Miracle-dz/UniFAR-FTUs huggingface dataset:
Adeno-associated virus (AAV) capsid engineering in liver-directed gene therapy

ABSTRACT Introduction: Gene therapy clinical trials with adeno-associated virus (AAV) vectors report impressive clinical efficacy data. Nevertheless, challenges have become apparent, such as the need for high vector doses and the induction of anti-AAV immune responses that cause the loss of vector-transduced hepatocytes. This fostered research focusing on development of next-generation AAV vectors capable of dealing with these hurdles. Areas Covered: While both the viral vector genome and the capsid are subjects to engineering, this review focuses on the latter. Specifically, we summarize the principles of capsid engineering strategies, and describe developments and applications of engineered capsid variants for liver-directed gene therapy. Expert Opinion: Capsid engineering is a promising strategy to significantly improve efficacy of the AAV vector system in clinical application. Reduction in vector dose will further improve vector safety, lower the risk of host immune responses and the cost of manufacturing. Capsid engineering is also expected to result in AAV vectors applicable to patients with preexisting immunity toward natural AAV serotypes.
Filling the Void: An Optimized Polymicrobial Interkingdom Biofilm Model for Assessing Novel Antimicrobial Agents in Endodontic Infection

There is a growing realization that endodontic infections are often polymicrobial, and may contain Candida spp. Despite this understanding, the development of new endodontic irrigants and models of pathogenesis remains limited to mono-species biofilm models and is bacterially focused. The purpose of this study was to develop and optimize an interkingdom biofilm model of endodontic infection and use this to test suitable anti-biofilm actives. Biofilms containing Streptococcus gordonii, Fusobacterium nucleatum, Porphyromonas gingivalis, and Candida albicans were established from ontological analysis. Biofilms were optimized in different media and atmospheric conditions, prior to quantification and imaging, and subsequently treated with chlorhexidine, EDTA, and chitosan. These studies demonstrated that either media supplemented with serum were equally optimal for biofilm growth, which were dominated by S. gordonii, followed by C. albicans. Assessment of antimicrobial activity showed significant effectiveness of each antimicrobial, irrespective of serum. Chitosan was most effective (3 log reduction), and preferentially targeted C. albicans in both biofilm treatment and inhibition models. Chitosan was similarly effective at preventing biofilm growth on a dentine substrate. This study has shown that a reproducible and robust complex interkingdom model, which when tested with the antifungal chitosan, supports the notion of C. albicans as a key structural component.
HNC0014, a Multi-Targeted Small-Molecule, Inhibits Head and Neck Squamous Cell Carcinoma by Suppressing c-Met/STAT3/CD44/PD-L1 Oncoimmune Signature and Eliciting Antitumor Immune Responses

Simple Summary Cancer stem cells (CSCs) in head and neck squamous cell carcinoma (HNSCC) possess unlimited self-renewal capacity, resist treatments and induce tumor repopulation after interventions. Here, we observed HNSCC CSCs secreted exosomes containing c-Met, STAT3 (also the phosphorylated form of c-Met and STAT3), CD44, and PD-L1 oncogenic signaling molecules. CSC-derived exosomes, in part, transform fibroblasts (NFs) into cancer-associated fibroblasts (CAFs), establish drug resistance, and an immune-evasive tumor microenvironment (TME). We demonstrated HNC0014, a novel small-molecule drug, suppresses HNSCC tumorigenesis, CSC generation and prevents CAF transformation by decreasing the aforementioned oncogenic signaling molecules’ expression in both HNSCC cells and CSC-derived exosomes. Abstract Despite advancements in diagnostic and standard treatment modalities, including surgery, radiotherapy, and chemotherapy, overall survival rates of advanced-stage head and neck squamous cell carcinoma (HNSCC) patients have remained stagnant for over three decades. Failure of these treatment modalities, coupled with post-therapy complications, underscores the need for alternative interventions and an in-depth understanding of the complex signaling networks involved in developing treatment resistance. Using bioinformatics tools, we identified an increased expression of c-Met, STAT3, and CD44 corresponding to a poor prognosis and malignant phenotype of HNSCC. Subsequently, we showed that tumorsphere-derived exosomes promoted cisplatin (CDDP) resistance and colony and tumorsphere formation in parental HNSCC cells, accompanied by an increased level of oncogenic/immune evasive markers, namely, c-Met, STAT3, CD44, and PD-L1. We then evaluated the therapeutic potential of a new small molecule, HNC0014. The molecular docking analysis suggested strong interactions between HNC0014 and oncogenic molecules; c-Met, STAT3, CD44, and PD-L1. Subsequently, we demonstrated that HNC0014 treatment suppressed HNSCC tumorigenic and expression of stemness markers; HNC0014 also reduced cancer-associated fibroblast (CAF) transformation by Exosp- and CAF-induced tumorigenic properties. HNC0014 treatment alone suppressed tumor growth in a cisplatin-resistant (SAS tumorspheres) mouse xenograft model and with higher inhibitory efficacy when combined with CDDP. More importantly, HNC0014 treatment significantly delayed tumor growth in a syngeneic mouse HNSCC model, elicited an antitumor immune profile, and reduced the total c-Met, STAT3, and their phosphorylated forms, PD-L1 and CD44, contents in serum exosomes. Collectively, our findings provide supports for HNC0014 as a multi-targeted immunotherapeutic lead compound for further development.
Differential TLR7-mediated cytokine expression by R848 in M-CSF- versus GM-CSF-derived macrophages after LCMV infection

Granulocyte-macrophage colony-stimulating factor (GM-CSF) and macrophage colony-stimulating factor (M-CSF) play an important role in macrophage (MФ) development by influencing their differentiation and polarization. Our goal was to explore the difference between M-CSF- and GM-CSF-derived bone marrow MФ responsiveness to TLR7-mediated signalling pathways that influence cytokine production early after infection in a model of acute virus infection. To do so, we examined cytokine production and TLR7-mediated signalling at 1 h post-lymphocytic choriomeningitis virus (LCMV) Armstrong (ARM) infection. We found that R848-induced cytokine expression was enhanced in these cells, with GM-CSF cells exhibiting higher proinflammatory cytokine expression and M-CSF cells exhibiting higher anti-inflammatory cytokine expression. However, R848-mediated signalling molecule activation was diminished in LCMV-infected M-CSF and GM-CSF macrophages. Interestingly, we observed that TLR7 expression was maintained during LCMV infection of M-CSF and GM-CSF cells. Moreover, TLR7 expression was significantly higher in M-CSF cells compared to GM-CSF cells. Taken together, our data demonstrate that although LCMV restrains early TLR7-mediated signalling, it primes differentiated MФ to enhance expression of their respective cytokine profiles and maintains levels of TLR7 expression early after infection.
Can We Define Dietary Requirements of Dispensable Amino Acids?

All of us in nutritional sciences learn early on that there are amino acids that can be synthesized de novo in our bodies, the dispensable amino acids (DAAs), and there are indispensable amino acids (IAAs) that we cannot synthesize and, thus, must consume in adequate amounts in our diet (1). The nitrogen (N) balance technique was initially used to define the estimated average requirement (EAR) and provide the RDA both for total protein and for individual IAAs. The EAR for protein was determined by placing test subjects on diets of high-quality protein where intakes ranged from deficient to surfeit, and N balance was measured. The EAR is the breakpoint where increasing protein intake causes N balance to go from negative to zero or positive. The EARs for individual IAAs can also be determined in the same manner, but in this case, subjects are placed on diets of crystalline amino acids where the test IAA’s intake is varied from low to high. The IAA EAR is again determined from the point where N balance shifts from negative to zero or positive. There are limitations to the N balance approach, and methods using 13C-labeled tracers of amino acids were developed to measure the amino acid oxidation response either directly (the 13C-labeled amino acid is the test IAA) or indirectly (the 13C-labeled amino acid is a different IAA from the test IAA) (1). Data from these amino acid tracer studies were used to increase EAR values for most IAAs from prior recommendations, e.g., from the 2002 report (2) to the current FAO/WHO/United Nations University (UNU) 2007 recommendation (3). Although both the direct and indirect amino acid oxidation methods have been shown to be effective at assessing individual IAA requirements, the indirect amino acid oxidation (IAAO) method (4) has advantages. First, the direct oxidation method uses a 13C-labeled tracer that is the same as the IAA being tested, and that tracer administration can distort results at low IAA intakes. However, the IAAO method uses a 13C-labeled tracer of an IAA different from that being tested, intake of which remains constant for all studies. Secondly, the IAAO method uses very short diet periods, allowing for much quicker study of subjects. Protein and amino acid requirements are difficult to determine in infants, children, and pregnant women using long adaptive diet periods because these dynamic stages of
Maximum weighted independent set and quantum alternating operator ansatz

We study the maximum weighted independent set problem of graph theory using the quantum approximate optimization algorithm. We perform simulations on the Rigetti Forrest simulator and analyze the dependence of the algorithm on the depth of the circuit, intial states and the wieghts of the vertices. We also numerically obtain an estimate of the expected approximation ratio of the algorithm for the circuit depths of p=1 and p=2 for a degree 2 graph.
Impact and effectiveness of a conjugate vaccine against invasive pneumococcal disease in Finland - a modelling approach

ABSTRACT The evaluation of the public health impact of a vaccination program is essential in monitoring its policy relevance. Vaccine impact (VI) is usually assessed in a before-after design, in which data on disease burden without vaccination program is required from a historical reference period. It takes into account the indirect effects and therefore aims to describe the public health performance of the vaccination program in the population. Vaccine effectiveness (VE), measured in parallel settings, quantifies the benefit for an individual of being vaccinated but does not address the indirect effects of a vaccination program. The motivation of this paper is to gain insight into patterns of how VI and VE have manifested under large-scale use of a ten-valent pneumococcal conjugate vaccine in Finnish children. We construct a simple pseudo-dynamic model that mimics typical post-vaccination trends in the incidences of pneumococcal carriage and invasive disease in children when the proportion of vaccine-type carriage decreases. In the context of the model, we define the parameters of interest for VI and VE and explore how their expected values evolve over time. For comparison, we demonstrate the application of VI and VE estimation by using register data.
The Arkansas Active Kids Study: Identifying contributing factors to metabolic health and obesity status in prepubertal school-age children

Background: We report the design, protocol and statistical analysis plan for the Arkansas Active Kids (AAK) Study. The study investigates the complex relationships between factors that contribute to metabolic health and obesity status in prepubertal school-age children in the state of Arkansas. Aim: We aim to identify modifiable behavioral and environmental factors and phenotypes related to metabolic health that are associated with obesity status that, if addressed effectively, can aid in designing effective intervention strategies to improve fitness and reduce obesity in children. Methods: We analyzed dietary and physical activity data from two national surveys (National Survey of Children’s Health and Youth Risk Behavior Surveillance System). We then conducted detailed surveys to collect dietary, physical activity, socio-demographic, and environmental data from a sample of 226 prepubertal Arkansas children. In the same sample of prepubertal children, we also collected extensive physiologic data to further study associations between physical activity and metabolic health. Results: All study visits included detailed measures of vital signs, energy expenditure, components of physical fitness, body composition and the collection of biological samples for determination of metabolic analytes. Conclusion: The observational, environmental and physiological results will be used to craft multivariate statistical models to identify which variables define ‘phenotype signatures’ that associate with fitness level and obesity status.
Rasch analysis of the Back Pain Attitudes Questionnaire (Back-PAQ)

Abstract Context As psychosocial factors have been recognised as significant predictors of the recovery trajectory from chronic back pain, the 34-item Back Pain Attitudes Questionnaire (Back-PAQ) was developed based on themes obtained from patient interviews, but previous psychometric analyses with a general population sample revealed uncertainty around the factor structure of the instrument. Objectives To provide more detailed information about the psychometric properties of the Back-PAQ when used with participants from the general population and also to test the internal validity of the tool for use with General Practitioners (GPs). Methods After applying partial-credit Rasch analysis with a sample of participants from the general population (n = 600), a replication analysis was conducted with a sample of GPs (n = 184). This approach permitted examination of sample-specific personal factors for differential item functioning. Subtests were used to differentiate between local dependency due to underlying dimensionality from local dependency due to method effects. Results A unidimensional fit to the Rasch model was achieved after 14 misfitting items had been deleted. The final 20-item solution also fit with a sample of 184 GPs. In both cases, the Back-PAQ-20 demonstrated good reliability (PSI ≥ 0.80), with no evidence of differential item functioning by personal factors. Conclusion The ordinal-to-interval conversion algorithms presented here further enhance the precision of the scale and permit analysis of Back-PAQ-20 scores using parametric statistics. The present study provided evidence for valid and reliable assessment of the back pain recovery beliefs of both users as well as providers of health services. IMPLICATIONS FOR REHABILITATION Psychosocial factors have been recognised as significant predictors of the recovery trajectory from chronic back pain. The 34-item Back Pain Attitudes Questionnaire (Back-PAQ) was developed based on themes obtained from patient interviews, but previous psychometric analyses with a general population sample revealed uncertainty around the factor structure of the instrument. The 20-item version of the Back Pain Attitudes Questionnaire (Back-PAQ) is shown here to have strong psychometric properties for administration with users and providers of health services.
Prototype Gluten-Free Breads from Processed Durum Wheat: Use of Monovarietal Flours and Implications for Gluten Detoxification Strategies

In this investigation, we reported the production of prototype breads from the processed flours of three specific Triticum turgidum wheat genotypes that were selected in our previous investigation for their potential low toxic/immunogenic activity for celiac disease (CD) patients. The flours were subjected to sourdough fermentation with a mixture of selected Lactobacillus strains, and in presence of fungal endoproteases. The breads were characterized by R5 competitive enzyme linked immunosorbent assay in order to quantify the residual gluten, and the differential efficacy in gluten degradation was assessed. In particular, two of them were classified as gluten-free (<20 ppm) and very low-gluten content (<100 ppm) breads, respectively, whereas the third monovarietal prototype retained a gluten content that was well above the safety threshold prescribed for direct consumption by CD patients. In order to investigate such a genotype-dependent efficiency of the detoxification method applied, an advanced proteomic characterization by high-resolution tandem mass spectrometry was performed. Notably, to the best of our knowledge, this is the first proteomic investigation which benefitted, for protein identification, from the full sequencing of the Triticum turgidum ssp. durum genome. The differences of the proteins’ primary structures affecting their susceptibility to hydrolysis were investigated. As a confirmation of the previous immunoassay-based results, two out of the three breads made with the processed flours presented an exhaustive degradation of the epitopic sequences that are relevant for CD immune stimulatory activity. The list of the detected epitopes was analyzed and critically discussed in light of their susceptibility to the detoxification strategy applied. Finally, in-vitro experiments of human gastroduodenal digestion were carried out in order to assess, in-silico, the toxicity risk of the prototype breads under investigation for direct consumption by CD patients. This approach allowed us to confirm the total degradation of the epitopic sequences upon gastro-duodenal digestion.
HCoV-NL63 and SARS-CoV-2 Share Recognized Epitopes by the Humoral Response in Sera of People Collected Pre- and during CoV-2 Pandemic

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause serious illness in older adults and people with chronic underlying medical conditions; however, children and young people are often asymptomatic or with mild symptoms. We evaluated the presence of specific antibodies (Abs) response against Human coronavirus NL63 (HCoV-NL63) S protein epitopes (NL63-RBM1, NL63-RBM2_1, NL63-RBM2_2, NL63-RBM3, NL63-SPIKE541–554, and NL63-DISC-like) and SARS-CoV-2 epitopes (COV2-SPIKE421–434 and COV2-SPIKE742–759) in plasma samples of pre-pandemic, mid-pandemic, and COVID-19 cohorts by indirect ELISA. Moreover, a competitive assay was performed to check for cross reactivity response between COV2-SPIKE421–434 and NL63-RBM3 among patients with a definitive diagnosis of SARS-CoV-2. Immune reaction against all SARS-CoV-2 and HCoV-NL63 epitopes showed a significantly higher response in pre-pandemic patients compared to mid-pandemic patients. The results indicate that probably antibodies against HCoV-NL63 may be able to cross react with SARS-CoV-2 epitopes and the higher incidence in pre-pandemic was probably due to the timing of collection when a high incidence of HCoV-NL63 is reported. In addition, the competitive assay showed cross-reactivity between antibodies directed against COV2-SPIKE421–434 and NL63-RBM3 peptides. Pre-existing HCoV-NL63 antibody response cross reacting with SARS-CoV-2 has been detected in both pre- and mid-pandemic individual, suggesting that previous exposure to HCoV-NL63 epitopes may produce antibodies which could confer a protective immunity against SARS-CoV-2 and probably reduce the severity of the disease.
The Queensland Birth Cohort Study for Early Childhood Caries: Results at 7 Years

Aims: This study investigated caries predictors in 378 children remaining from a birth cohort of 1,052 at 7 y and compared the efficacy of home visits (HVs) and telephone contacts (TCs) for early childhood caries (ECC) prevention. Methods: The HVs or TCs were made at ages 6, 12, 18, 30, and 42 mo with annual dental clinic examinations at ages 2 to 7 y. At every visit, the parents completed validated questionnaires regarding the children’s family, medical, dental, and dietary histories. Results: The caries prevalence increased from 2% and 6% at ages 2 and 3 y to 15%, 33%, 42%, and 52% at ages 4 to 7 y. The mean caries experience (decayed, missing, and teeth extracted due to caries) of the total cohort increased from 0.1 ± 0.5 at age 2 y to 0.2 ± 1.1 at 3 y, 0.5 ± 1.6 at 4 y, 1.1 ± 2.4 at 5 y, 1.6 ± 2.6 at 6 y, and 2.0 ± 2.7 at 7 y. The prevalence of mutans streptococci (MS) in the total cohort at years 2 to 7 was 22%, 36%, 42%, 42%, 39%, and 44%, respectively. MS was strongly correlated with caries prevalence for all years (all P < 0.001). Statistical modeling employing the generalized estimating equations identified caries predictors as holding a Health Care Card (low socioeconomic status) (P = 0.009; odds ratio [OR] = 2.05; confidence interval [CI]: 1.20–3.52), developmental defects of enamel (DDEs) (P < 0.001; OR = 1.09; CI: 1.05–1.14), and MS counts ≤105/mL (P = 0.001; OR = 1.63; CI: 1.24–2.14). By contrast, HVs were more protective than TCs for caries (P = 0.008; OR = 0.42; CI: 0.22–0.80). Conclusions: This study provides prospective, clinical evidence that MS, DDEs, and low socioeconomic status are strongly correlated with early childhood caries and that HVs are more efficacious than TCs in ECC prevention. Knowledge Transfer Statement: This 7-y birth cohort study provides longitudinal clinical evidence that mutans streptococci, developmental defects of enamel, and low socioeconomic status are key risk indicators of early childhood caries.
Multi-center study on overall clinical complexity of patients with prolonged disorders of consciousness of different etiologies

ABSTRACT Aim: to assess overall clinical complexity of patients with acquired disorders of consciousness (DoC) in vegetative state/unresponsive wakefulness syndrome (VS/UWS) vs. minimally conscious state- MCS) and in different etiologies. Design: Multi-center cross-sectional observational study. Setting: 23 intensive neurorehabilitation units. Subjects: 264 patients with DoC in the post-acute phase: VS/UWS = 141, and MCS = 123 due to vascular (n = 125), traumatic (n = 83) or anoxic (n = 56) brain injury. Main Measures: Coma Recovery Scale-Revised, and Disability Rating Scale (DRS); presence of medical devices (e.g., for eating or breathing); occurrence and severity of medical complications. Results: patients in DoC, and particularly those in VS/UWS, showed severe overall clinical complexity. Anoxic patients had higher overall clinical complexity, lower level of responsiveness/consciousness, higher functional disability, and higher needs of medical devices. Vascular patients had worse premorbid clinical comorbidities. The two etiologies showed a comparable rate of MC, higher than that observed in traumatic etiology. Conclusion: overall clinical complexity is significantly higher in VS/UWS than in MCS, and in non-traumatic vs. traumatic etiology. These findings could explain the worse clinical evolution reported in anoxic and vascular etiologies and in VS/UWS patients and contribute to plan patient-tailored care and rehabilitation programmes.