Miracle-dz/UniFAR-FTUs huggingface dataset:
The tyrosine phosphatase LAR acts as a receptor of the nidogen-tetanus toxin complex

Tetanus toxin is one of the most potent neurotoxins and is the causative agent of tetanus. This neurotoxin binds to the neuromuscular junction and, after internalisation into motor neurons, undergoes long-distance axonal transport and transcytosis into spinal cord inhibitory interneurons. Inside the cytoplasm of interneurons, the catalytic chain of the toxin blocks neurotransmitter release, leading to spastic paralysis. Whilst the effects of tetanus toxin intoxication have been extensively studied, the molecular composition of its receptor complex is still poorly understood. We have previously shown that the extracellular matrix proteins nidogens are essential for binding of the toxin to the neuromuscular junction. In this study, we show that the tyrosine phosphatase LAR interacts with the nidogen-tetanus toxin complex and enables its uptake into motor neurons. Binding of LAR to the toxin complex is mediated by its fibronectin III domains, which we have harnessed to inhibit tetanus toxin entry into motor neurons. Surprisingly, this function of LAR is independent of its role in regulating the neurotrophic activity of the TrkB receptor, which has previously been shown to augment the axonal transport of signalling endosomes containing tetanus neurotoxin. These findings identify a multi-subunit complex acting as a protein receptor for tetanus neurotoxin, and demonstrate a novel endocytic trafficking route for extracellular matrix proteins in neurons. Our study paves the way for dissecting the molecular mechanisms that control the recognition and uptake of physiological ligands and pathological proteins at the neuronal plasma membrane, as well as their targeting to the axonal retrograde pathway for long-distance transport within the nervous system.
Irreversible inhibition of TRF2TRFH recruiting functions: a strategy to induce telomeric replication stress in cancer cells

The shelterin component telomeric repeat-binding factor 2 (TRF2) is an essential regulator of telomere homeostasis and genomic stability. Mutations in the TRF2TRFH domain physically impair t-loop formation and prevent the recruitment of several factors that promote efficient telomere replication, resulting in a telomeric DNA damage response. Here, we design, synthesize, and biologically test covalent cyclic peptides that irreversibly target the TRF2TRFH domain. We identify APOD53 as our most promising compound. APOD53 forms a covalent adduct with a reactive cysteine residue present in the TRF2TRFH domain and induces phenotypes consistent with TRF2TRFH domain mutants. These include induction of a telomeric DNA damage response in the absence of fusions, increased telomeric replication stress, and impaired recruitment of regulator of telomere elongation helicase 1 (RTEL1) and structure-specific endonuclease subunit (SLX4) to telomeres. We demonstrate that APOD53 impairs cell growth in both a telomerase-positive and an ALT cell line, while sparing the viability of non-cancerous cells. Finally, we find that co-treatment with APOD53 and the G4 stabilizer RHPS4 further exacerbates telomere replication stress.
Endothelial cell derived microvesicles modulate cerebrovascular and brain aging via miR-17-5p and serve as potential biomarkers for vascular aging

Vascular aging, characterized by brain endothelial cells (ECs) senescence and dysfunction, has been known to lead to various age-related cerebrovascular and neurodegenerative diseases. However, its underlying mechanisms remain elusive. ECs derived microvesicles (EMVs) and exosomes (EEXs) carry the characteristics of parent cells and transfer their contents to modulate the functions of recipient cells, holding the potential to evaluate or regulate vascular aging. Here, we found that young or aged ECs released EMVs were more effective than their released EEXs on alleviating or aggravating mice cerebrovascular and brain aging as indicated by SA-β-gal staining, cerebral blood flow, blood brain barrier function, aging related markers and cognitive ability test. We further identified that these EMVs regulated cerebrovascular and brain aging by transferring miR-17-5p and could modulate ECs senescence and functions via miR-17-5p/PI3K/Akt pathway. Plasma EMVs and their contained miR-17-5p (EMV-miR-17-5p) were significantly increased or decreased in the elderly, and were closely correlated with vascular aging. Receiver Operating Characteristic (ROC) analysis showed that the area under the curve was 0.724 for EMVs, 0.77 for EMV-miR-17-5p and 0.815 for their combination for distinguishing vascular aging. Our results revealed the novel roles for EMVs that could more effectively modulate vascular and brain aging than EEXs by regulating ECs functions through miR-17-5p/PI3K/Akt pathway, and also suggested that EMVs and EMV-miR-17-5p represent promising biomarkers and therapeutic targets for vascular aging.
Thinking Ahead of the Tractor: Driver Safety and Situation Awareness

ABSTRACT Objective: Situation awareness has been identified as a key skill in maintaining safety in high-risk, dynamic industries. However, there is a lack of research evaluating situation awareness requirements and error types in agricultural operators. The aim of this study was to explore situation awareness among farmers in the United Kingdom (UK) when operating heavy agricultural machinery. Method: The study used an online qualitative survey to collect data in three main areas: situation awareness requirements, factors impacting situation awareness, and the safety context for UK farmers. A total of 57 farmers completed the survey, responding to seven open-ended questions. Data were analyzed using directed content analysis. Results: The results indicate the importance of situation awareness for safe and efficient work practice in farming. Situation awareness requirements span the machinery system, including awareness of internal cab systems and the status of implements attached to the external machine. Farmers needed to map and monitor the surrounding conditions in addition to considering personal requirements. Data also indicated the impact of a range of factors, including system-based elements such as blind spots, individual factors such as level of fatigue, and issues related to a lack of knowledge and failure to think ahead on the maintenance of situation awareness. Conclusion: This research highlights the situation awareness requirements for operating agricultural machinery in complex and dynamic environments. By taking a human factors approach, utilizing design and practical interventions, it may be possible to both support and enhance farmer situation awareness and, therefore, reduce errors and adverse incidents.
Computational analysis to investigate the anti-rheumatic potential of plant-based small molecule inhibitor targeting tumor necrosis factor α

Objective: This study aimed to assess the anti-rheumatic potential of Dodonaea viscosa and to evaluate its bioactive small molecules for their beneficial effects in the management of rheumatoid arthritis. Methods: In vitro bioactivity assays were performed to assess the healing potential of D. viscosa and statistical analysis was performed by using the linear regression technique. In silico analysis was performed to identify the key inhibitors of the disease to target TNF-α. The plant extract was prepared using ethanol solvent via the Soxhlet method. Phytochemical and bioactivity testing was performed. Gas chromatography–mass spectrometry (GC-MS) analysis was conducted for bioactive plant compounds. Disease-specific target was shortlisted by HUB gene analysis. Molecular docking and molecular dynamic simulations were run for validation of the results. Results: Phytochemical studies verified the presence of phenols, flavonoids, steroids, sterols, saponins, coumarins, tannins, and terpenoids. The significant antioxidant potential of plant extract was evaluated by the DPPH and Ferric Reducing Antioxidant Power (FRAP) assays, while the anti-inflammatory potential was evaluated by the protein denaturation and Human Red Blood Cell (HRBC) membrane stabilization assays. In silico studies revealed that nine of the 480 compounds found in D. viscosa (ethanol extract) had drug-like properties. Tumor necrosis factor alpha (TNF-α) was selected as a key disease gene through HUB gene analysis. Results of molecular docking and MD simulation analysis demonstrated that 4-(1-hydroxy-3-oxo-1H-isoindol-2-yl) benzoic acid (PubChemID 18873897), had the best binding affinity with TNF-α amongst all nine compounds. Conclusion: 4-(1-hydroxy-3-oxo-1H-isoindol-2-yl) benzoic acid (PubChemID 18873897), have the potential to be a good small molecule inhibitor of TNF-α against rheumatoid arthritis.
Acute injury to the mouse carotid artery provokes a distinct healing response

Treatment of vascular stenosis with angioplasty results in acute vascular damage, which may lead to restenosis. Owing to the highly complex cellularity of blood vessels, the healing response following this damage is incompletely understood. To gain further insight into this process, scRNA-seq of mouse carotid tissue after wire injury was performed. Stages of acute inflammation, resolution and remodeling were recapitulated in these data. To identify cell types which give rise to neointima, analyses focused on smooth muscle cell and fibroblast populations, and included data integration with scRNA-seq data from myocardial infarction and atherosclerosis datasets. Following carotid injury, a subpopulation of smooth muscle cells which also arises during atherosclerosis and myocardial infarction was identified. So-called stem cell/endothelial cell/monocyte (SEM) cells are candidates for repopulating injured vessels, and were amongst the most proliferative cell clusters following wire-injury of the carotid artery. Importantly, SEM cells exhibit specific transcriptional profiles which could be therapeutically targeted. SEM cell gene expression patterns could also be detected in bulk RNA-sequencing of neointimal tissue isolated from injured carotid vessels by laser capture microdissection. These data indicate that phenotypic plasticity of smooth muscle cells is highly important to the progression of lumen loss following acute carotid injury. Interference with SEM cell formation could be an innovative approach to combat development of restenosis.
The preliminary study on cardiac structure and function in Chinese patients with primary hyperparathyroidism

Purpose Recent evidences show that primary hyperparathyroidism (PHPT) patients have a high prevalence of cardiovascular diseases. However, the reported changes in cardiac status are inconsistent in previous studies. The present work evaluated the cardiac structure and function in PHPT patients by echocardiography. Methods PHPT patients and age- and sex-matched healthy controls were enrolled in this case-control study. Biochemical parameters were retrospectively collected from PHPT patients. Cardiac function and structure were assessed in all subjects using echocardiography. Results A total of 153 PHPT patients and 51 age- and sex-matched healthy controls were enrolled in this study. The mean serum calcium and parathyroid hormone (PTH) levels in PHPT patients were 2.84 ± 0.28mmol/L and 206.9 (130.0, 447.5) pg/ml, respectively. Left ventricular ejection fraction (LVEF) and early to late mitral annular velocity (E/A) were significantly lower in PHPT patients than in healthy controls (68.2 ± 6.0 vs. 70.7 ± 16.7%, 1.0 ± 0.5 vs. 1.4 ± 0.5, respectively, p both < 0.05). The left ventricular mass index (LVMI) and the relative wall thickness (RWT) were not significantly different between the two groups. However, the difference in LVEF between PHPT patients without hypertension and diabetes and the control groups disappeared. The majority of PHPT patients had normal cardiac geometry; however, a proportion of them exhibited concentric remodeling (normal LVMI, RWT≥0.42). Serum calcium, corrected calcium, ionized calcium and PTH were inversely related to E/A, whereas serum phosphorus and 24-hour urine calcium were positively related to E/A. Furthermore, biochemical parameters were not correlated with LVEF. Conclusions These findings demonstrate that PHPT patients exhibit diastolic cardiac dysfunction reflected by decreased E/A, as well as possible cardiac structural abnormalities. The serum calcium, phosphorus, and parathyroid hormone levels may influence cardiac structure and function.
The safety of combining immune checkpoint inhibitors and platinum-based chemotherapy for the treatment of solid tumors: A systematic review and network meta-analysis

Objective Combination treatment regimens consisting of both immune checkpoint inhibitors (ICI) and chemotherapeutic agents have emerged as the standard of care for a range of cancers. This network meta-analysis (NMA) examined the toxicity profiles and safety rankings of these different ICI-based combination regimens. Methods The PubMed, EMBASE, Web of Science, and Cochrane Library databases were searched for all randomized controlled trials (RCTs) published as of March 1, 2022 comparing two or more treatment regimens in which at least one arm was comprised of an ICI + platinum-based chemotherapeutic regimen. Treatment-related adverse events (AEs) of any grade and AEs of grade 3 or higher were the primary endpoints for this analysis, while specific AE types were secondary endpoints. This NMA combined both direct and indirect comparisons when analyzing odds ratios (ORs) and the surface under the cumulative ranking curve (SUCRA) for different ICI-based treatment regimens. Results In total, 33 RCTs enrolling 19,012 cancer patients were included in this NMA. Of the analyzed regimens, avelumab + chemotherapy and camrelizumab + chemotherapy were associated with a significantly greater risk of AEs of any grade relative to ipilimumab + chemotherapy, durvalumab + chemotherapy, or pembrolizumab + chemotherapy. No significant differences in the risk of AEs of grade 3 or higher were observed when comparing different ICI regimens. Hepatotoxicity and pyrexia were the most common AEs associated with atezolizumab + chemotherapy treatment. Ipilimumab + chemotherapy was associated with a relatively higher risk of gastrointestinal and skin toxicity. Skin toxicity and hypothyroidism were the major AEs associated with nivolumab + chemotherapy. Fatigue and pneumonia were the most common AEs respectively associated with sugemalimab + chemotherapy and pembrolizumab + chemotherapy regimens. Conclusions Of the evaluated regimens, camrelizumab + chemotherapy and avelumab + chemotherapy were associated with significantly higher rates of AEs of any grade, whereas durvalumab and sintilimab were relatively safe PD-L1 and PD-1 inhibitors, respectively, when administered in combination with platinum-based chemotherapy. However, none of the evaluated ICI + chemotherapy regimens exhibited any differences with respect to the incidence of grade 3 or higher AEs, offering guidance that may be of value in routine clinical practice.
Solidarity and strife after the Atlanta spa shootings: A mixed methods study characterizing Twitter discussions by qualitative analysis and machine learning

Background On March 16, 2021, a white man shot and killed eight victims, six of whom were Asian women at Atlanta-area spa and massage parlors. The aims of the study were to: (1) qualitatively summarize themes of tweets related to race, ethnicity, and racism immediately following the Atlanta spa shootings, and (2) examine temporal trends in expressions hate speech and solidarity before and after the Atlanta spa shootings using a new methodology for hate speech analysis. Methods A random 1% sample of publicly available tweets was collected from January to April 2021. The analytic sample included 708,933 tweets using race-related keywords. This sample was analyzed for hate speech using a newly developed method for combining faceted item response theory with deep learning to measure a continuum of hate speech, from solidarity race-related speech to use of violent, racist language. A qualitative content analysis was conducted on random samples of 1,000 tweets referencing Asians before the Atlanta spa shootings from January to March 15, 2021 and 2,000 tweets referencing Asians after the shooting from March 17 to 28 to capture the immediate reactions and discussions following the shootings. Results Qualitative themes that emerged included solidarity (4% before the shootings vs. 17% after), condemnation of the shootings (9% after), racism (10% before vs. 18% after), role of racist language during the pandemic (2 vs. 6%), intersectional vulnerabilities (4 vs. 6%), relationship between Asian and Black struggles against racism (5 vs. 7%), and discussions not related (74 vs. 37%). The quantitative hate speech model showed a decrease in the proportion of tweets referencing Asians that expressed racism (from 1.4% 7 days prior to the event from to 1.0% in the 3 days after). The percent of tweets referencing Asians that expressed solidarity speech increased by 20% (from 22.7 to 27.2% during the same time period) (p < 0.001) and returned to its earlier rate within about 2 weeks. Discussion Our analysis highlights some complexities of discrimination and the importance of nuanced evaluation of online speech. Findings suggest the importance of tracking hate and solidarity speech. By understanding the conversations emerging from social media, we may learn about possible ways to produce solidarity promoting messages and dampen hate messages.
Sport and mental health performance optimization in an adolescent gymnast: A case evaluation

The Optimum Performance Program in Sports (TOPPS) is a multi-component, sport-specific Family Behavior Therapy that has demonstrated improved sport performance, relationships, and mental health outcomes in adult and adolescent athletes with, and without, diagnosed mental health disorders in clinical trials. The current case trial demonstrates successful implementation of a novel component of TOPPS (i.e., talk aloud optimal sport performance imagery leading to dream mapping) in a biracial Latina and White adolescent gymnast without a mental health diagnosis. The participant demonstrated significant improvements from baseline to both post-treatment and 3-month follow-up in severity of mental health functioning, factors interfering with sports performance, and her relationships with teammates, coaches, and family. Results suggest it may be possible to optimize mental health through sport performance optimization.
Propagation strategies of Deyeuxia angustifolia in heterogeneous habitats

Plants utilize different strategies in different environments to maximize population expansion. Understanding plant reproductive strategies in heterogeneous habitats is therefore important for explaining plant ecological adaptability, and for effectively managing and conserving ecosystems. We wanted to explore the reproductive strategy transformation of D. angustifolia in heterogeneous habitats, as well as the environmental factors driving and affecting its reproductive characteristics. To do this we measured the reproductive characteristics of D. angustifolia, as well as the soil physical and chemical properties of these heterogeneous habitats. The density, biomass per unit area, and proportion of aboveground biomass in swampy meadows were significantly higher compared to other habitats. The proportion of rhizome node buds gradually increased from swampy to typical to miscellaneous grass meadows, while the proportion of tillering node buds decreased. The allocation of sexual reproduction within D. angustifolia populations was significantly and positively correlated with plant rhizome biomass and negatively correlated with the number of tillering node buds. The propagation strategies of D. angustifolia in heterogeneous habitats were consistent with CSR theory (Competitor, Stress-tolerator, and Ruderal). The proportions of inflorescence (2.07 ± 0.52%; 1.01 ± 0.15%) and root (23.8 ± 1.5%; 19.6 ± 1.4%) biomass in miscellaneous and typical meadows were high, which tended toward the “Ruderal” adaptation strategy. In swampy meadow, D. angustifolia invested mostly in vegetative growth to produce tiller node buds (14426.67 buds/m2; 46%) and ramets (1327.11 ± 102.10 plants/m2), which is characteristic of the “Competitor” strategy. Swamp D. angustifolia resisted flooding by maintaining a resource balance in its body, and was therefore biased toward the “Stress-tolerator” strategy. Environmental factors accounted for 74.63% of reproductive characteristic variation, in which the interpretative proportions of soil water content, dissolved organic carbon, ammonia nitrogen, and nitrate nitrogen were significant (p < 0.01). When soil water content, dissolved organic carbon, and nitrate nitrogen increased, D. angustifolia tended toward the C strategy; in contrast, when soil water content decreased, amine nitrogen and available phosphorus increased, and D. angustifolia tended toward the R strategy. In a stressful environment, the escape mechanism constitutes an increased rhizome and sexual reproduction investment. In contrast, for suitable habitats, tillering node buds increased in order to expand the population via new plant production, which was the propagation strategy of D. angustifolia in heterogeneous habitats.
To bead or not to bead: A review of Pseudomonas aeruginosa lung infection models for cystic fibrosis

Cystic fibrosis (CF) lung disease is characterised by recurring bacterial infections resulting in inflammation, lung damage and ultimately respiratory failure. Pseudomonas aeruginosa is considered one of the most important lung pathogens in those with cystic fibrosis. While multiple cystic fibrosis animal models have been developed, many fail to mirror the cystic fibrosis lung disease of humans, including the colonisation by opportunistic environmental pathogens. Delivering bacteria to the lungs of animals in different forms is a way to model cystic fibrosis bacterial lung infections and disease. This review presents an overview of previous models, and factors to consider when generating a new P. aeruginosa lung infection model. The future development and application of lung infection models that more accurately reflect human cystic fibrosis lung disease has the potential to assist in understanding the pathophysiology of cystic fibrosis lung disease and for developing treatments.
Advanced Monte Carlo simulator of the polarization-sensitive optical coherence tomography systems

Simulations of the optical coherence tomography (OCT) systems using the Monte Carlo method is a widely explored research area. However, there are several difficulties that need to be overcome in order to properly model the OCT imaging with the Monte Carlo algorithm. First of all, the temporal and the spatial coherence of the scattered light need to be considered, since OCT is based on the interference phenomenon. For the same reason, the polarization state of the scattered light need to be calculated. Moreover, the OCT systems use light beams that can be described by the Gaussian beam model. However, such beams cannot be directly simulated using the standard Monte Carlo algorithm. Different research groups have developed simulators dealing with some of these problems but the Monte Carlo simulator which considers all of them has not been published yet. Here we present the Monte Carlo program allowing to simulate OCT images of heterogeneous light scattering structures. The presented program considers all of the listed problems and allows to model complex sample geometries with layer boundaries described by a set of polygons.