as promising add-on therapeutic for further development in progressive MS.
Design and Modelling of a Continuum Robot for Distal Lung Sampling in Mechanically Ventilated Patients in Critical Care

In this paper, we design and develop a novel robotic bronchoscope for sampling of the distal lung in mechanically-ventilated (MV) patients in critical care units. Despite the high cost and attributable morbidity and mortality of MV patients with pneumonia which approaches 40%, sampling of the distal lung in MV patients suffering from range of lung diseases such as Covid-19 is not standardised, lacks reproducibility and requires expert operators. We propose a robotic bronchoscope that enables repeatable sampling and guidance to distal lung pathologies by overcoming significant challenges that are encountered whilst performing bronchoscopy in MV patients, namely, limited dexterity, large size of the bronchoscope obstructing ventilation, and poor anatomical registration. We have developed a robotic bronchoscope with 7 Degrees of Freedom (DoFs), an outer diameter of 4.5 mm and inner working channel of 2 mm. The prototype is a push/pull actuated continuum robot capable of dexterous manipulation inside the lung and visualisation/sampling of the distal airways. A prototype of the robot is engineered and a mechanics-based model of the robotic bronchoscope is developed. Furthermore, we develop a novel numerical solver that improves the computational efficiency of the model and facilitates the deployment of the robot. Experiments are performed to verify the design and evaluate accuracy and computational cost of the model. Results demonstrate that the model can predict the shape of the robot in <0.011s with a mean error of 1.76 cm, enabling the future deployment of a robotic bronchoscope in MV patients.
Bacteriophages Are Good Estimators of Human Viruses Present in Water

The detection of fecal viral pathogens in water is hampered by their great variety and complex analysis. As traditional bacterial indicators are poor viral indicators, there is a need for alternative methods, such as the use of somatic coliphages, which have been included in water safety regulations in recent years. Some researchers have also recommended the use of reference viral pathogens such as noroviruses or other enteric viruses to improve the prediction of fecal viral pollution of human origin. In this work, phages previously tested in microbial source tracking studies were compared with norovirus and adenovirus for their suitability as indicators of human fecal viruses. The phages, namely those infecting human-associated Bacteroides thetaiotaomicron strain GA17 (GA17PH) and porcine-associated Bacteroides strain PG76 (PGPH), and the human-associated crAssphage marker (crAssPH), were evaluated in sewage samples and fecal mixtures obtained from different animals in five European countries, along with norovirus GI + GII (NoV) and human adenovirus (HAdV). GA17PH had an overall sensitivity of ≥83% and the highest specificity (>88%) for human pollution source detection. crAssPH showed the highest sensitivity (100%) and specificity (100%) in northern European countries but a much lower specificity in Spain and Portugal (10 and 30%, respectively), being detected in animal wastewater samples with a high concentration of fecal indicators. The correlations between GA17PH, crAssPH, or the sum of both (BACPH) and HAdV or NoV were higher than between the two human viruses, indicating that bacteriophages are feasible indicators of human viral pathogens of fecal origin and constitute a promising, easy to use and affordable alternative to human viruses for routine water safety monitoring.