Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of EDS1-independent plant defense responses against bacterial pathogens using Duckweed/Pseudomonas pathosystems

ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) mediates the induction of defense responses against pathogens in most land plants. However, it has recently been shown that a few species have lost EDS1. It is unknown how defense against disease unfolds and evolves in the absence of EDS1. Here we utilize duckweeds; a collection of aquatic species that lack EDS1, to investigate this question. We successfully established duckweed-Pseudomonas pathosystems and were able to characterize pathogen-induced responses in an immune system that lacks the EDS1 signaling pathway. We show that the copy number of infection-associated genes and the infection-induced transcriptional responses of duckweeds differ from that of other model species. Moreover, we show that the conservation of canonical Microbe Triggered Immunity and Effector Triggered Immunity pathways varies between duckweed species. This work shows that pathogen defense has evolved along different trajectories and uncovers alternative genomic and transcriptional reprogramming. Specifically, the miAMP1 domain containing proteins, which are absent in Arabidopsis, show pathogen responsive upregulation in duckweeds. Despite such divergence between Arabidopsis and duckweed species, we find evidence for the conservation of upregulation of certain genes and the role of hormones in response to disease. Our work highlights the importance of expanding the pool of model species to study defense responses that have evolved in the plant kingdom, including those independent of EDS1.
Excitatory and inhibitory effects of HCN channel modulation on excitability of layer V pyramidal cells

Dendrites of cortical pyramidal cells are densely populated by hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, a.k. a. Ih channels. Ih channels are targeted by multiple neuromodulatory pathways, and thus are one of the key ion-channel populations regulating the pyramidal cell activity. Previous observations and theories attribute opposing effects of the Ih channels on neuronal excitability due to their mildly hyperpolarized reversal potential. These effects are difficult to measure experimentally due to the fine spatiotemporal landscape of the Ih activity in the dendrites, but computational models provide an efficient tool for studying this question in a reduced but generalizable setting. In this work, we build upon existing biophysically detailed models of thick-tufted layer V pyramidal cells and model the effects of over- and under-expression of Ih channels as well as their neuromodulation by dopamine (gain of Ih function) and acetylcholine (loss of Ih function). We show that Ih channels facilitate the action potentials of layer V pyramidal cells in response to proximal dendritic stimulus while they hinder the action potentials in response to distal dendritic stimulus at the apical dendrite. We also show that the inhibitory action of the Ih channels in layer V pyramidal cells is due to the interactions between Ih channels and a hot zone of low voltage-activated Ca2+ channels at the apical dendrite. Our simulations suggest that a combination of Ih-enhancing neuromodulation at the proximal apical dendrite and Ih-inhibiting modulation at the distal apical dendrite can increase the layer V pyramidal excitability more than any of the two neuromodulators alone. Our analyses uncover the effects of Ih-channel neuromodulation of layer V pyramidal cells at a single-cell level and shed light on how these neurons integrate information and enable higher-order functions of the brain.
Computational design and construction of an Escherichia coli strain engineered to produce a non-standard amino acid

Introducing heterologous pathways into host cells constitutes a promising strategy for synthesizing nonstandard amino acids (nsAAs) to enable the production of proteins with expanded chemistries. However, this strategy has proven challenging as the expression of heterologous pathways can disrupt cellular homeostasis of the host cell. Here, we sought to optimize the heterologous production of the nsAA para-aminophenylalanine (pAF) in Escherichia coli. First, we incorporated a heterologous pAF biosynthesis pathway into a genome-scale model of E. coli metabolism, and computationally identified metabolic interventions in the host’s native metabolism to improve pAF production. Next, we explored different ways of imposing these flux interventions experimentally and found that the upregulation of flux in chorismate biosynthesis pathway through the elimination of feedback inhibition mechanisms could significantly raise pAF titers (∼20 fold) while maintaining a reasonable pAF yield-growth rate trade-off. Overall, this study provides a promising strategy for the biosynthesis of nsAAs in engineered cells.
Surface microbiota of Mediterranean loggerhead sea turtles unravelled by 16S and 18S amplicon sequencing

Loggerhead sea turtle is considered a keystone species with major ecological role in Mediterranean marine environment. As with other wild reptiles, their outer microbiome is rarely studied. Although there are several studies on sea turtle’s macro-epibionts and endo-microbiota, there has been little research on epibiotic microbiota associated with sea turtles’ skin and carapace. Therefore, we provide the first identification of combined epibiotic eukaryotic and prokaryotic microbiota on Mediterranean loggerhead sea turtles. In this study, we sampled skin and carapace of 26 loggerheads from the Mediterranean Sea during 2018 and 2019. To investigate the overall microbial diversity and composition, amplicon sequencing of 16S and 18S rRNA genes was performed. We found that the Mediterranean loggerhead sea turtle epibiotic microbiota is a reservoir of a vast variety of microbial species. Microbial communities between samples mostly varied by different locations and seas, while within prokaryotic communities’ significant difference was observed between sampled body sites (carapace vs. skin). In terms of relative abundance, Proteobacteria and Bacteroidota were the most represented phyla within prokaryotes, while Alveolata and Stramenopiles thrived among eukaryotes. This study, besides providing a first survey of microbial eukaryotes on loggerheads via metabarcoding, identifies fine differences within both prokaryotic and eukaryotic microbial communities that seem to reflect the host anatomy and habitat. Multi-domain epi-microbiome surveys provide additional layers of information that are complementary with previous morphological studies and enable better understanding of the biology and ecology of these vulnerable marine reptiles.
Uma Abordagem para Verificação de Similaridade entre Sistemas Orientados a Objetos

This paper presents a quantitative approach for identifying similarity among object-oriented systems. This approach shows three contributions: (a) a mechanism that provides reference values for a specific metric, considering different class profiles; (b) a mechanism to obtain a subset of similar systems from a portfolio of systems according to a specific software metric and using well-known clustering techniques; and (c) a mechanism to obtain subsets of similar systems according to a set of software metrics and using standard graph theory concepts. We also describe a supporting tool and the application of our approach in a corpus of 86 open-source systems, comprising around 12 million lines of code. As a result, we have been able to found a group of 15 systems with strong indications of similarity. Our claim is that such systems very probably present similar levels of internal quality.
Identification of Differentially Expressed Genes Reveal Conserved Mechanisms in the Rice-Magnaporthe oryzae Interaction

Magnaporthe oryzae causes rice blast disease and is responsible for major losses in rice production worldwide. Although numerous studies have focused on the interactions between Oryza sativa and M. oryzae, to date, the conserved mechanisms remain in part unclear. In this study, a comparative analysis of transcriptomes of O. sativa L. ssp. japonica cv. ‘Nipponbare’ interacting with three M. oryzae strains (248, 235, and 163) were performed to explore the conserved molecular mechanisms. Differentially expressed genes with similar expression patterns in the interactions between cultivar ‘Nipponbare’ and three M. oryzae strains were defined as Conserved Differentially Expressed Genes (CDEGs). These included 3,647 O. sativa CDEGs and 3,655 M. oryzae CDEGs. Four rice CDEGs (LOC_Os03g19270, LOC_Os07g36600, LOC_Os05g28740, and LOC_Os01g32780) encoding universal stress protein (USP) were induced within 24 h post-inoculation (hpi) by three M. oryzae strains. Meanwhile, overexpression of LOC_Os07g36600 resulted in enhanced rice resistance against M. oryzae. Furthermore, four rice genes coding light-harvesting chlorophyll a/b-binding (LHC) protein (LOC_Os02g52650, LOC_Os09g12540, LOC_Os11g13850, LOC_Os05g22730) were also identified as CDEGs and were induced at 48 hpi, which might contribute to blast resistance through reactive oxygen species (ROS) accumulation. MoCDIP4 is M. oryzae effector inducing rice cell death and were verified that include AA9 CAZy domain (namely GH61 domain). In this study, we found seven MoCDIP4-homologous genes coding proteins with signal peptides and AA9 CAZy domains, which were continuously up-regulated across all infection stages relative to uninoculated control. This study uncovered that genes are required for conserved mechanisms of rice-M. oryzae interaction, which includes rice genes encoding USP proteins and LHC proteins, as well as M. oryzae genes encoding AA9 proteins. This study will help us to understand how O. sativa responds to M. oryzae infections and the molecular mechanisms of M. oryzae pathogenicity.
Perceptions of Telemental Health Care Delivery During COVID-19: A Cross-Sectional Study With Providers, February-March 2021

The COVID-19 pandemic accelerated adoption of telemental health (TMH). Providers with limited TMH experience faced challenges during the rapid switch to remote patient care. We investigated TMH providers’ perceptions about remote care one year into the pandemic according to when providers adopted telemedicine (i.e., before vs. after March 2020) and how much of their caseloads were served remotely (i.e., < 50% vs. ≥ 50%). Between February–March 2021, 472 TMH providers completed a cross-sectional, web-based survey that measured perceived benefits and satisfaction with telemedicine, therapeutic alliance, patient-centered communication, eHealth literacy, multicultural counseling self-efficacy, and facilitating factors of using telemedicine. Providers who began using telemedicine before the pandemic reported having better training, task-related therapeutic alliance with patients, and ability to conduct multicultural interventions, assessments, and session management. Providers who served ≥ 50% of their caseload remotely reported greater satisfaction with their practice, stronger beliefs about the benefits of telemedicine, and greater perceived effects of telemedicine on alleviating the impact of COVID-19. There were no differences in reports of patient-centered communication nor eHealth literacy. In conclusion, providers who adopted TMH more recently may require additional training and support to successfully establish a working alliance with their patients, especially with multicultural aspects of care.
BurnoutEnsemble: Augmented Intelligence to Detect Indications for Burnout in Clinical Psychology

Burnout, a state of emotional, physical, and mental exhaustion caused by excessive and prolonged stress, is a growing concern. It is known to occur when an individual feels overwhelmed, emotionally exhausted, and unable to meet the constant demands imposed upon them. Detecting burnout is not an easy task, in large part because symptoms can overlap with those of other illnesses or syndromes. The use of natural language processing (NLP) methods has the potential to mitigate the limitations of typical burnout detection via inventories. In this article, the performance of NLP methods on anonymized free text data samples collected from the online forum/social media platform Reddit was analyzed. A dataset consisting of 13,568 samples describing first-hand experiences, of which 352 are related to burnout and 979 to depression, was compiled. This work demonstrates the effectiveness of NLP and machine learning methods in detecting indicators for burnout. Finally, it improves upon standard baseline classifiers by building and training an ensemble classifier using two methods (subreddit and random batching). The best ensemble models attain a balanced accuracy of 0.93, test F1 score of 0.43, and test recall of 0.93. Both the subreddit and random batching ensembles outperform the single classifier baselines in the experimental setup.
Sharing or Not: Psychological Motivations of Brand Rumors Spread and the Stop Solutions

Brand rumors can harm brands’ image and bring significant impacts on customers’ decision-making and sharing behavior. Finding practical strategies for preventing the spread of brand rumors continues to be a challenge. Building on the social contagion theory, the current research enriches the discussion on understanding why people spread rumors and how to deal with the spreading of rumors. Sharing brand rumors is motivated by a variety of complex psychological reasons, but prior research didn’t adequately analyze the problem from a complexity perspective. Therefore, using a sample of 416 interviewers within eight types of brand rumors, this study employs fuzzy-set qualitative comparative analysis (fsQCA) to investigate the combination of rumor psychological communication motivations in brand activities and solutions to prevent the spread of brand rumors. The current study discoveries three and two first-level configurational solutions, respectively, that can promote positive and negative rumor spreading. To summarize, emotional stimulation is a key component in the spread of rumors; altruism and relationship management motivation can coexist at times; and untrusted rumors are disseminated through other motivation factors. Solutions to prevent rumors from spreading are also provided. Furthermore, the findings help to understand the psychology of configurational motivation and how it can help brands reduce the spread of brand rumors. Finally, these discoveries’ theoretical contributions and practical implications are presented.
Effects of Exercise Frequency and Intensity on Reducing Depressive Symptoms in Older Adults With Insomnia: A Pilot Randomized Controlled Trial

Background The effects of exercise frequency and intensity on alleviating depressive symptoms in older adults with insomnia are unclear. Purpose The purpose of this study was to investigate the influence of different exercise frequencies and intensities on prescribed aerobic-type physical activity (i.e., 75 min of vigorous-intensity exercise or 150 min of moderate-intensity exercise weekly) for reducing depressive symptoms in older adults living with insomnia, as recommended by the WHO. Design This study is a randomized, controlled, assessor-blinded trial. Setting This study is conducted at a single research site in Hong Kong. Participants This study includes older adults aged 50 years or above with depressive symptoms and insomnia. Intervention Participants were randomly assigned in a 1:1:1:1:1 ratio to the following groups: attention control (CON), moderate walking once weekly (MOD × 1/week), moderate walking thrice weekly (MOD × 3/week), vigorous walking once weekly (VIG × 1/week), and vigorous walking thrice weekly (VIG × 3/week). The total weekly exercise volumes among the walking groups were matched to the minimum recommended physical activity volume. Measurements Depression, anxiety, self-perceived sleep quality, insomnia severity, actigraphy-assessed 7-day sleep data, 7-day sleep diary, cardiorespiratory fitness, adherence, and habitual physical activity were examined at baseline and after 12 weeks of intervention. Results Both MOD × 3/week and VIG × 3/week groups demonstrated reduced depression (Hospital Anxiety and Depression Scale [HADS] – Depression: MOD × 3/wk: −68.6%; VIG × 3/week: −67.4%) and anxiety levels (HADS – Anxiety: MOD × 3/week: −54.3%; VIG × 3/week: −59.8%) compared with CON (both p < 0.01). Self-perceived sleep quality was improved in MOD × 3/week (−31.4% of the Pittsburgh Sleep Quality Index [PSQI]), VIG × 1/week (−34.1% of PSQI), and VIG × 3/week (−38.3% of PSQI), but not in MOD × 1/week, when compared with CON (p < 0.05). No serious adverse events were observed in this study. Conclusion The effects of walking training on reducing depressive symptoms appeared to be dependent on exercise frequency. Our findings suggest that three sessions of walking per week at either moderate or vigorous-intensity effectively alleviate depressive symptoms in older adults with insomnia. Additional research is needed to further verify the effects of exercise frequency on depression. Clinical Trial Registration [ClinicalTrials.gov], identifier [NCT04354922].
In silico Effects of Synaptic Connections in the Visual Thalamocortical Pathway

We have studied brain connectivity using a biologically inspired in silico model of the visual pathway consisting of the lateral geniculate nucleus (LGN) of the thalamus, and layers 4 and 6 of the primary visual cortex. The connectivity parameters in the model are informed by the existing anatomical parameters from mammals and rodents. In the base state, the LGN and layer 6 populations in the model oscillate with dominant alpha frequency, while the layer 4 oscillates in the theta band. By changing intra-cortical hyperparameters, specifically inhibition from layer 6 to layer 4, we demonstrate a transition to alpha mode for all the populations. Furthermore, by increasing the feedforward connectivities in the thalamo-cortico-thalamic loop, we could transition into the beta band for all the populations. On looking closely, we observed that the origin of this beta band is in the layer 6 (infragranular layers); lesioning the thalamic feedback from layer 6 removed the beta from the LGN and the layer 4. This agrees with existing physiological studies where it is shown that beta rhythm is generated in the infragranular layers. Lastly, we present a case study to demonstrate a neurological condition in the model. By changing connectivities in the network, we could simulate the condition of significant (P < 0.001) decrease in beta band power and a simultaneous increase in the theta band power, similar to that observed in Schizophrenia patients. Overall, we have shown that the connectivity changes in a simple visual thalamocortical in silico model can simulate state changes in the brain corresponding to both health and disease conditions.
CRISPR/Cas9-Mediated Disruption of Xylanase inhibitor protein (XIP) Gene Improved the Dough Quality of Common Wheat

The wheat dough quality is of great significance for the end-use of flour. Some genes have been cloned for controlling the protein fractions, grain protein content, starch synthase, grain hardness, etc. Using a unigene map of the recombinant inbred lines (RILs) for “TN 18 × LM 6,” we mapped a quantitative trait locus (QTL) for dough stability time (ST) and SDS-sedimentation values (SV) on chromosome 6A (QSt/Sv-6A-2851). The peak position of the QTL covered two candidate unigenes, and we speculated that TraesCS6A02G077000 (a xylanase inhibitor protein) was the primary candidate gene (named the TaXip gene). The target loci containing the three homologous genes TaXip-6A, TaXip-6B, and TaXip-6D were edited in the variety “Fielder” by clustered regularly interspaced short palindromic repeats–associated protein 9 (CRISPR/Cas9). Two mutant types in the T2:3 generation were obtained (aaBBDD and AAbbdd) with about 120 plants per type. The SVs of aaBBDD, AAbbdd, and WT were 31.77, 27.30, and 20.08 ml, respectively. The SVs of the aaBBDD and AAbbdd were all significantly higher than those of the wild type (WT), and the aaBBDD was significantly higher than the AAbbdd. The STs of aaBBDD, AAbbdd, and WT were 2.60, 2.24, and 2.25 min, respectively. The ST for the aaBBDD was significantly higher than that for WT and was not significantly different between WT and AAbbdd. The above results indicated that XIP in vivo can significantly affect wheat dough quality. The selection of TaXip gene should be a new strategy for developing high-quality varieties in wheat breeding programs.
LncRNA TUG1 Promotes Apoptosis, Invasion, and Angiogenesis of Retinal Endothelial Cells in Retinopathy of Prematurity via MiR-145-5p

Purpose Retinopathy of prematurity (ROP) is a common retinal vascular disease in premature neonates. In recent years, there is increasing evidence that the long non-coding RNA taurine upregulated gene 1 (TUG1) plays a regulatory role in vascular diseases, suggesting a potential role for TUG1 in vascular endothelial cells. We hypothesized that TUG1 may be associated with ROP. Our aim, therefore, was to explore the biological functions of TUG1 in aberrant retinal development. Methods We used the mouse oxygen-induced retinopathy (OIR) model to simulate the pathological changes of retinal in ROP. Quantitative real-time polymerase chain reaction was used to detect the expression of TUG1, miR-145-5p and cellular communication network factor 1 (CCN1). Human retinal endothelial cells (HRECs) were treated with CoCl2 to mimic hypoxia conditions. Cellular functional changes were observed after transfection with RNA interference (RNAi)-TUG1 and miR-145-5p mimics. The apoptosis of HRECs was detected by flow cytometry, the migration ability was detected by wound healing and transwell migration assays, and the ability of angiogenesis was detected by tube formation assay. The potential binding sites between TUG1, miR-145-5p, and CCN1 were verified by dual-luciferase reporter assays. The degree of retinopathy was evaluated by staining retinal sections with hematoxylin and eosin, and the expression of CCN1, HIF-1α, VEGF, caspase-3, Bcl-2, IL-1β, and TNF-α protein was analyzed by Western blotting and immunohistochemistry. Results In the retina tissue of OIR mice, TUG1, miR-145-5p, and CCN1 were differentially expressed. Knocking down TUG1 attenuated apoptosis, migration, and angiogenesis induced by hypoxia on HRECs, as did miR-145-5p overexpression. Results from reporter assays indicate direct interactions between TUG1, miR-145-5p, and CCN1. Intravitreal injection of miR-145-5p mimics reduced the degree of retinopathy. Conclusion TUG1 acts as a molecular sponge of miR-145-5p to regulate CCN1 expression and thus regulate the development of retinal neovascularization. This regulatory mechanism may provide a new theoretical basis for the prevention and treatment of ROP.