Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary Protein Intake and Transition between Frailty States in Octogenarians Living in New Zealand

Adequate nutritional status may influence progression to frailty. The purpose of this study is to determine the prevalence of frailty and examine the relationship between dietary protein intake and the transition between frailty states and mortality in advanced age. We used data from a longitudinal cohort study of Māori (80–90 years) and non-Māori (85 years). Dietary assessments (24-h multiple pass dietary recalls) were completed at the second year of follow-up (wave 2 and forms the baseline in this study). Frailty was defined using the Fried Frailty criteria. Multi-state modelling examined the association of protein intake and transitions between frailty states and death over four years. Over three quarters of participants were pre-frail or frail at baseline (62% and 16%, respectively). Those who were frail had a higher co-morbidity (p < 0.05), where frailty state changed, 44% showed a worsening of frailty status (robust → pre-frail or pre-frail → frail). Those with higher protein intake (g/kg body weight/day) were less likely to transition from robust to pre-frail [Hazard Ratio (95% Confidence Interval): 0.28 (0.08–0.91)] but also from pre-frail to robust [0.24 (0.06–0.93)]. Increased protein intake was associated with lower risk of transitioning from pre-frailty to death [0.19 (0.04–0.80)], and this association was moderated by energy intake [0.22 (0.03–1.71)]. Higher protein intake in this sample of octogenarians was associated with both better and worse outcomes.
Comparison of Supervised and Unsupervised Approaches for the Generation of Synthetic CT from Cone-Beam CT

Due to major artifacts and uncalibrated Hounsfield units (HU), cone-beam computed tomography (CBCT) cannot be used readily for diagnostics and therapy planning purposes. This study addresses image-to-image translation by convolutional neural networks (CNNs) to convert CBCT to CT-like scans, comparing supervised to unsupervised training techniques, exploiting a pelvic CT/CBCT publicly available dataset. Interestingly, quantitative results were in favor of supervised against unsupervised approach showing improvements in the HU accuracy (62% vs. 50%), structural similarity index (2.5% vs. 1.1%) and peak signal-to-noise ratio (15% vs. 8%). Qualitative results conversely showcased higher anatomical artifacts in the synthetic CBCT generated by the supervised techniques. This was motivated by the higher sensitivity of the supervised training technique to the pixel-wise correspondence contained in the loss function. The unsupervised technique does not require correspondence and mitigates this drawback as it combines adversarial, cycle consistency, and identity loss functions. Overall, two main impacts qualify the paper: (a) the feasibility of CNN to generate accurate synthetic CT from CBCT images, which is fast and easy to use compared to traditional techniques applied in clinics; (b) the proposal of guidelines to drive the selection of the better training technique, which can be shifted to more general image-to-image translation.
TCMacro: A Simple and Robust ImageJ-Based Method for Automated Measurement of Tail Coiling Activity in Zebrafish

Tail coiling is a reflection response in fish embryos that can be used as a model for neurotoxic analysis. The previous method to analyze fish tail coiling is largely based on third-party software. In this study, we aim to develop a simple and cost-effective method called TCMacro by using ImageJ macro to reduce the operational complexity. The basic principle of the current method is based on the dynamic change of pixel intensity in the region of interest (ROI). When the fish tail is moving, the average intensity is increasing. In time when the fish freeze, the peak of mean intensity is maintaining at a relatively low level. By using the optimized macro settings and excel VBA scripts, all the tail coiling measurement processes can be archived with few operation steps with high precision. Three major endpoints of tail coiling counts, tail coiling duration and tail coiling intervals can be obtained in batch. To validate this established method, we tested the potential neurotoxic activity of Tricaine (methanesulfonate, MS-222) and psychoactive compound of caffeine. Zebrafish embryos after Tricaine exposure displayed significantly less tail coiling activity in a dose-dependent manner, and were comparable to manual counting through the Wilcoxon test and Pearson correlation double validation. Zebrafish embryos after caffeine exposure displayed significantly high tail coiling activity. In conclusion, the TCMacro method presented in this study provides a simple and robust method that is able to measure the relative tail coiling activities in zebrafish embryos in a high-throughput manner.
Diet Intervention Study through Telemedicine Assistance for Systemic Nickel Allergy Syndrome Patients during the COVID-19 Pandemic

Background: Restrictions due to the COVID-19 pandemic limited patients’ access to hospital care. The aims of this study were to assess dietary nutritional status, quality of life (QoL), and adherence to dietary therapy before and after 30-day personalized diet therapy through telenutrition tools in patients with systemic nickel allergic syndrome (SNAS). Methods: Each SNAS patient underwent the following allergological procedures: (a) face-to-face visit (nutritional visit and QoL evaluation) with prescription of one out of five personalized and balanced dietary plans different for calorie intake, (b) video call visit for dietary evaluation and assessment of adherence to diet after 15 days, and (c) video call visit for dietary and QoL evaluation and assessment of adherence to diet therapy after 30 days (end of study). Results: We enrolled 20 SNAS patients. After 15 and 30 days, we found a statistically significant improvement in anthropometric findings after diet therapy, a significant adherence rate to low-nickel diet (60% and 80%, respectively), and an improvement in QoL with an increase in almost all psychometric indices. Conclusions: Our study demonstrates that telenutrition can be a valid tool to monitor nutritional status and adherence to balanced low-Ni diet positively affecting QoL in SNAS patients during the COVID-19 pandemic.
Restoring the Molecular Clockwork within the Suprachiasmatic Hypothalamus of an Otherwise Clockless Mouse Enables Circadian Phasing and Stabilization of Sleep-Wake Cycles and Reverses Memory Deficits

The timing and quality of sleep-wake cycles are regulated by interacting circadian and homeostatic mechanisms. Although the suprachiasmatic nucleus (SCN) is the principal clock, circadian clocks are active across the brain and the respective sleep-regulatory roles of SCN and local clocks are unclear. To determine the specific contribution(s) of the SCN, we used virally mediated genetic complementation, expressing Cryptochrome1 (Cry1) to establish circadian molecular competence in the suprachiasmatic hypothalamus of globally clockless, arrhythmic male Cry1/Cry2-null mice. Under free-running conditions, the rest/activity behavior of Cry1/Cry2-null controls expressing EGFP (SCNCon) was arrhythmic, whereas Cry1-complemented mice (SCNCry1) had coherent circadian behavior, comparable to that of Cry1,2-competent wild types (WTs). In SCNCon mice, sleep-wakefulness, assessed by electroencephalography (EEG)/electromyography (EMG), lacked circadian organization. In SCNCry1 mice, however, it matched WTs, with consolidated vigilance states [wake, rapid eye movement sleep (REMS) and non-REMS (NREMS)] and rhythms in NREMS δ power and expression of REMS within total sleep (TS). Wakefulness in SCNCon mice was more fragmented than in WTs, with more wake-NREMS-wake transitions. This disruption was reversed in SCNCry1 mice. Following sleep deprivation (SD), all mice showed a homeostatic increase in NREMS δ power, although the SCNCon mice had reduced NREMS during the inactive (light) phase of recovery. In contrast, the dynamics of homeostatic responses in the SCNCry1 mice were comparable to WTs. Finally, SCNCon mice exhibited poor sleep-dependent memory but this was corrected in SCNCry1mice. In clockless mice, circadian molecular competence focused solely on the SCN rescued the architecture and consolidation of sleep-wake and sleep-dependent memory, highlighting its dominant role in timing sleep. SIGNIFICANCE STATEMENT The circadian timing system regulates sleep-wake cycles. The hypothalamic suprachiasmatic nucleus (SCN) is the principal circadian clock, but the presence of multiple local brain and peripheral clocks mean the respective roles of SCN and other clocks in regulating sleep are unclear. We therefore used virally mediated genetic complementation to restore molecular circadian functions in the suprachiasmatic hypothalamus, focusing on the SCN, in otherwise genetically clockless, arrhythmic mice. This initiated circadian activity-rest cycles, and circadian sleep-wake cycles, circadian patterning to the intensity of non-rapid eye movement sleep (NREMS) and circadian control of REMS as a proportion of total sleep (TS). Consolidation of sleep-wake established normal dynamics of sleep homeostasis and enhanced sleep-dependent memory. Thus, the suprachiasmatic hypothalamus, alone, can direct circadian regulation of sleep-wake.
Social Support and Cognitive Impairment: Results from a Portuguese 4-Year Prospective Study

(1) Background: In an ageing society, social relationships may benefit cognitive performance with an impact on the health of older people. This study aims to estimate the effect of different social support sources on the risk of cognitive impairment in a sample of older Portuguese people. (2) Methods: From the Portuguese EpiPorto cohort study, we followed a sample of participants with 60 to 85 years (N = 656) between 2009 and 2015 (4.63 mean years of follow-up). The participants’ perception of social support from family, friends and significant others was evaluated. Cox’s regression models were used to investigate the association between this and sociodemographic variables. (3) Results: It was found that social support from friends reduces the risk of cognitive impairment. Men, participants aged 60 to 64 and those not married have a lower risk of cognitive impairment after adjusting for other variables. Participants between 80 and 85 years old (p = 0.021), those with less than four years of education (p < 0.001), and those with cognitive impairment (p = 0.007) have perception of less social support from friends. (4) Conclusions: A social support network from friends reduces the risk of cognitive impairment for older people.
Diagnostic Performance of Electromagnetic Navigation Bronchoscopy-Guided Biopsy for Lung Nodules in the Era of Molecular Testing

Electromagnetic navigation bronchoscopy (ENB) is an emerging technique used to evaluate peripheral lung lesions. The aim of this study was to determine the diagnostic yield, safety profile, and adequacy of specimens obtained using ENB for molecular testing. This single-center, prospective pilot study recruited patients with peripheral pulmonary nodules that were not suitable for biopsy via percutaneous transthoracic needle biopsy methods. The possibility of molecular testing, including epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), and programmed death ligand 1 (PD-L1), was identified with non-small cell lung cancer (NSCLC) tissue obtained using ENB. ENB-guided biopsy was performed on 30 pulmonary nodules in 30 patients. ENB-guided biopsy was successfully performed in 96.6% (29/30) of cases, but one case failed to approach the target lesion. The diagnostic accuracy of ENB-guided biopsy was 68.0% (17/25). Biopsy-related pneumothorax occurred in one patient and there was no major bleeding or deaths related to the procedure. Among 13 patients diagnosed with NSCLC, molecular testing was successfully performed in 92.3% (12/13). ENB-guided biopsy demonstrated acceptable accuracy and excellent sample adequacy, with a high possibility of achieving molecular testing and a good safety profile to evaluate peripheral pulmonary nodules, even when the percutaneous approach was difficult and/or dangerous.
Mesenchymal Stem Cells, Bioactive Factors, and Scaffolds in Bone Repair: From Research Perspectives to Clinical Practice

Mesenchymal stem cell-based therapies are promising tools for bone tissue regeneration. However, tracking cells and maintaining them in the site of injury is difficult. A potential solution is to seed the cells onto a biocompatible scaffold. Construct development in bone tissue engineering is a complex step-by-step process with many variables to be optimized, such as stem cell source, osteogenic molecular factors, scaffold design, and an appropriate in vivo animal model. In this review, an MSC-based tissue engineering approach for bone repair is reported. Firstly, MSC role in bone formation and regeneration is detailed. Secondly, MSC-based bone tissue biomaterial design is analyzed from a research perspective. Finally, examples of animal preclinical and human clinical trials involving MSCs and scaffolds in bone repair are presented.
Treatment-Free Remission—A New Aim in the Treatment of Chronic Myeloid Leukemia

Tyrosine kinases inhibitors (TKIs) revolutionized chronic myeloid leukemia (CML) treatment for many years, prolonging patients’ life expectancy to be comparable to age-matched healthy individuals. According to the latest the European LeukemiaNet (ELN) recommendations, CML treatment aims to achieve long-term remission without treatment (TFR), which is feasible in more than 40% of patients. Nearly all molecular relapses occur during the first 6 months after TKI withdrawal and do not progress to clinical relapse. The mechanisms that are responsible for CML relapses remain unexplained. It is suggested that maintaining TFR is not directly related to the total disposing of the gene transcript BCR-ABL1, but it might be a result of the restoration of the immune surveillance in CML. The importance of the involvement of immunocompetent cells in the period of TKI withdrawal is also emphasized by the presence of specific symptoms in some patients with “withdrawal syndrome”. The goal of this review is to analyze data from studies regarding TFRs in order to characterize the elements of the immune system of patients that might prevent CML molecular relapse. The role of modern droplet digital polymerase chain reaction (ddPCR) and next-generation sequencing (NGS) in better identification of low levels of BCR-ABL1 transcripts was also taken into consideration for refining the eligibility criteria to stop TKI therapy.
Biochemical and Clinical Effects of Vitamin E Supplementation in Hungarian Smith-Lemli-Opitz Syndrome Patients

Smith-Lemli-Opitz syndrome (SLOS) is a severe monogenic disorder resulting in low cholesterol and high 7-dehydrocholesterol (7-DHC) levels. 7-DHC-derived oxysterols likely contribute to disease pathophysiology, and thus antioxidant treatment might be beneficial because of high oxidative stress. In a three-year prospective study, we investigated the effects of vitamin E supplementation in six SLOS patients already receiving dietary cholesterol treatment. Plasma vitamin A and E concentrations were determined by the high-performance liquid chromatography (HPLC) method. At baseline, plasma 7-DHC, 8-dehydrocholesterol (8-DHC) and cholesterol levels were determined by liquid chromatography–tandem mass spectrometry (LC-MS/MS) method. The clinical effect of the supplementation was assessed by performing structured parental interviews. At baseline, patients were characterized by low or low–normal plasma vitamin E concentrations (7.19–15.68 μmol/L), while vitamin A concentrations were found to be normal or high (1.26–2.68 μmol/L). Vitamin E supplementation resulted in correction or significant elevation of plasma vitamin E concentration in all patients. We observed reduced aggression, self-injury, irritability, hyperactivity, attention deficit, repetitive behavior, sleep disturbance, skin photosensitivity and/or eczema in 3/6 patients, with notable individual variability. Clinical response to therapy was associated with a low baseline 7-DHC + 8-DHC/cholesterol ratio (0.2–0.4). We suggest that determination of vitamin E status is important in SLOS patients. Supplementation of vitamin E should be considered and might be beneficial.
Age and Sex Specific Trends in Incidence of Juvenile Idiopathic Arthritis in Danish Birth Cohorts from 1992 to 2002: A Nationwide Register Linkage Study

This study reports age- and sex-specific incidence rates of juvenile idiopathic arthritis (JIA) in complete Danish birth cohorts from 1992 through 2002. Data were obtained from the Danish registries. All persons born in Denmark, from 1992–2002, were followed from birth and until either the date of first diagnosis recording, death, emigration, 16th birthday or administrative censoring (17 May 2017), whichever came first. The number of incident JIA cases and its incidence rate (per 100,000 person-years) were calculated within sex and age group for each of the birth cohorts. A multiplicative Poisson regression model was used to analyze the variation in the incidence rates by age and year of birth for boys and girls separately. The overall incidence of JIA was 24.1 (23.6–24.5) per 100,000 person-years. The rate per 100,000 person-years was higher among girls (29.9 (29.2–30.7)) than among boys (18.5 (18.0–19.1)). There were no evident peaks for any age group at diagnosis for boys but for girls two small peaks appeared at ages 0–5 years and 12–15 years. This study showed that the incidence rates of JIA in Denmark were higher for girls than for boys and remained stable over the observed period for both sexes.
Genetics of Diabetic Retinopathy, a Leading Cause of Irreversible Blindness in the Industrialized World

Diabetic retinopathy (DR) is a chronic complication of diabetes and a leading cause of blindness in the industrialized world. Traditional risk factors, such as glycemic control and duration of diabetes, are unable to explain why some individuals remain protected while others progress to a more severe form of the disease. Differences are also observed in DR heritability as well as the response to anti-vascular endothelial growth factor (VEGF) treatment. This review discusses various aspects of genetics in DR to shed light on DR pathogenesis and treatment. First, we discuss the global burden of DR followed by a discussion on disease pathogenesis as well as the role genetics plays in the prevalence and progression of DR. Subsequently, we provide a review of studies related to DR’s genetic contribution, such as candidate gene studies, linkage studies, and genome-wide association studies (GWAS) as well as other clinical and meta-analysis studies that have identified putative candidate genes. With the advent of newer cutting-edge technologies, identifying the genetic components in DR has played an important role in understanding DR incidence, progression, and response to treatment, thereby developing newer therapeutic targets and therapies.
The Simple Biology of Flipons and Condensates Enhances the Evolution of Complexity

The classical genetic code maps nucleotide triplets to amino acids. The associated sequence composition is complex, representing many elaborations during evolution of form and function. Other genomic elements code for the expression and processing of RNA transcripts. However, over 50% of the human genome consists of widely dispersed repetitive sequences. Among these are simple sequence repeats (SSRs), representing a class of flipons, that under physiological conditions, form alternative nucleic acid conformations such as Z-DNA, G4 quartets, I-motifs, and triplexes. Proteins that bind in a structure-specific manner enable the seeding of condensates with the potential to regulate a wide range of biological processes. SSRs also encode the low complexity peptide repeats to patch condensates together, increasing the number of combinations possible. In situations where SSRs are transcribed, SSR-specific, single-stranded binding proteins may further impact condensate formation. Jointly, flipons and patches speed evolution by enhancing the functionality of condensates. Here, the focus is on the selection of SSR flipons and peptide patches that solve for survival under a wide range of environmental contexts, generating complexity with simple parts.
Liquid Biopsy for Disease Monitoring in Non-Small Cell Lung Cancer: The Link between Biology and the Clinic

Introduction: Cell-free DNA (cfDNA) analysis offers a non-invasive method to identify sensitising and resistance mutations in advanced Non-Small Cell Lung Cancer (NSCLC) patients. Next-generation sequencing (NGS) of circulating free DNA (cfDNA) is a valuable tool for mutations detection and disease′s clonal monitoring. Material and methods: An amplicon-based targeted gene NGS panel was used to analyse 101 plasma samples of advanced non-small cell lung cancer (NSCLC) patients with known oncogenic mutations, mostly EGFR mutations, serially collected at different clinically relevant time points of the disease. Results: The variant allelic frequency (VAF) monitoring in consecutive plasma samples demonstrated different molecular response and progression patterns. The decrease in or the clearance of the mutant alleles was associated with response and the increase in or the emergence of novel alterations with progression. At the best response, the median VAF was 0% (0.0% to 3.62%), lower than that at baseline, with a median of 0.53% (0.0% to 9.9%) (p = 0.004). At progression, the VAF was significantly higher (median 4.67; range: 0.0–36.9%) than that observed at the best response (p = 0.001) and baseline (p = 0.006). These variations anticipated radiographic changes in most cases, with a median time of 0.86 months. Overall, the VAF evolution of different oncogenic mutations predicts clinical outcomes. Conclusion: The targeted NGS of circulating tumour DNA (ctDNA) has clinical utility to monitor treatment response in patients with advanced lung adenocarcinoma.