Miracle-dz/UniFAR-FTUs huggingface dataset:
European Stroke Organisation guideline on endarterectomy and stenting for carotid artery stenosis

Atherosclerotic stenosis of the internal carotid artery is an important cause of stroke. The aim of this guideline is to analyse the evidence pertaining to medical, surgical and endovascular treatment of patients with carotid stenosis. These guidelines were developed based on the ESO standard operating procedure and followed the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) approach. The working group identified relevant questions, performed systematic reviews and meta-analyses of the literature, assessed the quality of the available evidence, and wrote recommendations. Based on moderate quality evidence, we recommend carotid endarterectomy (CEA) in patients with ≥60–99% asymptomatic carotid stenosis considered to be at increased risk of stroke on best medical treatment (BMT) alone. We also recommend CEA for patients with ≥70–99% symptomatic stenosis, and we suggest CEA for patients with 50–69% symptomatic stenosis. Based on high quality evidence, we recommend CEA should be performed early, ideally within two weeks of the last retinal or cerebral ischaemic event in patients with ≥50–99% symptomatic stenosis. Based on low quality evidence, carotid artery stenting (CAS) may be considered in patients < 70 years old with symptomatic ≥50–99% carotid stenosis. Several randomised trials supporting these recommendations were started decades ago, and BMT, CEA and CAS have evolved since. The results of another large trial comparing outcomes after CAS versus CEA in patients with asymptomatic stenosis are anticipated in the near future. Further trials are needed to reassess the benefits of carotid revascularisation in combination with modern BMT in subgroups of patients with carotid stenosis.
Serum GFAP for stroke diagnosis in regions with limited access to brain imaging (BE FAST India)

Introduction Despite a high burden of stroke, access to rapid brain imaging is limited in many middle- and low-income countries. Previous studies have described the astroglial protein GFAP (glial fibrillary acidic protein) as a biomarker of intracerebral hemorrhage. The aim of this study was to test the diagnostic accuracy of GFAP for ruling out intracranial hemorrhage in a prospective cohort of Indian stroke patients. Patients and methods This study was conducted in an Indian tertiary hospital (Christian Medical College, Ludhiana). Patients with symptoms suggestive of acute stroke admitted within 12 h of symptom onset were enrolled. Blood samples were collected at hospital admission. Single Molecule Array technology was used for determining serum GFAP concentrations. Results A total number of 155 patients were included (70 intracranial hemorrhage, 75 ischemic stroke, 10 stroke mimics). GFAP serum concentrations were elevated in intracranial hemorrhage patients compared to ischemic stroke patients [median (interquartile range) 2.36 µg/L (0.61–7.16) vs. 0.18 µg/L (0.11–0.38), p < 0.001]. Stroke mimics patients had a median GFAP serum level of 0.14 µg/L (0.09–0.26). GFAP values below the cut-off of 0.33 µg/L (area under the curve 0.871) ruled out intracranial hemorrhage with a negative predictive value of 89.7%, (at a sensitivity for detecting intracranial hemorrhage of 90.0%). Discussion The high negative predictive value of a GFAP test system allows ruling out patients with intracranial hemorrhage. Conclusion In settings where immediate brain imaging is not available, this would enable to implement secondary prevention (e.g., aspirin) in suspected ischemic stroke patients as soon as possible.
Cognition and Emotion in Extreme Political Action: Individual Differences and Dynamic Interactions

Who is most likely to join and engage in extreme political action? Although traditional theories have focused on situational factors or group identity, an emerging science illustrates that tendencies for extreme political action may also be rooted in individuals’ idiosyncratic cognitive and affective dispositions. This article synthesizes cutting-edge evidence demonstrating that individuals’ cognitive and affective architecture shapes their willingness to support ideological violence. In the cognitive domain, traits such as cognitive rigidity, slow perceptual strategies, and poor executive functions are linked to heightened endorsement for ideological violence. In the emotion domain, characteristics associated with emotional reactivity and impaired emotional regulation, such as sensation seeking and impulsivity, can facilitate readiness for extreme political action. The review homes in on the roles of cognitive rigidity and sensation seeking as traits heightening proclivities for extreme pro-group behavior and recommends that future research should assess cognition-emotion interactions to reveal different subprofiles of political actors. A theoretical framework focused on cognitive and affective information-processing traits—and their interactions—opens up tractable empirical questions and a future research agenda. Identifying subsets of ideologues is an endeavor with potential to inform the design of evidence-based interventions aimed at reducing ideological extremism and fostering social understanding.
SPEAR: a proteomics approach for simultaneous protein expression and redox analysis

Oxidation and reduction of protein cysteinyl thiols serve as molecular switches, which is considered the most central mechanism for redox regulation of biological processes, altering protein structure, biochemical activity, subcellular localization, and binding affinity. Redox proteomics allows for the global identification of redox-modified cysteine (Cys) sites and quantification of their oxidation/reduction responses, serving as a hypothesis-generating platform to stimulate redox biology mechanistic research. Here, we developed Simultaneous Protein Expression and Redox (SPEAR) analysis, a new redox-proteomics approach based on differential labeling of oxidized and reduced cysteines with light and heavy isotopic forms of commercially available isotopically-labeled N-ethylmaleimide (NEM). The presented method does not require enrichment for labeled peptides, thus enabling simultaneous quantification of Cys oxidation state and protein abundance. Using SPEAR, we were able to quantify the in-vivo oxidation state of thousands of cysteines across the Arabidopsis proteome under steady-state and oxidative stress conditions. Functional assignment of the identified redox-sensitive proteins demonstrated the widespread effect of oxidative conditions on various cellular functions and highlighted the enrichment of chloroplast-targeted proteins. SPEAR provides a simple, straightforward, and cost-effective means of studying redox proteome dynamics. The presented data provide a global quantitative view of cysteine oxidation of well-known redox-regulated active sites and many novel redox-sensitive sites whose role in plant acclimation to stress conditions remains to be further explored.
ACES: Analysis of Conservation with Expansive Species

Motivation An abundance of new reference genomes are becoming available through large-scale sequencing efforts. While the reference FASTA for each genome is available, there is currently no automated mechanism to query a specific sequence across all new reference genomes. Results We developed ACES (Analysis of Conservation with Expansive Species) as a computational workflow to query specific sequences of interest (e.g., enhancers, promoters, exons) against reference genomes with an available reference FASTA. This automated workflow generates BLAST hits against each of the reference genomes, a multiple sequence alignment file, a graphical fragment assembly file, and a phylogenetic tree file. These data files can then be used by the researcher in several ways to provide key insights into conservation of the query sequence. Availability ACES is available at https://github.com/TNTurnerLab/ACES Contact tychele@wustl.edu Supplementary information Supplementary Figure 1 is available on bioRxiv.
Bacterial factors drive the differential targeting of Guanylate Binding Proteins to Francisella and Shigella

Guanylate-Binding Proteins (GBPs) are interferon-inducible GTPases that play a key role in cell autonomous responses against intracellular pathogens. Seven GBPs are present in humans. Despite sharing high sequence similarity, subtle differences among GBPs translate into functional divergences that are still largely not understood. A key step for the antimicrobial activity of GBPs towards cytosolic bacteria is the formation of supramolecular GBP complexes on the bacterial surface. Such complexes are formed when GBP1 binds lipopolysaccharide (LPS) from Shigella and Salmonella and further recruits GBP2, 3, and 4. Here, we investigated GBPs recruitment on Francisella novicida, a professional cytosol-dwelling pathogen with an atypical tetra-acylated LPS. Co-infection experiments demonstrated that GBPs target preferentially S. flexneri compared to F. novicida. F. novicida was coated by GBP1 and GBP2 in human macrophages but escaped targeting by GBP3 and GBP4. GBP1 and GBP2 features that drive recruitment to F. novicida were investigated revealing that GBP1 GDPase activity is required to initiate GBP recruitment to F. novicida but facultative to target S. flexneri. Furthermore, analysis of chimeric GBP2/5 proteins identified a central domain in GBP2 necessary and sufficient to target F. novicida. Finally, a F. novicida ΔlpxF mutant with a penta-acylated lipid A was targeted by GBP3 suggesting that lipid A tetra-acylation contributes to escape from GBP3. Altogether our results indicate that GBPs have different affinity for different bacteria and that the repertoire of GBPs recruited onto cytosolic bacteria is dictated by GBP-intrinsic features and specific bacterial factors, including the structure of the lipid A. IMPORTANCE Few bacteria have adapted to thrive in the hostile environment of the cell cytosol. As a professional cytosol-dwelling pathogen, S. flexneri secretes several effectors to block cytosolic immune effectors, including GBPs. This study illustrates a different approach of adapting to the host cytosol: the stealth strategy developed by F. novicida. F. novicida bears an atypical hypoacylated LPS, which does not elicit neither TLR4 nor caspase-11 activation. Here, this atypical LPS was shown to promote escape from GBP3 targeting. Furthermore, the lower affinity of GBPs for F. novicida allowed to decipher the different domains that govern GBP recruitment to the bacterial surface. This study illustrates the importance of investigating different bacterial models to broaden our understanding of the intricacies of host-pathogen interactions.
State transitions in the statistically stable place cell population are determined by rate of perceptual change

The hippocampus plays a central role in mammalian navigation and memory, yet an implementational understanding of the rules that govern the granularity of location encoding and the spatial-statistics of the population as a whole are lacking. We analysed large numbers of CA1 place fields recorded while rats foraged in environments up to 8.75 m2. We found that place cell propensities to form fields were proportional to open-field area, gamma-distributed, and conserved across environments. The properties of place fields varied positionally with a denser distribution of smaller fields near boundaries. Remarkably, field size and density were in a dynamic equilibrium, such that population-level activity statistics remained constant. We showed that the rate of transition through the statistically stable place cell population matched the rate of change in the animals’ visual scenes - demonstrating that the resolution of the spatial-memory system is bounded by perceptual information afforded by the environment.
Spatial structure, phase, and the contrast of natural images

The sensitivity of the human visual system is thought to be shaped by environmental statistics. A major endeavour in vision science, therefore, is to uncover the image statistics that predict perceptual and cognitive function. When searching for targets in natural images, for example, it has recently been proposed that target detection is inversely related to the spatial similarity of the target to its local background. We tested this hypothesis by measuring observers’ sensitivity to targets that were blended with natural image backgrounds. Targets were designed to have a spatial structure that was either similar or dissimilar to the background. Contrary to masking from similarity, we found that observers were most sensitive to targets that were most similar to their backgrounds. We hypothesised that a coincidence of phase-alignment between target and background results in a local contrast signal that facilitates detection when target-background similarity is high. We confirmed this prediction in a second experiment. Indeed, we show that, by solely manipulating the phase of a target relative to its background, the target can be rendered easily visible or undetectable. Our study thus reveals that, in addition to its structural similarity, the phase of the target relative to the background must be considered when predicting detection sensitivity in natural images.
Dopamine enhanced auditory perceptual learning in humans via long-term memory consolidation

Dopamine is known to modulate sensory plasticity in animal brain, but how it impacts perceptual learning in humans remains largely unknown. In a placebo-controlled, double-blinded training experiment with young healthy adults (both male and female), oral administration of Madopar, a dopamine precursor, during each of multiple training sessions was shown to enhance auditory perceptual learning, particularly in late training sessions. Madopar also enhanced learning and transfer to working memory when tested outside the time widow of drug effect, which appeared to retain for at least 20 days. To test whether such learning modulation was mediated by the dopaminergic working memory network, the same dopamine manipulation was applied to working memory training, but to little influence on learning or transfer. Further, a neural network model of auditory perceptual learning revealed distinctive behavioural modulation patterns for proposed dopaminergic functions in the auditory cortex: trial-by-trial reinforcement signals (reward/reward prediction error and expected reward) and across-session memory consolidation. Only the memory consolidation simulations matched experimental observations. The results thus demonstrate that dopamine modulates human perceptual learning, mostly likely via enhancing memory consolidation over extended time scales.
Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules

We describe MIP-1 and MIP-2, novel paralogous C. elegans germ granule components that interact with the intrinsically disordered MEG-3 protein. These proteins promote P granule condensation, form granules independently of MEG-3 in the postembryonic germ line, and balance each other in regulating P granule growth and localization. MIP-1 and MIP-2 each contain two LOTUS domains and intrinsically disordered regions and form homo- and heterodimers. They bind and anchor the Vasa homolog GLH-1 within P granules and are jointly required for coalescence of MEG-3, GLH-1, and PGL proteins. Animals lacking MIP-1 and MIP-2 show temperature-sensitive embryonic lethality, sterility, and mortal germ lines. Germline phenotypes include defects in stem cell self-renewal, meiotic progression, and gamete differentiation. We propose that these proteins serve as scaffolds and organizing centers for ribonucleoprotein networks within P granules that help recruit and balance essential RNA processing machinery to regulate key developmental transitions in the germ line.
Analysis of conditional colocalization relationships and hierarchies in three-color microscopy images

Colocalization analysis of multicolor microscopy images is a cornerstone approach in cell biology. It provides information on the localization of molecules within various subcellular compartments and allows the interrogation of molecular interactions in their cellular context. However, almost all colocalization analyses are designed for two-color images. This limits their applicability and the type of information that they reveal, leading to underutilization of multicolor microscopy images. Here we describe an approach, termed “conditional colocalization analysis,” for analyzing the colocalization relationships between three molecular entities in three-color microscopy images. Going beyond the question of whether colocalization is present or not, it addresses the question of whether the colocalization between two entities is influenced, positively or negatively, by their colocalization with a third entity. We showcase two applications of conditional colocalization analysis, one addressing the question of compartmentalization of molecular interactions, and one investigating the hierarchy of molecular interactions in a multimolecular complex. The software for conditional colocalization analysis is available at https://github.com/kjaqaman/conditionalColoc.
Behavioral and nociceptor states of inflammatory pain across timescales in 2D and 3D

Inflammatory pain represents a complex state involving sensitization of peripheral and central neuronal signalling. Resolving this high-dimensional interplay at the cellular and behavioral level is key to effective therapeutic development. Here, using the carrageenan model of local inflammation of the hind paw, we determine how carrageenan alters both the physiological state of sensory neurons and behaviors at rapid and continuous timescales. We identify higher excitability of sensory neurons innervating the site of inflammation by profiling their physiological state at different time points. To identify millisecond-resolved sensory-reflexive signatures evoked by inflammatory pain, we used a combination of supervised and unsupervised algorithms, and uncovered abnormal paw placement as a defining behavioral feature. For long-term detection and characterization of spontaneous behavioral signatures representative of affective-motivational pain states, we use computer vision coupled to unsupervised machine learning in an open arena. Using the non-steroidal anti-inflammatory drug meloxicam to characterize analgesic states during rapid and ongoing timescales, we identify a return to pre-injury states of some sensory-reflexive behaviors, but by and large, many spontaneous, affective-motivational pain behaviors remain unaffected. Taken together, this comprehensive exploration across cellular and behavioral dimensions reveals peripheral versus centrally mediated pain signatures that define the inflamed state, providing a framework for scaling the pain experience at unprecedented resolution. Highlights Automated identification of millisecond-resolved behaviors that separate inflammation-induced mechanical allodynia versus hyperalgesia. Sensory neurons innervating the inflamed paw show heightened excitability and nociceptive channel activity. Automated identification of spontaneous inflammation-induced behaviors uncovered by computer vision/machine learning during exploratory behavior in an open arena. Reduction in evoked pain signatures by an anti-inflammatory drug does not equal return to pre-injury state.
Title: Scanning ethyl methanesulphonate effects on the whole genome of Lotus japonicus using second generation sequencing analysis Authors:

Genetic structure can be altered by chemical mutagenesis, which is a common method applied in molecular biology and genetics. Second generation sequencing provides a platform to reveal base alterations occurring in the whole genome due to mutagenesis. A model legume, Lotus japonicus ecotype Miyakojima, was chemically mutated with alkylating ethyl methanesulphonate for the scanning of DNA lesions throughout the genome. Using second generation sequencing, two individually mutated third generation progeny (M3, named AM and AS) were sequenced and analysed to identify single nucleotide polymorphisms and reveal ethyl methanesulphonate effects on nucleotide sequences in these mutant genomes. Single nucleotide polymorphisms were found in every 208 kb (AS) and 202 kb (AM) with a bias mutation of G/C-to-A/T changes at low percentage. Most mutations were intergenic. The mutation spectrum of the genomes was comparable in their individual chromosomes however; each mutated genome has unique alterations, which are useful to identify causal mutations for their phenotypic changes. The data obtained demonstrate that whole genomic sequencing is applicable as a high throughput tool to investigate genomic changes due to mutagenesis. The identification of these single point
Enhancing Availability of Services in Multi-Tenant Environment Using Software-Defined Networking

The immense growth of client requirements imposed on data center and cloud providers results in a conflict with traditional networking concepts lacking the required agility. In order to promote flexibility, which data center providers promise to their clients, this discrepancy needs to be resolved, for instance by employing the novel concept of Software Defined Networking (SDN). This diploma thesis utilises this concept in order to minimise service downtime while performing live virtual machine migration. The work is aimed at small/mediumsized data centers and hence the findings are based on real communication patterns found within such environments. The results of the thesis and implemented application show that latency and packet loss is slightly diminished thanks to the proactive approach taken during network topology changes when compared to the traditional approach based on L2 forwarding. Hence, the overall service availability within the virtual machine undergoing live migration is enhanced.
Michigan Neuroprosthetics Design Team Independent Research

Michigan Neuroprosthetics Design Team strives to develop cost effective, 3D printed, transradial arm prostheses. Our clients are children who cannot afford to invest in a neurologically controlled prosthesis that will be quickly outgrown. As a member of the mechanical subteam, I am responsible for designing the arm in Fusion 360. The design goals for the 2020 design cycle were to reduce the weight of the forearm, separate the battery compartment for simplified charging, redesign the string channels in the palm to reduce tangling, and perform mechanical testing to address design weaknesses. These goals, along with additional design changes, were met with the exception of physical mechanical testing. COVID-19 prohibited in-person meeting, so Finite Element Analysis (FEA) testing was performed instead.
A Study on Neuro Fuzzy Systems and Fuzzy Set

:The Neuro Fuzzy System is an intelligence system that is used to render systems intelligent. The Fuzzy System is an artificial intelligence technique focused on fuzzy logic, and neural networks are often used together. The combination of fuzzy logic and neural networks is used to minimize the issue of each system and its inherent limitations. It is referred to as the Neuro-Fuzzy method when fuzzy logic is used in neural networks. When they get input patterns, fuzzy logic and rules are modified in the fuzzy system. The Neuro-fuzzy system is a smart system used to execute the different programmers of artificial intelligence. The Neuro fuzzy system has numerous applications and uses that inventors and authors settle on.Neuro fuzzy system has different applications and uses according to which inventors and authors decide different models. This paper shows the different uses and applications of the neuro fuzzy systems advantage of using fuzzy logic in any system to make it smart.This paper also discusses the advantage of fuzzy systems.