Miracle-dz/UniFAR-FTUs huggingface dataset:
A strategy for mapping biophysical to abstract neuronal network models applied to primary visual cortex

A fundamental challenge for the theoretical study of neuronal networks is to make the link between complex biophysical models based directly on experimental data, to progressively simpler mathematical models that allow the derivation of general operating principles. We present a strategy that successively maps a relatively detailed biophysical population model, comprising conductance-based Hodgkin-Huxley type neuron models with connectivity rules derived from anatomical data, to various representations with fewer parameters, finishing with a firing rate network model that permits analysis. We apply this methodology to primary visual cortex of higher mammals, focusing on the functional property of stimulus orientation selectivity of receptive fields of individual neurons. The mapping produces compact expressions for the parameters of the abstract model that clearly identify the impact of specific electrophysiological and anatomical parameters on the analytical results, in particular as manifested by specific functional signatures of visual cortex, including input-output sharpening, conductance invariance, virtual rotation and the tilt after effect. Importantly, qualitative differences between model behaviours point out consequences of various simplifications. The strategy may be applied to other neuronal systems with appropriate modifications. Author summary A hierarchy of theoretical approaches to study a neuronal network depends on a tradeoff between biological fidelity and mathematical tractibility. Biophysically-detailed models consider cellular mechanisms and anatomically defined synaptic circuits, but are often too complex to reveal insights into fundamental principles. In contrast, increasingly abstract reduced models facilitate analytical insights. To better ground the latter to the underlying biology, we describe a systematic procedure to move across the model hierarchy that allows understanding how changes in biological parameters - physiological, pathophysiological, or because of new data - impact the behaviour of the network. We apply this approach to mammalian primary visual cortex, and examine how the different models in the hierarchy reproduce functional signatures of this area, in particular the tuning of neurons to the orientation of a visual stimulus. Our work provides a navigation of the complex parameter space of neural network models faithful to biology, as well as highlighting how simplifications made for mathematical convenience can fundamentally change their behaviour.
Judgments of agency are affected by sensory noise without recruiting metacognitive processing

Judgments of agency, our sense of control over our actions and the environment, often occur in noisy conditions. We examined the computations underlying judgments of agency, in particular under the influence of sensory noise. Building on previous literature, we studied whether judgments of agency incorporate uncertainty in the same way that confidence judgments do, which would imply that the former share computational mechanisms with metacognitive judgments. In two tasks, participants rated agency, or confidence in a decision about their agency, over a virtual hand that tracked their movements, either synchronously or with a delay and either under high or low noise. We compared the predictions of two computational models to participants’ ratings and found that agency ratings, unlike confidence, were best explained by a model involving no estimates of sensory noise. We propose that agency judgments reflect first-order measures of the internal signal, without involving metacognitive computations, challenging the assumed link between the two cognitive processes.
Identification and correction of phase switches with Hi-C data in the Nanopore and HiFi chromosome-scale assemblies of the dikaryotic leaf rust fungus Puccinia triticina

Background Most animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust fungi are such species with two nuclei (karyons) that contain a full set of haploid chromosomes each. The physical separation of haplotypes in dikaryons means that, unlike in diploids, Hi-C chromatin contacts between haplotypes are false positive signals. Results We generate the first chromosome-scale, fully-phased assembly for the dikaryotic leaf rust fungus Puccinia triticina and compare Nanopore MinION and PacBio HiFi sequence-based assemblies. We show that false positive Hi-C contacts between haplotypes are predominantly caused by phase switches rather than by collapsed regions or Hi-C read mis-mappings. We introduce a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs, including a phase switch correction step. In the HiFi assembly, relatively few phase switches occur, and these are predominantly located at haplotig boundaries and can be readily corrected. In contrast, phase switches are widespread throughout the Nanopore assembly. We show that haploid genome read coverage of 30-40 times using HiFi sequencing is required for phasing of the leaf rust genome (~0.7% heterozygosity) and that HiFi sequencing resolves genomic regions with low heterozygosity that are otherwise collapsed in the Nanopore assembly. Conclusions This first Hi-C based phasing pipeline for dikaryons and comparison of long-read sequencing technologies will inform future genome assembly and haplotype phasing projects in other non-haploid organisms.
Refined Quantification of Infection Bottlenecks and Pathogen Dissemination with STAMPR

Barcoded bacteria are often employed to monitor pathogen population dynamics during infection. The accuracy of these measurements is diminished by unequal bacterial expansion rates. ABSTRACT Pathogen population dynamics during infection are critical determinants of infection susceptibility and define patterns of dissemination. However, deciphering these dynamics, particularly founding population sizes in host organs and patterns of dissemination between organs, is difficult because measuring bacterial burden alone is insufficient to observe these patterns. Introduction of allelic diversity into otherwise identical bacteria using DNA barcodes enables sequencing-based measurements of these parameters, in a method known as STAMP (Sequence Tag-based Analysis of Microbial Populations). However, bacteria often undergo unequal expansion within host organs, resulting in marked differences in the frequencies of barcodes in input and output libraries. Here, we show that these differences confound STAMP-based analyses of founding population sizes and dissemination patterns. We present STAMPR, a successor to STAMP, which accounts for such population expansions. Using data from systemic infection of barcoded extraintestinal pathogenic E. coli, we show that this new framework, along with the metrics it yields, enhances the fidelity of measurements of bottlenecks and dissemination patterns. STAMPR was also validated on an independent barcoded Pseudomonas aeruginosa data set, uncovering new patterns of dissemination within the data. This framework (available at https://github.com/hullahalli/stampr_rtisan), when coupled with barcoded data sets, enables a more complete assessment of within-host bacterial population dynamics. IMPORTANCE Barcoded bacteria are often employed to monitor pathogen population dynamics during infection. The accuracy of these measurements is diminished by unequal bacterial expansion rates. Here, we develop computational tools to circumvent this limitation and establish additional metrics that collectively enhance the fidelity of measuring within-host pathogen founding population sizes and dissemination patterns. These new tools will benefit future studies of the dynamics of pathogens and symbionts within their respective hosts and may have additional barcode-based applications beyond host-microbe interactions.
AGENT: the Arabidopsis Gene Regulatory Network Tool for Exploring and Analyzing GRNs

Gene regulatory networks (GRNs) are complex networks that capture multi-level regulatory events between one or more regulatory macromolecules, such as transcription factors (TFs), and their target genes. Advancements in screening technologies such as enhanced yeast-one-hybrid screens have allowed for high throughput determination of GRNs. However, visualization of GRNs in Arabidopsis has been limited to ad hoc networks and are not interactive. Here, we describe the Arabidopsis GEne Network Tool (AGENT) that houses curated GRNs and provides tools to visualize and explore them. AGENT features include expression overlays, subnetwork motif scanning, and network analysis. We show how to use AGENT’s multiple built-in tools to identify key genes that are involved in flowering and seed development along with identifying temporal multi-TF control of a key transporter in nitrate signaling. AGENT can be accessed at https://bar.utoronto. ca/AGENT.
Synchrotron X-ray diffraction studies of proton transfer in hydrogen bonded molecular complexes

The technique of single crystal synchrotron X-ray diffraction is applied in the study of solid state proton transfer processes in hydrogen bonded molecular complexes. Proton transfer processes are of interest where they are responsible for a number of physical and chemical properties within solid state functional materials; their study gives insight into the occurrence of such properties and where they may be targeted and tuned in future materials. The synchrotron X-ray diffraction technique has been trialled with respect to the potential it offers for high throughput capability for studying proton transfer processes as a function of an external stimulus or across a number of molecular systems. Chapter 1 contains a review of the literature of the hydrogen bond, including its role in crystal engineering and proton transfer effects. In Chapter 2, the theory behind the analytical techniques used in the study of hydrogen bonded molecular complexes, in which crystallographic methods are fundamental, are described. In Chapter 3 the research project aims and objectives are presented; these objectives are targeted at the use of single crystal synchrotron X-ray diffraction in the study and rationalisation of solid state proton transfer processes. In Chapter 4, the experimental methods implemented in this research project to achieve these research goals are reported. Chapter 5 is the first of the result chapters and applies the synchrotron single crystal X-ray diffraction technique in the study of variable temperature proton disorder in centrosymmetric hydrogen bonded carboxylic acid dimers. Chapter 6 focuses on the design of proton transfer systems implementing a number of crystal engineering strategies in the design of short strong hydrogen bonds (SSHBs) for potential proton migration studies. Chapter 7 applies a combination of diffraction methods (synchrotron and laboratory X-ray diffraction) and refinement strategies in the study of temperature dependent proton migration across SSHBs, allowing the potential of these methods in the study of proton migration to be assessed. Chapter 8 is the final application of the synchrotron technique in studies of proton transfer behaviour investigating static proton transfer behaviour in molecular complexes of the proton sponge 1,8-bis(dimethylamino)naphthalene with organic acids. The urea-acid inclusion materials presented in Chapter 9 additionally allow the investigation of the hydrogen bond as a crystal engineering tool in the design of hydrogen bonded solvent-inclusion networks. In the last chapter, Chapter 10, conclusions from the findings in Chapters 5 to 9 are pulled together and patterns explored. Drawing on these overall findings, some suggestions for future work are also made.
Topological analysis of separation phenomena in liquid metal flow in sudden expansions. Part 2. Magnetohydrodynamic flow

A numerical study has been carried out to analyse liquid metal flows in a sudden expansion of electrically conducting rectangular ducts under the influence of an imposed uniform magnetic field. Separation phenomena are investigated by selecting a reference Reynolds number and by increasing progressively the applied magnetic field. The magnetic effects leading to the reduction of the size of separation zones that form behind the cross-section enlargement are studied by considering modifications of flow topology, streamline patterns and electric current density distribution. In the range of parameters investigated, the magnetohydrodynamic flow undergoes substantial transitions from a hydrodynamic-like flow to one dominated by electromagnetic forces, where the influence of inertia and viscous forces is confined to thin internal layers aligned with the magnetic field and to boundary layers that form along the walls. Scaling laws describing the reattachment length and the pressure drop in the sudden expansion are derived for intense magnetic fields.
A qnr-plasmid allows aminoglycosides to induce SOS in Escherichia coli

The plasmid-mediated quinolone resistance (PMQR) genes have been shown to promote high-level bacterial resistance to fluoroquinolone antibiotics, potentially leading to clinical treatment failures. In Escherichia coli, sub-inhibitory concentrations (sub-MIC) of the widely used fluoroquinolones are known to induce the SOS response. Interestingly, the expression of several PMQR qnr genes is controlled by the SOS master regulator. During the characterization of a small qnrD-plasmid carried in E. coli, we observed that the aminoglycosides become able to induce the SOS response in this species, thus leading to the transcription of qnrD. We found that induction of the SOS response is due to nitric oxide (NO) accumulation in presence of sub-MIC of aminoglycosides. We demonstrated that the NO accumulation is driven by two plasmid genes, ORF3 and ORF4, whose products act at two levels. ORF3 encode a FAD-binding oxidoreductase which helps NO synthesis, while ORF4 code for an FNR-type transcription factor, related to an O2-responsive regulator of hmp expression, able to repress the Hmp-mediated NO detoxification pathway of E. coli. Thus, this discovery, that other major classes of antibiotics may induce the SOS response could have worthwhile implications for antibiotic stewardship efforts in preventing the emergence of resistance.
Comparative Effectiveness of Pharmacological Interventions for Covid-19: A Systematic Review and Network Meta-Analysis

Background: Several pharmacological interventions are now under investigation for the treatment of Covid-19, and the evidence is evolving rapidly. Our aim is to assess the comparative efficacy and safety of these drugs. Methods and Findings: We performed a systematic review and network meta-analysis searching Medline, Pubmed, Embase, Cochrane Covid-19 register, international trial registers, medRxiv, bioRxiv, and arXiv up to December 10, 2020. We included all randomised controlled trials (RCTs) comparing any pharmacological intervention for Covid-19 against any drugs, placebo or standard care (SC). Data extracted from published reports were assessed for risk of bias in accordance with the Cochrane tool, and using the GRADE framework. Primary outcomes were all-cause mortality, adverse events (AEs) and serious adverse events (SAEs). We estimated summary risk ratio (RR) using pairwise and network meta-analysis with random effects (Prospero, number CRD42020176914). We performed a systematic review and network meta-analysis searching Medline, Pubmed, Embase, Cochrane Covid-19 register, international trial registers, medRxiv, bioRxiv, and arXiv up to December 10, 2020. We included all randomised controlled trials (RCTs) comparing any pharmacological intervention for Covid-19 against any drugs, placebo or standard care (SC). Data extracted from published reports were assessed for risk of bias in accordance with the Cochrane tool, and using the GRADE framework. Primary outcomes were all-cause mortality, adverse events (AEs) and serious adverse events (SAEs). We estimated summary risk ratio (RR) using pairwise and network meta-analysis with random effects (Prospero, number CRD42020176914). We included 96 RCTs, comprising of 34,501 patients. The network meta-analysis showed in terms of all-cause mortality, when compared to SC or placebo, only corticosteroids significantly reduced the mortality rate (RR 0.90, 95%CI 0.83, 0.97; moderate certainty of evidence). Corticosteroids significantly reduced the mortality rate also when compared to hydroxychloroquine (RR 0.83, 95%CI 0.74, 0.94; moderate certainty of evidence). Remdesivir proved to be better in terms of SAEs when compared to SC or placebo (RR 0.75, 95%CI 0.63, 0.89; high certainty of evidence) and plasma (RR 0.57, 95%CI 0.34, 0.94; high certainty of evidence). The combination of lopinavir and ritonavir proved to reduce SAEs when compared to plasma (RR 0.49, 95%CI 0.25, 0.95; high certainty of evidence). Most of the RCTs were at unclear risk of bias (42 of 96), one third were at high risk of bias (34 of 96) and 20 were at low risk of bias. Certainty of evidence ranged from high to very low. Conclusion: At present, corticosteroids reduced all-cause mortality in patients with Covid-19, with a moderate certainty of evidence. Remdesivir appeared to be a safer option than SC or placebo, while plasma was associated with safety concerns. These preliminary evidence-based observations should guide clinical practice until more data are made public.
Desulfovibrio Bacteria Are Associated With Parkinson’s Disease

Parkinson’s disease (PD) is the most prevalent movement disorder known and predominantly affects the elderly. It is a progressive neurodegenerative disease wherein α-synuclein, a neuronal protein, aggregates to form toxic structures in nerve cells. The cause of Parkinson’s disease (PD) remains unknown. Intestinal dysfunction and changes in the gut microbiota, common symptoms of PD, are evidently linked to the pathogenesis of PD. Although a multitude of studies have investigated microbial etiologies of PD, the microbial role in disease progression remains unclear. Here, we show that Gram-negative sulfate-reducing bacteria of the genus Desulfovibrio may play a potential role in the development of PD. Conventional and quantitative real-time PCR analysis of feces from twenty PD patients and twenty healthy controls revealed that all PD patients harbored Desulfovibrio bacteria in their gut microbiota and these bacteria were present at higher levels in PD patients than in healthy controls. Additionally, the concentration of Desulfovibrio species correlated with the severity of PD. Desulfovibrio bacteria produce hydrogen sulfide and lipopolysaccharide, and several strains synthesize magnetite, all of which likely induce the oligomerization and aggregation of α-synuclein protein. The substances originating from Desulfovibrio bacteria likely take part in pathogenesis of PD. These findings may open new avenues for the treatment of PD and the identification of people at risk for developing PD.
Hypoxia-Induced MALAT1 Promotes the Proliferation and Migration of Breast Cancer Cells by Sponging MiR-3064-5p

Hypoxia, a common process during tumor growth, can lead to tumor aggressiveness and is tightly associated with poor prognosis. Long noncoding RNAs (lncRNAs) are long ribonucleotides (>200 bases) with limited ability to translate proteins, and are known to affect many aspects of cellular function. One of their regulatory mechanisms is to function as a sponge for microRNA (miRNA) to modulate its biological functions. Previously, MALAT1 was identified as a hypoxia-induced lncRNA. However, the regulatory mechanism and functions of MALAT1 in breast cancer are still unclear. Therefore, we explored whether MALAT1 can regulate the functions of breast cancer cells through miRNAs. Our results showed the expression levels of MALAT1 were significantly up-regulated under hypoxia and regulated by HIF-1α and HIF-2α. Next, in contrast to previous reports, nuclear and cytoplasmic fractionation assays and fluorescence in situ hybridization indicated that MALAT1 was mainly located in the cytoplasm. Therefore, the labeling of MALAT1 as a nuclear marker should be done with the caveat. Furthermore, expression levels of miRNAs and RNA immunoprecipitation using antibody against AGO2 showed that MALAT1 functioned as a sponge of miRNA miR-3064-5p. Lastly, functional assays revealed that MALAT1 could promote cellular migration and proliferation of breast cancer cells. Our findings provide evidence that hypoxia-responsive long non-coding MALAT1 could be transcriptionally activated by HIF-1α and HIF-2α, act as a miRNA sponge of miR-3064-5p, and promote tumor growth and migration in breast cancer cells. These data suggest that MALAT1 may be a candidate for therapeutic targeting of breast cancer progression.
Comparison of Antioxidant and Antibacterial Activities of Camellia Oil From Hainan With Camellia Oil From Guangxi, Olive Oil, and Peanut Oil

Background/Aim: Camellia oil from Hainan (SY) is a unique vegetable oil in Hainan, China, due to the geographical environment and oil extraction only through simple physical treatments. To compare SY with camellia oil from Guangxi (SC), olive oil (GL), and peanut oil (HS), this study analyzed the antioxidant and antibacterial activity of four vegetable oils. Methods: Using Gallic acid, BHT as the control, Saccharomyces cerevisiae as the model organism, the antioxidant activities of vegetable oils were measured in vitro and in vivo, and the antibacterial activity was measured with the minimum inhibitory concentration (MIC) method. Results: The major contents of SY, SC, and HS were oleic Acid; the major content of GL was squalene. The highest total flavonoids content of SY was 39.50 ± 0.41 mg RE/g DW; and the highest total phenolic content of SC was 47.05 ± 0.72 mg GAE/g DW. SY exhibited the strongest scavenging activity of hydroxyl radical (HO·) and superoxide anions (O2-·), the IC50 value were 2.06 mg/mL, 0.62 mg/mL, respectively; and SC showed the strongest DPPH· and ABTS· scavenging activity and the reducing abilities. SY showed excellent effect on survival rate, protection rate, flavonoids uptake of S. cerevisiae cells, decreased MDA content and ROS level, inhibited CAT, POD, and GR enzyme activity. The absorption of SC total phenols was the highest by cells. The activity showed GL had a broad-spectrum antibacterial activity. Conclusion: Thus, SY shows potential antioxidant activity and provides an important reference value for people to choose edible vegetable oils.