Miracle-dz/UniFAR-FTUs huggingface dataset:
PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave

Immune responses triggered by pathogen-associated molecular patterns (PAMPs) are key to pathogen defense, but drivers of the genetic reprogramming required to reach the immune state remain incompletely understood in plants. Here, we report a time-course study of the establishment of PAMP-triggered immunity (PTI) using cap analysis of gene expression (CAGE). Our results show that as much as 15% of all PAMP response genes display alternative transcription initiation. In several cases, use of alternative TSSs may be regulatory as it determines inclusion of target peptides or protein domains, or occurrence of upstream open reading frames (uORFs) in mRNA leader sequences. We also find that 60% of PAMP-response genes respond much earlier than previously thought. In particular, a previously unnoticed cluster of rapidly and transiently PAMP-induced genes is enriched in transcription factors whose functions, previously associated with biological processes as diverse as abiotic stress adaptation and stem cell activity, appear to converge on growth restriction. Furthermore, some examples of known potentiators of PTI, in one case under direct MAP kinase control, support the notion that the rapidly induced transcription factors could constitute direct links to PTI signaling pathways and drive gene expression changes underlying establishment of the immune state.
In-cell structures of a conserved supramolecular array at the mitochondria-cytoskeleton interface in mammalian sperm

Mitochondria-cytoskeleton interactions modulate cellular physiology by regulating mitochondrial transport, positioning, and immobilization. However, there is very little structural information defining mitochondria-cytoskeleton interfaces in any cell type. Here, we use cryo-focused ion beam milling-enabled cryo-electron tomography to image mammalian sperm, where mitochondria wrap around the ciliary cytoskeleton. We find that mitochondria are tethered to their neighbors through inter-mitochondrial linkers and are anchored to the cytoskeleton through ordered arrays on the outer mitochondrial membrane. We use subtomogram averaging to resolve in-cell structures of these arrays from three mammalian species, revealing they are conserved across species despite variations in mitochondrial dimensions and cristae organization. We find that the arrays consist of boat-shaped particles anchored on a network of membrane pores whose arrangement and dimensions are consistent with voltage dependent anion channels. Proteomics and in-cell cross-linking mass spectrometry suggest that the conserved arrays are composed of glycerol kinase-like proteins. Ordered supramolecular assemblies may serve to stabilize similar contact sites in other cell types where mitochondria need to be immobilized in specific subcellular environments, such as in muscles and neurons.
Cerebellum regulates the timing of periaqueductal grey neural encoding of fear memory and the expression of fear conditioned behaviours

The pivotal role of the periaqueductal grey (PAG) in fear learning is reinforced by the identification of neurons in rat ventral (vPAG) that encode fear memory through signalling the onset and offset of an auditory conditioned stimulus during retrieval. Within this framework, understanding of cerebellar contributions to survival circuits is advanced by the discovery that: (i) reversible inactivation of the medial cerebellar nucleus (MCN) during fear consolidation (a) reduces the temporal precision of vPAG offset, but not onset responses and (b) increases rearing behaviour during retrieval, and (ii) chemogenetic inhibition of the MCN-vPAG projection during fear acquisition (a) reduces the emission of fear-related ultrasonic vocalisations and (b) slows the extinction rate of fear-related freezing. These findings show that the cerebellum regulates fear memory processes at multiple timescales and in multiple ways. The current findings indicate that dysfunctional interactions in the cerebellar-survival network may underlie fear-related disorders and comorbidities. Impact Statement Cerebellar-periaqueductal grey interactions contribute to fear conditioned processes and, as such, provide a novel target for treating psychological conditions including post-traumatic stress disorder.
Multidimensional Single-Nuclei RNA-Seq Reconstruction of Adipose Tissue Reveals Adipocyte Plasticity Underlying Thermogenic Response

Adipose tissue has been classified based on its morphology and function as white, brown, or beige / brite. It plays an essential role as a regulator of systemic metabolism through paracrine and endocrine signals. Recently, multiple adipocyte subtypes have been revealed using RNA sequencing technology, going beyond simply defined morphology but by their cellular origin, adaptation to metabolic stress, and plasticity. Here, we performed an in-depth analysis of publicly available single-nuclei RNAseq from adipose tissue and utilized a workflow template to characterize adipocyte plasticity, heterogeneity, and secretome profiles. The reanalyzed dataset led to the identification of different subtypes of adipocytes including three subpopulations of thermogenic adipocytes and provided a characterization of distinct transcriptional profiles along the adipocyte trajectory under thermogenic challenges. This study provides a useful resource for further investigations regarding mechanisms related to adipocyte plasticity and trans-differentiation. Highlights Multidimensional transcriptome analysis at single-nucleus resolution recovers nuclei of cell types in adipose tissue Adaptative thermogenic response results in 3 distinct mature adipose cell types Single-nuclei transcriptomic-based secretome analysis reveals adipose cell-type-specific genes The in vivo trajectory of adipocyte plasticity for thermogenic response reveals sets of trans-differentiation genes Graphic Abstract
Optical activation of TrkB neurotrophin receptor in mouse ventral hippocampus promotes plasticity and facilitates fear extinction

Successful extinction of traumatic memories depends on neuronal plasticity in the fear extinction network. However, the mechanisms involved in the extinction process remain poorly understood. Here, we investigated the fear extinction network by using a new optogenetic technique that allows temporal and spatial control of neuronal plasticity in vivo. We optimized an optically inducible TrkB (CKII-optoTrkB), the receptor of the brain-derived neurotrophic factor, which can be activated upon blue light exposure to increase plasticity specifically in pyramidal neurons. The activation of CKII-optoTrkB facilitated the induction of LTP in Schaffer collateral-CA1 synapses after brief theta-burst stimulation and increased the expression of FosB in the pyramidal neurons of the ventral hippocampus, indicating enhanced plasticity in that brain area. We showed that optical stimulation of the CA1 region of the ventral hippocampus during fear extinction training led to an attenuated conditioned fear memory. This was a specific effect only observed when combining extinction training with CKII-optoTrkB activation, and not when using either intervention alone. Thus, TrkB activation in ventral CA1 pyramidal neurons promotes a state of neuronal plasticity that allows extinction training to guide neuronal network remodeling to overcome fear memories. Our methodology is a powerful tool to induce neuronal network remodeling in the adult brain, and can attenuate neuropsychiatric symptoms caused by malfunctioning networks.
Comparative analysis of Alzheimer’s disease knock-in model brain transcriptomes implies changes to energy metabolism as a causative pathogenic stress

Energy production is the most fundamentally important cellular activity supporting all other functions, particularly in highly active organs such as brains. Here, we summarise transcriptome analyses of young adult (pre-disease) brains from a collection of eleven early-onset familial Alzheimer’s disease (EOfAD)-like and non-EOfAD-like mutations in three zebrafish genes. The one cellular activity consistently predicted as affected by only the EOfAD-like mutations is oxidative phosphorylation that produces most of the brain’s energy. All the mutations were predicted to affect protein synthesis. We extended our analysis to knock-in mouse models of APOE alleles and found the same effect for the late onset Alzheimer’s disease risk allele ɛ4. Our results support a common molecular basis for initiation of the pathological processes leading to both early and late onset forms of Alzheimer’s disease and illustrate the utility of both zebrafish and knock-in, single EOfAD mutation models for understanding the causes of this disease.
Reporter gene assay for membrane fusion of extracellular vesicles

Abstract Extracellular vesicles (EVs) secreted by living cells are expected to deliver biological cargo molecules, including RNA and proteins, to the cytoplasm of recipient cells. There is an increasing need to understand the mechanism of intercellular cargo delivery by EVs. However, the lack of a feasible bioassay has hampered our understanding of the biological processes of EV uptake, membrane fusion, and cargo delivery to recipient cells. Here, we describe a reporter gene assay that can measure the membrane fusion efficiency of EVs during cargo delivery to recipient cells. When EVs containing tetracycline transactivator (tTA)-fused tetraspanins are internalized by recipient cells and fuse with cell membranes, the tTA domain is exposed to the cytoplasm and cleaved by protease to induce tetracycline responsive element (TRE)-mediated reporter gene expression in recipient cells. This assay (designated as EV-mediated tetraspanin-tTA delivery assay, ETTD assay), enabled us to assess the cytoplasmic cargo delivery efficiency of EVs in recipient cells. With the help of a vesicular stomatitis virus-derived membrane fusion protein, the ETTD assay could detect significant enhancement of cargo delivery efficiency of EVs. Furthermore, the ETTD assay could evaluate the effect of potential cargo delivery enhancers/inhibitors. Thus, the ETTD assay may contribute to a better understanding of the underlying mechanism of the cytoplasmic cargo delivery by EVs.
Isolation and Characterisation of Bacteriophages with Activity against Invasive Non-Typhoidal Salmonella Causing Bloodstream Infection in Malawi

In recent years, novel lineages of invasive non-typhoidal Salmonella (iNTS) serovars Typhimurium and Enteritidis have been identified in patients with bloodstream infection in sub-Saharan Africa. Here, we isolated and characterised 32 phages capable of infecting S. Typhimurium and S. Enteritidis, from water sources in Malawi and the UK. The phages were classified in three major phylogenetic clusters that were geographically distributed. In terms of host range, Cluster 1 phages were able to infect all bacterial hosts tested, whereas Clusters 2 and 3 had a more restricted profile. Cluster 3 contained two sub-clusters, and 3.b contained the most novel isolates. This study represents the first exploration of the potential for phages to target the lineages of Salmonella that are responsible for bloodstream infections in sub-Saharan Africa.
Multispecies site occupancy modeling and study design for spatially replicated environmental DNA metabarcoding

Environmental DNA (eDNA) metabarcoding has become widely applied to gauge biodiversity in a noninvasive and cost-efficient manner. The detection of species using eDNA metabarcoding is, however, imperfect owing to various factors that can cause false negatives in the inherent multi-stage workflow. Imperfect detection in the multi-stage workflow of eDNA metabarcoding also raises an issue of study design: namely, how available resources should be allocated among the different stages to optimize survey efficiency. Here, we propose a variant of the multispecies site occupancy model for eDNA metabar-coding studies where samples are collected at multiple sites within a region of interest. This model describes the variation in sequence reads, the unique output of the high-throughput sequencers, in terms of the hierarchical workflow of eDNA metabarcoding and interspecific heterogeneity, allowing the decomposition of the sources of variation in the detectability of species throughout the different stages of the workflow. We also introduced a Bayesian decision analysis framework to identify the study design that optimizes the efficiency of species detection with a limited budget. An application of the model to freshwater fish communities in the Lake Kasumigaura watershed, in Japan, highlighted a remarkable inhomogeneity in the detectability of species, indicating a potential risk of the biased detection of specific species. Species with lower site occupancy probabilities tended to be difficult to detect as they had lower capture probabilities and lower dominance of the sequences. The expected abundance of sequence reads was predicted to vary by up to 23.5 times between species. An analysis of the study design suggested that ensuring multiple within-site replications of the environmental samples is preferred in order to achieve better species detection efficiency, provided that a throughput of tens of thousands of sequence reads was secured. The proposed framework makes the application of eDNA metabarcoding more error-tolerant, allowing ecologists to monitor ecological communities more efficiently.
A phosphorylation of RIPK3 kinase initiates an intracellular apoptotic pathway that promotes corpus luteum regression

Receptor-interacting serine/threonine-protein kinase 3 (RIPK3) normally signals to necroptosis by phosphorylating MLKL. We report here that when the cellular RIPK3 chaperone Hsp90/CDC37 level is low, RIPK3 also signals to apoptosis. The apoptotic function of RIPK3 requires phosphorylation of the serine 165/threonine 166 sites on its kinase activation loop, resulting in inactivation of RIPK3 kinase activity while gaining the ability to recruit RIPK1, FADD, and caspase-8 to form a cytosolic caspase-activating complex, thereby triggering apoptosis. We found that PGF2α induces RIPK3 expression in luteal granulosa cells in the ovary to cause luteal regression through this RIPK3-mediated apoptosis pathway. Mice carrying homozygous phosphorylation-resistant RIPK3 S165A/T166A knockin mutations failed to respond to PGF2α but retained pro-necroptotic function, whereas mice with phospho-mimicking S165D/T166E homozygous knockin mutation underwent spontaneous apoptosis in multiple RIPK3-expressing tissues and died shortly after birth. Thus, RIPK3 signals to either necroptosis or apoptosis depending on its serine 165/threonine 166 phosphorylation status.
Interfacial oxygen migration and its effect on the magnetic anisotropy in Pt/Co/MgO/Pt films

This paper reports the interfacial oxygen migration effect and its induced magnetic anisotropy evolution in Pt/Co/MgO/Pt films. During depositing the MgO layer, oxygen atoms from the MgO combine with the neighboring Co atoms, leading to the formation of CoO at the Co/MgO interface. Meanwhile, the films show in-plane magnetic anisotropy (IMA). After annealing, most of the oxygen atoms in CoO migrate back to the MgO layer, resulting in obvious improvement of Co/MgO interface and the enhancement of effective Co-O orbital hybridization. These favor the evolution of magnetic anisotropy from IMA to perpendicular magnetic anisotropy (PMA). The oxygen migration effect is achieved by the redox reaction at the Co/MgO interface. On the contrary, the transfer from IMA to PMA cannot be observed in Pt/Co/Pt films due to the lack of interfacial oxygen migration.
FORMULATION AND CHARACTERIZATION OF ALOE VERA COSMETIC HERBAL HYDROGEL

Present study deals with the development and characterization of aloe vera cosmetic herbal hydrogel preparation using inner part of aloe vera leaf, acacia, hydroxy propyl methyl cellulose (HPMC), carbopol 934, glycerine, tartaric acid, potassium sorbate and sodium benzoate. Aloe vera liquid was prepared by heating at low temperature and the hydrogel was prepared by simple dissolving method of other ingredients in a specific manner. Four formulations were developed which differ in the ratio of hydrogel forming polymers. Formulation A1, A2, A3 and A4 were composed of acacia, HPMC, carbopol 934 in the ratio of 1:1:1, 1:2:1, 2:1:1 and 1:1:2 respectively. All the formulations were evaluated for percentage moisture content, transparency, smoothness, weight on drying, viscosity, pH and microbial growth. On the basis of evaluation parameter formulation A4 was selected as developed formulation. On the basis of evaluation study, it can be concluded that aloe vera cosmetic herbal hydrogel may be used for cosmetic purpose.
Blockchain sentiment on sector analysis: LSTM approach

In this thesis, an LSTM architecture is presented to perform sentence-level sentiment analysis for blockchain news articles. An in-depth look into the model specification and the choice of different model parameters is given. Around 25000 articles from April 2013 to April 2019 were gathered from the business section of Coindesk (2019) using a dynamic Web-scraper. Various methods like SMOTE oversampling are introduced to account for an imbalanced training dataset. The model performance is compared to an SVM model, and it could be shown that LSTM is better suited for sentiment analysis as it is superior in modelling long term semantic dependencies in text data. Furthermore, a static contemporaneous Regression is employed to explain the relationship between blockchain sentiment and returns in different US Sectors. After identifying the most promising US sectors with stronger ties to the blockchain news sentiment, the regression model could not establish a significant influence of blockchain sentiment on US sector returns. However, the hypothesis that blockchain sentiment today increases the conditional volatility in returns tomorrow could be established for specific sectors by implementing a GARCH model.
The Relationship between Public Service Efficiency of Government and Residential Political Trust in Hong Kong

Hong Kong has a long history with its high efficiency and clean and self-disciplined government. Within the past over 20 years, different social development trend has occurred in Hong Kong. The article observed the relationship between political trust from residence and public service efficiency of government in Hong Kong from 1992 to 2015 and found that the value of public service efficiency has a significant effect on political trust in Hong Kong government, the higher the efficiency of public services, the higher the political trust. The author tried to find the path for the Hong Kong government to improve its public service quality and efficiency after testifying the positive correlation between public service efficiency and residential political trust with empirical analysis.
University of Southern Denmark Right Ventricular and Pulmonary Vascular Function are Influenced by Age and Volume Expansion in Healthy Humans Wolsk,

Citation for pulished version (APA): Wolsk, E. , Bakkestrøm, R. , Kristensen, C. B. , Aagaard Myhr, K. , Thomsen, J. H. , Balling, L. , Andersen, M. J., Dahl, J. S. , Shah, S. J., Gustafsson, F. , Hassager, C. , & Møller, J. E. (2019). Right Ventricular and Pulmonary Vascular Function are Influenced by Age and Volume Expansion in Healthy Humans. Journal of Cardiac Failure, 25(1), 51-59. https://doi.org/10.1016/j.cardfail. 2018.11. 013
Chemical composition and antimicrobial and antioxidant activities of Tunisian, France and Austrian Laurus nobilis (Lauraceae) essential oils

Essential oil (EO) of Laurus nobilis, from Tunisian, France and Austrian were screened for their chemical composition, antioxidant and antimicrobial activities and compared. GC-MS analysis showed that leaves of Tunisian L. nobilis had camphor (34.43%), 1,8-cineole (20.21%) and α-terpineol (7%) as major components. France and Austrian EOs had a high content of 1,8-cineole (45.8% and 43.4%, respectively) followed by bornyl acetate (13.8% and 17.7% respectively) and methyl eugenol (7.7% and 10.9% respectively). Antioxidant potential was measured by ABTS and DPPH tests. Tunisian L. nobilis EO showed greater radical scavenging by ABTS activity (IC50=44.8±0.1 mg/L) than the France and Austrian EOs (76.4±3.2 mg/L and 81.4±4.0 mg/L, respectively). However, for DPPH test system, French and Austrian EOs activities were excellent (IC50=176.1±5.1 mg/L and 236.3±2.9 mg/L respectively) then Tunisian L. nobilis EO (IC50=2859.7±99.0 mg/L). A good Antimicrobial activity was observed on the yeasts and fungi for all EOs. Tunisian laurel EO show a better antibacterial activity against gram-negative bacteria (Klebsiella pneumonial, E. coli and Salmonella enterica CMI: 0.004 mg/ml) than gram-positive ones (Bacilus subtilis, Staphylococcus aureus and Listeria monocytogenes CMI: 0.01 mg/ml). A significant antifungal activity of Tunisian EO was also observed against fungi and yeasts species (CMI: 0.004 mg/ml). France essential oil shows better activities against all organisms tested wail Austrian oil activity is more important against yeasts species tested and Mucor ramannianus (fungi). Chemical composition, antimicrobial and antioxidant activity of Tunisian L. nobilis essential oil, were different from that of France and Austrian and it give the opportunity for its uses in new pharmaceuticals and natural therapies of infectious diseases.
A Feasibility Trial of HoloLens 2™; Using Mixed Reality Headsets to Deliver Remote Bedside Teaching During COVID-19

Background COVID-19 has had a catastrophic impact measured in human lives. Medical education has also been impacted: appropriately stringent infection control policies have precluded medical trainees from attending clinical teaching. Lecture-based education has been easily transferred to a digital platform, but bedside teaching has not transitioned so well. The aim of this study was to assess the feasibility of using a mixed reality (MR) headset to deliver remote bedside teaching to trainee doctors during the COVID-19 pandemic.Methods Two MR sessions were led by senior specialty registrars (the clinical trainers) wearing the HoloLens™ headset. The trainers selected patients admitted with pathology requiring their specialist input; thus, the educational sessions were opportunistic. The headset allowed bi-directional video and audio communication between the trainer and trainee doctors during the consultation. Trainee doctor conceptions of bedside teaching, impact of COVID-19 on bedside teaching and technical success of the session was evaluated using pre- and post-round questionnaires using 1 (‘strongly disagree’ or ‘never’) to 7 (‘strongly agree’ or ‘always’) Likert scales and white space questions. Feedback on acceptability of the round was collected verbally from patients after each encounter. Data related to clinician exposure to at risk patients and use of PPE were also collected.Results Pre-questionnaire respondents (n=24) strongly agreed that bedside teaching is key to educating clinicians (7, IQR 6-7). It was also apparent that bedside teaching had become a rarity during COVID-19 (2, IQR 2-4). Session 1 feedback (n=6) was adversely affected by a loose microphone connection. With the issue rectified for session 2 (n=4), most respondents strongly agreed that they felt like they were physically present for the session (7, IQR 6.75-7). Mixed-reality versus in-person teaching led to a 79.5% reduction in cumulative clinician exposure time and 83.3% reduction in PPE use. Conclusions This study is proof of principle that HoloLens™ can be used effectively to deliver high-quality clinical bedside teaching. This novel format confers significant advantages in terms of: minimising exposure of trainees to COVID-19; saving PPE; enabling larger attendance; and convenient accessible real-time clinical training.