Miracle-dz/UniFAR-FTUs huggingface dataset:
Toll-like receptor agonists as cancer vaccine adjuvants

ABSTRACT Cancer immunotherapy has emerged as a promising strategy to treat cancer patients. Among the wide range of immunological approaches, cancer vaccines have been investigated to activate and expand tumor-reactive T cells. However, most cancer vaccines have not shown significant clinical benefit as monotherapies. This is likely due to the antigen targets of vaccines, “self” proteins to which there is tolerance, as well as to the immunosuppressive tumor microenvironment. To help circumvent immune tolerance and generate effective immune responses, adjuvants for cancer vaccines are necessary. One representative adjuvant family is Toll-Like receptor (TLR) agonists, synthetic molecules that stimulate TLRs. TLRs are the largest family of pattern recognition receptors (PRRs) that serve as the sensors of pathogens or cellular damage. They recognize conserved foreign molecules from pathogens or internal molecules from cellular damage and propel innate immune responses. When used with vaccines, activation of TLRs signals an innate damage response that can facilitate the development of a strong adaptive immune response against the target antigen. The ability of TLR agonists to modulate innate immune responses has positioned them to serve as adjuvants for vaccines targeting infectious diseases and cancers. This review provides a summary of various TLRs, including their expression patterns, their functions in the immune system, as well as their ligands and synthetic molecules developed as TLR agonists. In addition, it presents a comprehensive overview of recent strategies employing different TLR agonists as adjuvants in cancer vaccine development, both in pre-clinical models and ongoing clinical trials.
Co-designing a nature-based intervention to promote postnatal mental health for mothers and their infants: a complex intervention development study in England

Objectives There is burgeoning evidence for the potential of nature-based interventions to improve wellbeing. However, the role of nature in enhancing maternal mental health, child development and early relationships remains relatively unexplored. This study aimed to develop a co-designed nature-based intervention to improve postnatal mothers’ and infants’ wellbeing. Design, setting and participants Person-based and co-design approaches informed the planning and design of the postnatal nature-based intervention. In stage 1, a multidisciplinary team was formed to agree research questions and appropriate methodology, and a scoping review was conducted. Six qualitative focus groups were then held with 30 mothers and 15 professional stakeholders. In stage 2, intervention guiding principles and a logic model were developed, and a stakeholder consensus meeting was convened to finalise the prototype intervention. The research was conducted in Bristol, UK, across voluntary, educational and community-based healthcare settings. Results Stakeholder consultation indicated significant enthusiasm for a postnatal nature-based intervention. A scoping review identified little existing research in this area. Focus group data are reported according to four broad themes: (1) perceived benefits of a group postnatal nature-based intervention, (2) potential drawbacks and barriers to access, (3) supporting attendance and implementation, and (4) ideas for intervention content. The developed intervention was tailored for mothers experiencing, or at risk of, postnatal mental health difficulties. It was identified that the intervention should facilitate engagement with the natural world through the senses, while taking into account a broad range of postnatal-specific practical and psychological needs. Conclusions To our knowledge, this is the first reported use of person-based and co-design approaches to develop a postnatal nature-based intervention. The resulting intervention was perceived by target users to address their needs and preferences. Further research is needed to determine the feasibility, clinical and cost-effectiveness of this approach.
Safer and More Convenient Modern Curative Radiotherapy for Patients With Early Prostate Cancer

Background/Aim: New fractionation schedules with modern tools are a very rapidly developing area in curative radiotherapy (RT) for early prostate cancer (PC). To apply these techniques in everyday clinical practice, we planned this phase II trial with different fractionation schedules and followed up patients using careful health-related quality of life (QoL) questionnaires for three years. Patients and Methods: Seventy-three PC patients with one or two intermediate PC risk factors according to the National Comprehensive Cancer Network criteria were recruited. Forty-two patients were treated with 78/2 Gy (conventional fractionation, CF) or 60/3 Gy (moderately hypofractionation RT, MHF), and 31 patients were treated with 36.25/7.25 Gy (stereotactic body RT, SBRT). Their PSA levels were measured, and QoL data were assessed for genitourinary (GU), gastrointestinal (GI), and sexual well-being between the baseline and three years after treatment. A Rectafix™ (RF) fixation device was used in 30 patients in the CF/MHF group. Results: Three years after radiotherapy (RT), there were no differences between the groups regarding GU, GI, sexual well-being, PSA response, or clinical outcomes. On QoL questionnaires, men in the SBRT group were more satisfied with their QoL at the end of RT. Urinary symptoms (p=0.004) and urinary incontinence were more common in the CF/MHF group (p=0.016) three months after RT. The use of RF reduced GI toxicity, especially urgency (p=0.002), at three years after RT. Conclusion: Modern, short, five-fraction stereotactic radiotherapy as a local curative treatment for PC is well tolerated and safe. Our novel results showing a decrease in GI toxicity using Rectafix™ fixation should be confirmed in future randomized trials.
Baryscapus rugglesi (Rohwer, 1919) (Hymenoptera: Eulophidae) discovered in western North America: Redescription, notes on biology, and implications as a parasitoid of its host, Agrilus cuprescens (Ménétries, 1832) (Coleoptera: Buprestidae)

Abstract. Eulophid larvae discovered in galleries of Agrilus cuprescens (Ménétries, 1832) within canes of Rubus sp. (Rosaceae) in the Pacific Northwest, U.S.A. region between 2018 and 2021 were identified as Baryscapus rugglesi (Rohwer, 1919) (subfamily Tetrastichinae). This species had previously only been found in eastern North America. Identification was based on numerous specimens reared from larvae collected from eight disparate locations in western Oregon and Washington State, U.S.A. , in 2019 and 2021, and examination against its type series from 1919 in Minnesota, U.S.A. and specimens from 1938 in New York, U.S.A (Mundinger 1941). Both sexes of B. rugglesi are herein redescribed and illustrated. Additionally, DNA sequences from specimens collected in 2019 were direct sequence matches with original specimens collected in 2018. The ubiquitous occurrence of B. rugglesi suggests it is likely a predominant parasitoid of A. cuprescens in the region. Baryscapus rugglesi is a gregarious larval parasitoid of several native Agrilus spp. in North America, so it is presumably native to the Nearctic region and has adapted as an alternative parasitoid of A. cuprescens, a Eurasian-native pest introduced into North America. However, COI sequences of B. rugglesi were similar to those of an unidentified eulophid from Europe in the Barcode of Life Database (almost 96% identity), possibly indicating a Holarctic distribution. Observed wasp biology, behavior, and perspectives on the potential role of B. rugglesi as a natural enemy within integrated pest management programs for A. cuprescens control are discussed.
The role of recombination, niche‐specific gene pools and flexible genomes in the ecological speciation of bacteria

Abstract Bacteria diversify into genetic clusters analogous to those observed in sexual eukaryotes, but the definition of bacterial species is an ongoing problem. Recent work has focused on adaptation to distinct ecological niches as the main driver of clustering, but there remains debate about the role of recombination in that process. One view is that homologous recombination occurs too rarely for gene flow to constrain divergent selection. Another view is that homologous recombination is frequent enough in many bacterial populations that barriers to gene flow are needed to permit divergence. Niche‐specific gene pools have been proposed as a general mechanism to limit gene flow. We use theoretical models to evaluate additional hypotheses that evolving genetic architecture, specifically the effect sizes of genes and gene gain and loss, can limit gene flow between diverging populations. Our model predicts that (a) in the presence of gene flow and recombination, ecological divergence is concentrated in few loci of large effect and (b) high rates of gene flow plus recombination promote gene loss and favor the evolution of niche‐specific genes. The results show that changing genetic architecture and gene loss can facilitate ecological divergence, even without niche‐specific gene pools. We discuss these results in the context of recent studies of sympatric divergence in microbes.
Reshaping neuroimmunology: diagnosis and treatment in the era of precision medicine

Abstract Precision medicine has revolutionized the field of neuroimmunology, with innovative approaches that characterize diseases based on their biology, deeper understanding of the factors leading to heterogeneity within the same disease, development of targeted therapies, and strategies to tailor therapies to each patient. This review explores the impact of precision medicine on various neuroimmunological conditions, including multiple sclerosis (MS), neuromyelitis optica spectrum disorder (NMOSD), myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD), optic neuritis, autoimmune encephalitis, and immune-mediated neuropathies. We discuss advances in disease subtyping, recognition of novel entities, promising biomarkers, and the development of more selective monoclonal antibodies and cutting-edge synthetic cell-based immunotherapies in neuroimmunological disorders. In addition, we analyze the challenges related to affordability and equity in the implementation of these emerging technologies, especially in situations with limited resources.
Mass spectrometry and NMR spectroscopy profiles of red and pink Rhododendron flower petals establish them as rich sources of bioactive secondary metabolites

Rhododendron petals are considered high-value owing to their commercial utility, national/state flower status in certain countries, and bioactive potential from recent studies. Profiling and quantitative analysis of the bioactive metabolites would evaluate if they can be natural sources. This study is focused on comprehensive profiling of secondary metabolites in the petals of Red and Pink Rhododendron flowers (R. arboreum and R. campanulatum) using Mass Spectrometry (GC-MS, LC-MS/MS) and Proton-Nuclear Magnetic Resonance (1H-NMR) Spectroscopy. The profiling highlighted the presence of secondary metabolites belonging to phenolic acids and flavonoids. Specifically, the flowers are rich in promising bioactive molecules such as quinic acid, chlorogenic acid (3-O-caffeoyl quinic acid), protocatechuic acid, coumaroyl quinic acids, catechin, epigallocatechin, and shikimic acid. The profiles are correlated with the metabolic pathways which reflected the activity of shikimic acid, phenolic acid and flavonoid biosynthetic pathways. These metabolites are well reported for their bioactive potential as anti-oxidative, anti-viral, anti-cancerous, anti-diabetic, anti-inflammatory, etc. While the quantitative and multivariate analysis showed variations in the levels of phenolic acids and flavonoids, it is established that red and pink Rhododendron flower petals are a rich source of bioactive phytochemicals of interest to the phytochemical Industry.
Phosphatases of regenerating liver balance F-actin rearrangements during T cell activation through WD repeat containing protein 1

Phosphatases of regenerating liver (PRLs) have been proposed to regulate actin dynamics in lymphoid cells. However, the mechanism mediating this role remained unknown. Here we showed the interaction of the PRLs with the actin regulator WD repeat containing protein 1 (WDR1). The interaction of the PRLs with WDR1 was dependent on F-actin integrity and the proper recruitment of the PRLs to cell membranes through the CAAX motif. Endogenous PRLs and WDR1 were distributed to the Immunological Synapse (IS) and perturbed expression of PRL-1 or PRL-2 by CRISPR/Cas9 mediated genome editing showed that the PRLs were required for proper distribution of WDR1 to filamentous (F)-actin at the IS. Further, perturbed expression of the PRLs or WDR1 resulted in defective IS assembly with deregulated F-actin rearrangements, altered positioning of LFA-1, and reduced IL-2 production. Interestingly, balanced expression of PRLs was required for accumulation of CD3ε at the IS and early activating signalling. We propose that PRLs regulate early T cell signalling and are required for proper F-actin dynamics by regulating the WDR1 access to F-actin networks. As a consequence, PRLs regulate LFA-1 positioning at the IS and proper cytokine secretion.
A computational account of joint SSRI and anti-inflammatory treatment

We present a computational model that elucidates the interplay between inflammation, serotonin levels, and brain activity. The model delineates how inflammation impacts extracellular serotonin, while cerebral activity reciprocally influences serotonin concentration. Understanding the reciprocal interplay between the immune system and brain dynamics is important, as unabated inflammation can lead to relapsing depression. The model predicts dynamics within the prefrontal cortex (PFC) and subcallosal cingulate cortex (SCC), mirroring patterns observed in depressive conditions. It also accommodates pharmaceutical interventions that encompass anti-inflammatory and antidepressant agents, concurrently evaluating their efficacy with regard to the severity of depressive symptoms.
S1 hydrophobic residues alter the voltage sensing phosphatase enzymatic function and voltage sensing

The voltage sensing domain (VSD) is a four-helix modular protein domain that converts electrical signals into conformational changes, leading to open pores and active enzymes. In most voltage sensing proteins, the VSDs do not interact with one another and the S1-S3 helices are considered mainly as scaffolding. The two exceptions are the voltage sensing phosphatase (VSP) and the proton channel (Hv). VSP is a voltage-regulated enzyme and Hv’s are channels that only have VSDs. To investigate the S1 contribution to VSP function, we individually mutated four hydrophobic amino acids in S1 to alanine (F127, I131, I134 and L137). We also combined these mutations to generate quadruple mutation designated S1-Q. Most of these mutations shifted the voltage dependence of activity to higher voltages though interestingly, not all substrate reactions were the same. The kinetics of enzymatic activity were also altered with some mutations significantly slowing down dephosphorylation. The voltage dependence of VSD motions were consistently shifted to lower voltages and indicated a second voltage dependent motion. Co-immunoprecipitation demonstrated that none of the mutations broke the VSP dimer indicating that the S1 impact could stem from intersubunit interactions. Lastly, when the same alanine mutations were introduced into a genetically encoded voltage indicator, they dramatically altered the optical readings, making some of the kinetics faster and shifting the voltage dependence. These results indicate that the S1 helix in VSP plays a critical role in tuning the enzyme’s conformational response to membrane potential transients and influencing the function of the VSD.
Abscisic acid signaling gates salt-specific responses of plant roots

Soil salinity presents a dual challenge for plants, involving both osmotic and ionic stress. In response, plants deploy distinct yet interconnected mechanisms to cope with these facets of salinity stress. In this investigation, we observed a substantial overlap in the salt (NaCl)-induced transcriptional responses of Arabidopsis roots with those triggered by osmotic stress or the plant stress hormone abscisic acid (ABA), as anticipated. Notably, a specific cluster of genes responded uniquely to sodium (Na+) ions. Surprisingly, expression of sodium-induced genes exhibited a negative correlation with the ABA response and preceded the activation of genes induced by the osmotic stress component of salt. Elevated exogenous ABA levels resulted in the complete abolition of sodium-induced responses. Consistently, ABA signalling mutants displayed prolonged sodium-induced gene expression, coupled with increased root cell damage under high salinity conditions. Moreover, ABA signalling mutants were unable to redirect root growth to avoid high sodium concentrations and failed to contain their root cell swelling in the presence of elevated salt levels. In summary, our findings unveil an unexpected and pivotal role for ABA signaling in mitigating cellular damage induced by salinity stress and modulating sodium-specific responses in plant roots.
Chemical probes to interrogate the extreme environment of mosquito larval guts

Mosquito control methods are vital for the spread of life-threatening illnesses such as dengue fever, malaria, and yellow fever. Vector control technologies must be selective to minimize deleterious effects to our ecosystem. Successful methods that control mosquito larva populations utilize the uniquely high alkaline nature of the midgut. Here, we present novel protected triazabutadienes (pTBD) which are deprotected under basic conditions of the larval midgut, releasing an aryl diazonium ion (ADI) that results in protein modification. The probes contain a bioorthogonal terminal alkyne handle, enabling a selective Cu-click reaction with an azido-fluorophore for quantification by SDS PAGE and visualization using fluorescence microscopy. A control TBD, unable to release an ADI, did not label the midgut. We envision our chemical probes will aid in the development of new selective mosquito control methods thus preventing the spread of mosquito-borne illnesses with minimal impact on other organisms in the ecosystem.
MERITS: a web-based integrated Mycobacterial PE/PPE protein database

Motivation PE/PPE proteins, highly abundant in the Mycobacterium genome, play a vital role in virulence and immune modulation. Understanding their functions is key to comprehending the internal mechanisms of Mycobacterium. However, a lack of dedicated resources has limited research into PE/PPE proteins. Results Addressing this gap, we introduce MERITS, a comprehensive 3D structure database specifically designed for PE/PPE proteins. MERITS hosts 22,353 non-redundant PE/PPE proteins, encompassing details like physicochemical properties, subcellular localisation, post-translational modification sites, protein functions, and measures of antigenicity, toxicity, and allergenicity. MERITS also includes data on their secondary and tertiary structure, along with other relevant biological information. MERITS is designed to be user-friendly, offering interactive search and data browsing Features to aid researchers in exploring the potential functions of PE/PPE proteins. MERITS is expected to become a crucial resource in the field, aiding in developing new diagnostics and vaccines by elucidating the sequence-structure-functional relationships of PE/PPE proteins. Availability and implementation MERITS is freely accessible at http://merits.unimelb-biotools.cloud. edu.au/.
Pharmacological modulation of dopamine D1 and D2 receptors reveals distinct neural networks related to probabilistic learning in non-human primates

The neurotransmitter dopamine (DA) has a multifaceted role in healthy and disordered brains through its action on multiple subtypes of dopaminergic receptors. How modulation of these receptors controls behavior by altering connectivity across intrinsic brain-wide networks remains elusive. Here we performed parallel behavioral and resting-state functional MRI experiments after administration of two different DA receptor antagonists in macaque monkeys. Systemic administration of SCH-23390 (D1 antagonist) disrupted probabilistic learning when subjects had to learn new stimulus-reward associations and diminished functional connectivity (FC) in cortico-cortical and fronto-striatal connections. By contrast, haloperidol (D2 antagonist) improved learning and broadly enhanced FC in cortical connections. Further comparison between the effect of SCH-23390/haloperidol on behavioral and resting-state FC revealed specific cortical and subcortical networks associated with the cognitive and motivational effects of DA, respectively. Thus, we reveal the distinct brain-wide networks that are associated with the dopaminergic control of learning and motivation via DA receptors.
Hypoxia Sensing in Resident Cardiac Macrophages Regulates Monocyte Fate Specification following Ischemic Heart Injury

Myocardial infarction initiates cardiac remodeling and is central to heart failure pathogenesis. Following myocardial ischemia reperfusion injury, monocytes enter the heart and differentiate into diverse subpopulations of macrophages. The mechanisms and dynamics of monocyte differentiation within this context are unknown. We investigated the role of macrophage hypoxia sensing on monocyte differentiation following reperfused myocardial infarction. We show that deletion of Hif1α, a hypoxia response transcription factor, in resident cardiac macrophages led to increased remodeling and overrepresentation of a macrophage subset marked by arginase 1 (Arg1) expression. Arg1+ macrophages displayed an inflammatory gene signature and were predicted to represent an intermediate state within the monocyte differentiation cascade. Lineage tracing of Arg1+ macrophages revealed the existence of a monocyte differentiation trajectory consisting of multiple transcriptionally distinct macrophage states. We further showed that deletion of Hif1α in resident cardiac macrophages resulted in arrested progression through this trajectory and accumulation of an inflammatory intermediate state marked by persistent Arg1 expression. Collectively, our findings unveil distinct trajectories of monocyte differentiation and identify hypoxia sensing as an important determinant of monocyte differentiation following myocardial infarction.
Online Behaviour Indicator Extraction for Enhanced Cancer Patient Management using Real-World Data

Mental health issues of breast cancer patients and survivors are detrimental to their recovery, reintegration to normal living, and quality of life. With the increasing popularity of social media platforms and online browsing, combined with the rise of Natural Language Processing (NLP), there exists great potential in analyzing textual information of various online user activities to infer important indicators about a person’s online behaviour and emotional well-being. This work proposes a NLP-based framework for emotion extraction from social media posts and for user interest identification from browser history data. We experimented with contextual representations by fine-tuning pre-trained models like BERT combined with a fully connected layer, stacked LSTM and Bi-LSTM layers, and external resources in the form of emotion lexicons and self-attention. We evaluated our models on curated datasets derived from the combination of open datasets and achieved state-of-the-art performance. Overall, our work provides evidence of the potential for non-obtrusive extraction of online behaviour indicators that reflect the emotional well-being of patients.