Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal Prognostic Factors for Metastatic and Inoperable Sarcomas Treated With Pazopanib, Eribulin, and Trabectedin

Background/Aim: The prognosis of metastatic and inoperable sarcomas is extremely poor, and intensive chemotherapy-based treatment is typically administered to prolong survival. Currently, pazopanib, eribulin, and trabectedin are key drugs used in patients with these sarcomas. The aim of the study was to identify prognostic factors for metastatic and inoperable bone and soft tissue sarcomas. Patients and Methods: Clinicopathological data of 46 patients with metastatic and inoperable sarcomas treated with pazopanib, eribulin, and trabectedin between January 2013 and February 2022 at our institution were retrospectively analyzed. Age, sex, primary tumor location, adverse effects, history of doxorubicin and radiation therapy, performance status scores, maximum tumor response, and survival duration were evaluated. The significant prognostic factors were identified using Cox proportional hazards models. Moreover, the 5-year survival rate was evaluated using the Kaplan-Meier method. Results: The median survival duration after treatment was 13.3 months, where the 5-year overall survival rate was estimated to be 9.85%. Both univariate and multivariate analyses revealed significant relationships among patient prognosis, performance status, and tumor response. Conclusion: Performance status scores and tumor response were significantly associated with patient prognosis. Therefore, regardless of age, sex, primary tumor location, adverse effects, and history of doxorubicin and radiation therapy, use of cutting-edge drugs, such as pazopanib, eribulin, and trabectedin, may be advantageous in patients with advanced sarcomas, if their drug response and performance status scores are good.
MyCOACH (COnnected Advice for Cognitive Health): a digitally delivered multidomain intervention for cognitive decline and risk of dementia in adults with mild cognitive impairment or subjective cognitive decline–study protocol for a randomised controlled trial

Introduction Digital health interventions are cost-effective and easily accessible, but there is currently a lack of effective online options for dementia prevention especially for people at risk due to mild cognitive impairment (MCI) or subjective cognitive decline (SCD). Methods and analysis MyCOACH (COnnected Advice for Cognitive Health) is a tailored online dementia risk reduction programme for adults aged ≥65 living with MCI or SCD. The MyCOACH trial aims to evaluate the programme’s effectiveness in reducing dementia risk compared with an active control over a 64-week period (N=326). Eligible participants are randomly allocated to one of two intervention arms for 12 weeks: (1) the MyCOACH intervention programme or (2) email bulletins with general healthy ageing information (active control). The MyCOACH intervention programme provides participants with information about memory impairments and dementia, memory strategies and different lifestyle factors associated with brain ageing as well as practical support including goal setting, motivational interviewing, brain training, dietary and exercise consultations, and a 26-week post-intervention booster session. Follow-up assessments are conducted for all participants at 13, 39 and 65 weeks from baseline, with the primary outcome being exposure to dementia risk factors measured using the Australian National University-Alzheimer’s Disease Risk Index. Secondary measures include cognitive function, quality of life, functional impairment, motivation to change behaviour, self-efficacy, morale and dementia literacy. Ethics and dissemination Ethical approval was obtained from the University of New South Wales Human Research Ethics Committee (HC210012, 19 February 2021). The results of the study will be disseminated in peer-reviewed journals and research conferences. Trial registration number ACTRN12621000977875.
Use of immersive virtual reality for stress reduction during botulinum toxin injection for spasticity (RVTOX): a study protocol of a randomised control trial

Introduction Botulinum toxin injection is a common way to help reduce spasticity in the body caused by central neurological damage such as cerebral stroke, multiple sclerosis or traumatic brain injury. The pain felt during the injection causes most patients to experience significant stress for further injections, the level of which is variable between patients. Immersive virtual reality is a digital technique that simulates the three-dimensional spatial and sound environment around a person said to be immersed in this virtualised world. The effectiveness of virtual reality comes from the intensity of this multisensory immersion, known as the feeling of presence (ie, subjective experience of being in one place or one environment, even when you are physically in another one). Only one research article in paediatrics has shown that immersive reality technique has a positive impact on the level of pain and agitation suffered during botulinum toxin injections. The purpose of this study is therefore to evaluate with sufficient assurance the following research hypothesis: virtual reality can help adults cope with the stress and pain of botulinum toxin treatment injection. Methods and analysis The research hypothesis will be tested using a randomised stepped-wedge method versus a non-invasive technique (headset with virtual reality session) to its control (headset with no image nor audio). The design leads to considering the injection as a statistical unit as all participants will undergo the standard condition, the control technique and virtual reality technique. Ethics and dissemination Patients will be fully and fairly informed in terms of their understanding of the objectives and constraints of the study and the possible risks involved. They will also be entitled to refuse the study and/or withdraw, and this refusal will have no impact on their follow-up as part of their pathology. Dissemination of the results of this study will be through peer-reviewed publications, and national and international conferences. Ethics were approved by the Comité de Protection des Personnes Nord-Ouest in January 2022. Trial registration number NCT05364203.
Phylogenetic diversity and functional potential of large and cell-associated viruses in the Bay of Bengal

The Bay of Bengal (BoB), the largest bay in the world, provides valuable ecosystem services such as fishing and recreation to millions of people living along its coast and has a significant economic value. The BoB is impacted by various environmental factors such as seasonal monsoons and multiple freshwater inputs, and this region is particularly vulnerable to sea-level rise and increased frequency of devastating cyclones that are predicted to be exacerbated due to global climate change. These factors are also compounded by anthropogenic influences from tourism and development, making it an important ecosystem to understand and study from a global change perspective. Despite its importance, microbial diversity and ecology have remained largely understudied in this region. In this study, we describe the diversity and putative functional importance of large and cell-associated (that is, originating from the cellular size fraction) viruses from two coastal sites in the BoB, with an emphasis on giant viruses and large phages. Sites chosen for this study include Cox’s Bazar, a populated beach with multiple freshwater inputs, and Saint Martin Island, a resort island that has considerably less human influence compared to Cox’s Bazar. Through metagenomic sequencing, we were able to identify a more abundant and more diverse viral community at Cox’s Bazar consisting of many viruses that are indicators of freshwater intrusion and runoff. Overall, 1962 putative phage genome bins were obtained ranging from 10 - 655 kilobase pairs (kbp) in sizes. Of these genomes, 16 from Saint Martin were found to be larger than 100kbp which we deemed “large” phages, and we were able to reconstruct a phylogeny of these large phages using the TerL gene as a marker. This phylogeny revealed clades enriched in large phages and a high diversity of large phage candidates in the Bay of Bengal coast. Protein annotation analysis showed a wide variety of functionality from both sites with more auxiliary metabolic genes (AMGs) found in the Cox’s Bazar viral community. Five giant virus (Phylum Nucleocytoviricota) genomes were also reconstructed from Cox’s Bazar and identified as belonging to the orders Imitervirales and Pandoravirales. These genomes ranged from 83 - 876 kbp in size and contained a wide range of encoded functionalities. To the best of our knowledge, our study represents the first insights on the phylogenetic and functional diversity of viruses in the Bay of Bengal. These results thus provide an important foundation for further studies on the impact of host-virus interactions on biogeochemical cycles and microbial food web in this understudied marine environment.
Length-dependent Intramolecular Coil-to-Globule Transition in Poly(ADP-ribose) Induced by Cations

Poly(ADP-ribose) (PAR), a non-canonical nucleic acid, is essential for DNA/RNA metabolism and protein condensation, and its dysregulation is linked to cancer and neurodegeneration. However, key structural insights into PAR’s functions remain largely uncharacterized, hindered by the challenges in synthesizing and characterizing PAR, which are attributed to its length heterogeneity. A central issue is how PAR, comprised solely of ADP-ribose units, attains specificity in its binding and condensing proteins based on chain length. Here, we integrate molecular dynamics simulations with small-angle X-ray scattering to analyze PAR structures. We reveal the diverse structural ensembles of PAR and the factors influencing them, including a notable length-dependent compaction of PAR upon the addition of small amounts of Mg2+ ions. Unlike PAR15, PAR22 forms ADP-ribose bundles via local intramolecular coil-to-globule transitions. Understanding these length-dependent structural changes could be central to deciphering the specific biological functions of PAR.
Viral genomic features predict orthopoxvirus reservoir hosts

Orthopoxviruses (OPVs), including the causative agents of smallpox and mpox have led to devastating outbreaks in human populations worldwide. However, the discontinuation of smallpox vaccination, which also provides cross-protection against related OPVs, has diminished global immunity to OPVs more broadly. We apply machine learning models incorporating both host ecological and viral genomic features to predict likely reservoirs of OPVs. We demonstrate that incorporating viral genomic features in addition to host ecological traits enhanced the accuracy of potential OPV host predictions, highlighting the importance of host-virus molecular interactions in predicting potential host species. We identify hotspots for geographic regions rich with potential OPV hosts in parts of southeast Asia, equatorial Africa, and the Amazon, revealing high overlap between regions predicted to have a high number of potential OPV host species and those with the lowest smallpox vaccination coverage, indicating a heightened risk for the emergence or establishment of zoonotic OPVs. Our findings can be used to target wildlife surveillance, particularly related to concerns about mpox establishment beyond its historical range.
GCN5L1-mediated acetylation prevents Rictor degradation in cardiac cells after hypoxic stress

Cardiomyocyte apoptosis and cardiac fibrosis are the leading causes of mortality in patients with ischemic heart disease. As such, these processes represent potential therapeutic targets to treat heart failure resulting from ischemic insult. We previously demonstrated that the mitochondrial acetyltransferase protein GCN5L1 regulates cardiomyocyte cytoprotective signaling in ischemia- reperfusion injury in vivo and hypoxia-reoxygenation injury in vitro. The current study investigated the mechanism underlying GCN5L1-mediated regulation of the Akt/mTORC2 cardioprotective signaling pathway. Rictor protein levels in cardiac tissues from human ischemic heart disease patients were significantly decreased relative to non-ischemic controls. Rictor protein levels were similarly decreased in cardiac AC16 cells following hypoxic stress, while mRNA levels remained unchanged. The reduction in Rictor protein levels after hypoxia was enhanced by the knockdown of GCN5L1, and was blocked by GCN5L1 overexpression. These findings correlated with changes in Rictor lysine acetylation, which were mediated by GCN5L1 acetyltransferase activity. Rictor degradation was regulated by proteasomal activity, which was antagonized by increased Rictor acetylation. Finally, we found that GCN5L1 knockdown restricted cytoprotective Akt signaling, in conjunction with decreased mTOR abundance and activity. In summary, these studies suggest that GCN5L1 promotes cardioprotective Akt/mTORC2 signaling by maintaining Rictor protein levels through enhanced lysine acetylation.
Synthetic Peptide Nucleic Acids in Action: In Vivo Interference of the groEL Gene from Pea Aphid Endosymbiont Buchnera aphidicola

The unculturable nature of intracellular obligate symbionts presents a significant challenge for elucidating gene functionality, necessitating the development of gene manipulation techniques. One of the best-studied obligate symbioses is that between aphids and the bacterial endosymbiont Buchnera aphidicola. Given the extensive genome reduction observed in Buchnera, the remaining genes are crucial for understanding the host-symbiont relationship, but a lack of tools for manipulating gene function in the endosymbiont has significantly impeded the exploration of the molecular mechanisms underlying this mutualism. In this study, we introduced a novel gene manipulation technique employing synthetic single-stranded peptide nucleic acids (PNAs). We targeted the critical Buchnera groEL using specially designed antisense PNAs conjugated to an arginine-rich cell-penetrating peptide (CPP). Within 24 h of PNA administration via microinjection, we observed a significant reduction in groEL expression and Buchnera cell count. Notably, the interference of groEL led to profound morphological malformations in Buchnera, indicative of impaired cellular integrity. The gene knockdown technique developed in this study, involving the microinjection of CPP-conjugated antisense PNAs, provides a potent approach for in vivo gene manipulation of unculturable intracellular symbionts, offering valuable insights into their biology and interactions with hosts.
Ethambutol and Meropenem/Clavulanate Synergy Promotes Enhanced Extracellular and Intracellular Killing of Mycobacterium tuberculosis

Increasing evidence supports the repositioning of beta-lactams for tuberculosis (TB) therapy. However, additional research on the interaction of these drugs with conventional anti-TB agents is still warranted. Since the complex cell envelope of Mycobacterium tuberculosis (Mtb) may pose an additional obstacle to the diffusion of beta-lactams, an improved activity upon combination with drugs that inhibit the synthesis of outer cell wall elements is particularly relevant. In this context, we aimed to determine potential synergies between beta-lactams and the antimycobacterial drugs ethambutol and isoniazid. This was followed by experiments that aimed to confirm if the increased antimicrobial effects remained within the intracellular milieu and if they promoted heightened immune responses. Results of checkerboard assays with H37Rv and eight clinical isolates, including four drug-resistant Mtb strains, exposed that only the treatments containing ethambutol and beta-lactams achieved synergistic effects, while the standard ethambutol and isoniazid association failed to produce synergy in any of the tested isolates. In Mtb-infected THP-1 macrophages, combinations of ethambutol with increasing meropenem concentrations consistently displayed superior killing activities over the individual antibiotics. Flow cytometry with BODIPY FL vancomycin, which binds directly to the peptidoglycan, confirmed an increased exposure of this layer after co-treatment. This was reinforced by the high IL-1β secretion levels found in infected macrophages after incubation with concentrations of meropenem above 5 mg/L, which indicated an exposure of the host innate response sensors to pathogen-associated molecular patterns in the PG. Our findings show that the proposed impaired access of beta-lactams to periplasmic transpeptidases is counteracted by concomitant administration with ethambutol. The efficiency of this combination may be attributed to the synchronized inhibition of arabinogalactan and peptidoglycan synthesis, two key cell wall components. Given that beta-lactams exhibit a time-dependent bactericidal activity, a more effective pathogen recognition and killing prompted by this association may be highly beneficial to optimize TB regimens containing carbapenems.
Homologs of SD6 and ICE2 from rice may be involved in regulation of ABA in woody perennial buds

The availability of ABA, a central component in the regulation of the dormancy cycle in grapevine buds, is controlled by coordinated and opposite regulation of NCED and ABA8OX expression, as shown during natural dormancy release and following treatment with Hydrogen Cyanamide (HC). This implies the existence of a shared regulatory entity, which serves as an upstream switch. A molecular switch for integrated and opposite regulation of NCED and ABA8OX was recently described in rice, involving a pair of bHLH transcription factors (OsSD6-OsICE2) that directly regulate ABA8OX3 expression and indirectly regulate NCED2 expression, by direct regulation of the expression of the NCED repressor OsbHLH048. Here, we tested whether expression of the Vitis homologs of the rice SD6 and ICE2 are regulated by dormancy release stimuli, and whether the direction of regulation agrees with that of ABA8OX. Treatment with two independent stimuli of bud break (HC and hypoxia), as well as natural dormancy release, resulted in upregulation of OsSD6 homologs and down regulation of OsICE2 homologs, in agreement with the rice model. In unexpected contrast, the homolog of OsbHLH048 was down-regulated. Our results suggest a grapevine model in which (1) the homologs of OsSD6 and OsICE2 act as direct activators and repressors of ABA8OX3 expression, as for rice, (2) they have opposed effects on the expression of an OsbHLH048 homolog, which serves as direct activator of NCED expression, as for Arabidopsis, and (3) together they act as a switch that allows removal of ABA repression, followed by meristem reactivation and bud break. HIGHLIGHT A molecular switch for integrated and opposite regulation of NCED and ABA8OX in rice seeds, operated by three bHLH transcription factors, is conserved in grapevine buds and regulates dormancy release
Pharmacologically inducing regenerative cardiac cells by small molecule drugs

In contrast to lower organisms, adult mammals cannot regenerate damaged hearts through de-differentiation of cardiomyocytes (CMs) into cells with regenerative capacity. Development of an enabling condition to induce such naturally unavailable cells with potential to proliferate and differentiate into CMs, i.e., regenerative cardiac cells (RCCs), in mammals will provide new insights and tools for heart regeneration. Here, a two-compound combination (2C), CHIR99021 and A-485, was identified to robustly induce RCCs from human embryonic stem cell (hESC) derived TNNT2+ CMs in vitro, which was confirmed by lineage tracing experiments. Functional analyses revealed that RCCs expressed a spectrum of genes essential for cardiogenesis and exhibited potential to become functional CMs, endothelial cells (ECs) and smooth muscle cells (SMCs). Consistent with the results in human cells, 2C-induced generation of RCCs were also observed in neonatal rats CMs in vitro and in vivo. Remarkably, administration of 2C can induce RCCs in adult mouse hearts and significantly improve survival and heart function in the mice undergoing myocardial infarction. Mechanistically, CHIR99021 is indispensable for transcriptional and epigenetic activation of genes essential for RCC, whereas A-485 mainly function to epigenetically down-regulate H3K27Ac and particularly H3K9Ac in CMs. Their combination specifically enhances both H3K27Ac and H3K9Ac on RCC genes, facilitating the establishment of RCC state dedifferentiated from CMs. Therefore, our findings demonstrated the feasibility and revealed the mechanisms of pharmacological induction of RCCs from endogenous CMs, which could offer a promising regenerative strategy to repair injured hearts.
Transdifferentiation of fibroblasts into muscle cells to constitute cultured meat with tunable intramuscular fat deposition

Current studies on cultured meat mainly focused on the muscle tissue reconstruction in vitro, but lack the formation of intramuscular fat which is a crucial factor in determining taste, texture and nutritional contents. Therefore, incorporating fat into cultured meat is of superior value. In this study, we employed the myogenic/lipogenic transdifferentiation of chicken fibroblasts in 3D to produce muscle mass and deposit fat into the same cells without the co-culture or mixture of different cells or fat substances. The immortalized chicken embryonic fibroblasts were implanted into the hydrogel scaffold and the cell proliferation and myogenic transdifferentiation were conducted in 3D to produce the whole-cut meat mimics. Compare to 2D, cells grown in 3D matrix showed elevated myogenesis and collagen production. We further induced fat deposition in the transdifferentiated muscle cells and the triglyceride content could be manipulated to match and exceed the levels of chicken meat. The gene expression analysis indicated that both lineage-specific and multi-functional signalings could contribute to the generation of muscle/fat matrix. Overall, we were able to precisely modulate muscle, fat, and extracellular matrix contents according to balanced or specialized meat preferences. These findings provide new avenues for customized cultured meat production with desired intramuscular fat contents that can be tailored to meet the diverse demands of consumers. Graphical Abstract
Developing small Cas9 hybrids using molecular modeling

The RNA-guided CRISPR-Cas9 from Streptococcus pyogenes is the best characterized enzyme for gene editing. Its large size, however, precludes it from being packaged together with its single guide (sg)RNA into a single adeno-associated virus, limiting in vivo applications. Here, we developed smaller Cas9 hybrids, made of the PAM interacting domain (PID) of S. pyogenes and the catalytic domains of the smaller Cas9 orthologues, as well as sgRNA cognate hybrids. Molecular modeling revealed that the presence of a sgRNA stabilizes Cas9. Making the D10A mutation to turn Cas9 into a nickase dramatically alters its binding energy to the sgRNA, showing that the approach can identify functionally relevant changes. However, we found that the four Cas9/sgRNA hybrid pairs tested in human cells failed to edit target sequences. We conclude that in silico approaches can identify functional changes caused by point mutations but are not sufficient for designing Cas9/sgRNA hybrids.