Miracle-dz/UniFAR-FTUs huggingface dataset:
cellHarmony: Cell-level matching and comparison of single-cell transcriptomes

To understand the molecular etiology of human disease, precision analyses of individual cell populations and their molecular alternations are desperately needed. Single-cell genomics represents an ideal platform to enable to the quantification of specific cell types, the discovery of transcriptional cell states and underlying molecular differences that can be compared across specimens. We present a new computational approach called cellHarmony, to consistently classify individual cells from a query (i.e., mutant) against a reference (i.e., wild-type) dataset to discover crucial differences in discrete or transitional cell-populations. CellHarmony performs a supervised classification of new scRNA-Seq data against a priori delineated cell populations and associated genes to visualize the combined datasets and derive consistent annotations in a platform-independent manner. Such analyses enable the comparison of results from distinct single-cell platforms against well-curated references or against orthogonal profiles from a related experiment. In addition, cellHarmony produces differential expression results from non-confounded aligned cell populations to explore the impact of chemical, genetic, environmental and temporal perturbations. This approach works seamlessly with the unsupervised classification and annotation of cell-states using the software ICGS in AltAnalyze. Using cellHarmony, we demonstrate novel molecular and population insights in scRNA-Seq data from models of Acute Myeloid Leukemia, across technological platforms and using references derived from the Human Cell Atlas project.
Emplοying body-fixed sensors and machine learning to predict physical activity in military personnel

Introduction This was a feasibility pilot study aiming to develop and validate an activity recognition system based on a custom-made body-fixed sensor and driven by an algorithm for recognising basic kinetic movements in military personnel. The findings of this study are deemed essential in informing our development process and contributing to our ultimate aim which is to develop a low-cost and easy-to-use body-fixed sensor for military applications. Methods Fifty military participants performed a series of trials involving walking, running and jumping under laboratory conditions in order to determine the optimal, among five machine learning (ML), classifiers. Thereafter, the accuracy of the classifier was tested towards the prediction of these movements (15 183 measurements) and in relation to participants’ gender and fitness level. Results Random forest classifier showed the highest training and validation accuracy (98.5% and 92.9%, respectively) and classified participants with differences in type of activity, gender and fitness level with an accuracy level of 83.6%, 70.0% and 62.2%, respectively. Conclusions The study showed that accurate prediction of various dynamic activities can be achieved with high sensitivity using a low-cost easy-to-use sensor and a specific ML model. While this technique is in a development stage, our findings demonstrate that our body-fixed sensor prototype alongside a fully trained validated algorithm can strategically support military operations and offer valuable information to commanders controlling operations remotely. Further stages of our developments include the validation of our refined technique on a larger range of military activities and groups by combining activity data with physiological variables to predict phenomena relating to the onset of fatigue and performance decline.
Molecular detection of Borrelia anserina in Argas persicus (Acari: Argasidae) ticks collected from Lorestan province, west of Iran

Borrelia anserina is the agent of avian borreliosis, an acute septicemic disease of a variety of avian species in tropical and warm temperate regions of the world. Avian borreliosis is one of the most widespread poultry diseases in Iran, and is of great economic importance. The present study was designed to detect B. anserina in Argas persicus ticks. Specimens were collected from the cracks of aviary in Lorestan province of Iran. Then the salivary glands, ovaries and uterus of ticks were dissected to detect B. anserina within the specific organ using molecular methods. DNA was extracted by Phenol-chloroform method and then a fragment of flagellin gene ( fla B) of B. anserina was amplified by polymerase chain reaction. According to our results, the fla B target fragment was detected in Argas persicus ticks collected from Lorestan province. It seems that B. anserina is widely distributed in A. persicus vector ticks. Based on the result, B. anserina strain of Iran is similar to B. anserina fla B sequences reported from other parts the world.
Can the Consumption of Ultra-Processed Food Be Associated with Anthropometric Indicators of Obesity and Blood Pressure in Children 7 to 10 Years Old?

The consumption of ultra-processed foods plays an important role in the development of obesity and hypertension. The present study investigated the association between consumption of food according to the degree of processing and anthropometric indicators of obesity and blood pressure in children. This is a cross-sectional study with 164 children aged 7–10 years. The body mass index (BMI) for age, waist circumference (WC), and waist-to-height ratio (WHtR) was evaluated. Food consumption was analyzed by three 24-h dietary recalls, and classified as: G1—unprocessed or minimally processed; G2—culinary ingredients and processed food; and G3—ultra-processed food. Linear regression analyses were used to investigate the associations among variables. The average energy consumption was 1762.76 kcal/day, split into 45.42%, 10.88%, and 43.70%, provided by G1, G2, and G3, respectively. Adjusted linear regression analyses identified that the caloric contribution of G1 was inversely associated with DBP, showing that for each 10% increase in the energy intake of minimally processed foods, there was a reduction of 0.96 mmHg in the DBP (β:−0.10; 95% CI:−0.19 to −0.01; r2 = 0.20). There was no association between the caloric contribution of food groups and BMI, WC, WHtR, and SBP. Increasing consumption of G1 could be a strategy for the prevention and treatment of hypertension in schoolchildren.
Uvaol Improves the Functioning of Fibroblasts and Endothelial Cells and Accelerates the Healing of Cutaneous Wounds in Mice

Uvaol is a natural pentacyclic triterpene that is widely found in olives and virgin olive oil, exerting various pharmacological properties. However, information remains limited about how it affects fibroblasts and endothelial cells in events associated with wound healing. Here, we report the effect of uvaol in the in vitro and in vivo healing process. We show the positive effects of uvaol on migration of fibroblasts and endothelial cells in the scratch assay. Protein synthesis of fibronectin and laminin (but not collagen type I) was improved in uvaol-treated fibroblasts. In comparison, tube formation by endothelial cells was enhanced after uvaol treatment. Mechanistically, the effects of uvaol on cell migration involved the PKA and p38-MAPK signaling pathway in endothelial cells but not in fibroblasts. Thus, the uvaol-induced migratory response was dependent on the PKA pathway. Finally, topical treatment with uvaol caused wounds to close faster than in the control treatment using experimental cutaneous wounds model in mice. In conclusion, uvaol positively affects the behavior of fibroblasts and endothelial cells, potentially promoting cutaneous healing.
Spontaneous Coronary Artery Dissection

Supplemental Digital Content is available in the text. Background: Spontaneous coronary artery dissection (SCAD) occurs when an epicardial coronary artery is narrowed or occluded by an intramural hematoma. SCAD mainly affects women and is associated with pregnancy and systemic arteriopathies, particularly fibromuscular dysplasia. Variants in several genes, such as those causing connective tissue disorders, have been implicated; however, the genetic architecture is poorly understood. Here, we aim to better understand the diagnostic yield of rare variant genetic testing among a cohort of SCAD survivors and to identify genes or gene sets that have a significant enrichment of rare variants. Methods: We sequenced a cohort of 384 SCAD survivors from the United Kingdom, alongside 13 722 UK Biobank controls and a validation cohort of 92 SCAD survivors. We performed a research diagnostic screen for pathogenic variants and exome-wide and gene-set rare variant collapsing analyses. Results: The majority of patients within both cohorts are female, 29% of the study cohort and 14% validation cohort have a remote arteriopathy. Four cases across the 2 cohorts had a diagnosed connective tissue disorder. We identified pathogenic or likely pathogenic variants in 7 genes (PKD1, COL3A1, SMAD3, TGFB2, LOX, MYLK, and YY1AP1) in 14/384 cases in the study cohort and in 1/92 cases in the validation cohort. In our rare variant collapsing analysis, PKD1 was the highest-ranked gene, and several functionally plausible genes were enriched for rare variants, although no gene achieved study-wide statistical significance. Gene-set enrichment analysis suggested a role for additional genes involved in renal function. Conclusions: By studying the largest sequenced cohort of SCAD survivors, we demonstrate that, based on current knowledge, only a small proportion have a pathogenic variant that could explain their disease. Our findings strengthen the overlap between SCAD and renal and connective tissue disorders, and we highlight several new genes for future validation.
Comparative effectiveness clinical trial of magnetic seizure therapy and electroconvulsive therapy in major depressive disorder.

BACKGROUND Magnetic seizure therapy (MST) has demonstrated fewer cognitive side effects than electroconvulsive therapy (ECT) in antidepressant efficacy trials. However, there are no effectiveness trials examining antidepressant efficacy and cognitive side effects against ECT. The aims of this study were to evaluate the comparative effectiveness of MST vs ECT in major depressive disorder (MDD), and compare the cognitive side effects of MST and ECT. METHODS In this open-label study, patients were assigned to either ECT or high-dose MST twice a week for 5 sessions based on the clinician's and the patient's decision-making. Efficacy was primarily assessed by the Hamilton Depression Rating Scale-21 (HAMD-21); cognitive side effects were assessed by time to reorientation (TRO) and cognitive battery. RESULTS Sixty patients were enrolled. Efficacy was similar between those assigned to MST (n = 30) and ECT (n = 30). Post-treatment HAMD-21 mean scores were 12.33 after MST, 12.80 after bitemporal (BT) ECT (n = 15), and 27.93 after right unilateral (RUL) ECT (n = 15). Magnetic seizure therapy had a significantly faster TRO of 1.8 minutes (standard deviation [SD] = 0.37) compared with ECT (RUL: 18.9 minutes [SD = 8.25]; BT: 50.2 minutes [SD = 5.89]) and had fewer cognitive side effects. CONCLUSIONS Magnetic seizure therapy was effective for the treatment of MDD in real-world clinical care, with fewer cognitive side effects than ECT. Future studies are warranted to replicate these findings.
Loss of Parkin Results in Altered Muscle Stem Cell Differentiation during Regeneration

The high capacity of the skeletal muscle to regenerate is due to the presence of muscle stem cells (MuSCs, or satellite cells). The E3 ubiquitin ligase Parkin is a key regulator of mitophagy and is recruited to mitochondria during differentiation of mouse myoblast cell line. However, the function of mitophagy during regeneration has not been investigated in vivo. Here, we have utilized Parkin deficient (Parkin–/–) mice to investigate the role of Parkin in skeletal muscle regeneration. We found a persistent deficiency in skeletal muscle regeneration in Parkin–/– mice after cardiotoxin (CTX) injury with increased area of fibrosis and decreased cross-sectional area (CSA) of myofibres post-injury. There was also a significant modulation of MuSCs differentiation and mitophagic markers, with altered mitochondrial proteins during skeletal muscle regeneration in Parkin–/– mice. Our data suggest that Parkin-mediated mitophagy plays a key role in skeletal muscle regeneration and is necessary for MuSCs differentiation.
Increased Psychological Distress during COVID-19 and Quarantine in Ireland: A National Survey

Background: The emergence of the coronavirus pneumonia (COVID-19) resulted in a global pandemic. The psychological impact of an epidemic is multifaceted and acute, with long-term consequences. Methods: A cross-sectional online survey-based design was employed, assessing the psychological impact of COVID-19 on members of the Irish public during the quarantine period of COVID-19 in Ireland. Participants were invited to complete the Depression, Anxiety, and Stress Scale-21 (DASS-21) retrospectively (prior to quarantine) and during the quarantine period, as well as measures of illness perceptions, well-being, and a bespoke measure (the Effects of COVID Questionnaire, ECQ), which assessed perceptions of COVID-related stresses associated with personal concerns, caring for children, caring for aging parents, as well as gratitude. Results: A total of n = 1620 entered the survey platform, with a total of n = 847 surveys completed by members of the Irish public. Entry into COVID-19 quarantine was associated with significant increases in clinically significant symptoms of depression, stress, and anxiety. The ECQ reliably assessed a range of COVID-19-related stresses and had large and significant correlations with the DASS-21. Conclusions: The COVID-19 quarantine was associated with stresses and significant increases in symptoms of depression, anxiety, and stress in a national Irish cohort. The public require increased access to mental health services to meet this increase in COVID-19-related psychological distress.
Multiplexed tat-Targeting CRISPR-Cas9 Protects T Cells from Acute HIV-1 Infection with Inhibition of Viral Escape

HIV-1 cure strategy by means of proviral knock-out using CRISPR-Cas9 has been hampered by the emergence of viral resistance against the targeting guide RNA (gRNA). Here, we proposed multiple, concentrated gRNA attacks against HIV-1 regulatory genes to block viral escape. The T cell line were transduced with single and multiple gRNAs targeting HIV-1 tat and rev using lentiviral-based CRISPR-Cas9, followed by replicative HIV-1NL4-3 challenge in vitro. Viral p24 rebound was observed for almost all gRNAs, but multiplexing three tat-targeting gRNAs maintained p24 suppression and cell viability, indicating the inhibition of viral escape. Multiplexed tat gRNAs inhibited acute viral replication in the 2nd round of infection, abolished cell-associated transmission to unprotected T cells, and maintained protection through 45 days, post-infection (dpi) after a higher dose of HIV-1 infection. Finally, we describe here for the first time the assembly of all-in-one lentiviral vectors containing three and six gRNAs targeting tat and rev. A single-vector tat-targeting construct shows non-inferiority to the tat-targeting multi-vector in low-dose HIV-1 infection. We conclude that Cas9-induced, DNA repair-mediated mutations in tat are sufficiently deleterious and deplete HIV-1 fitness, and multiplexed disruption of tat further limits the possibility of an escape mutant arising, thus elevating the potential of CRISPR-Cas9 to achieve a long-term HIV-1 cure.
Feature extraction of EEG signals based on functional data analysis and its application to recognition of driver fatigue state

Objective: Our objective is to study how to obtain features which can reflect the continuity and internal dynamic changes of electroencephalography (EEG) signals and study an effective method for fatigued driving state recognition based on the obtained features. Approach: A method of EEG signalfeature extraction based on functional data analysis is proposed. Combined with kernel principal component analysis method, the obtained features are applied to the recognition of driver fatigue state, and a corresponding recognition model of fatigued driving state is constructed. Main results: The recognition model is tested on the real collected driver fatigue EEG signals by selecting a suitable classifier. The test results show that the proposed driver fatigue state recognition method has good recognition effect, especially on the classifier based on decision tree, with an average accuracy of 99.50%. Significance: The extracted features well reflect the continuityand internal dynamic changes of the EEG signals, and it is of great significance and application value to study an effective method of fatigued driver state recognition based on the features.
Genomic Diversity in Sporadic Breast Cancer in a Latin American Population

Among Latin American women, breast cancer incidences vary across populations. Uruguay and Argentina have the highest rates in South America, which are mainly attributed to strong, genetic European contributions. Most genetic variants associated with breast cancer were described in European populations. However, the vast majority of genetic contributors to breast cancer risk remain unknown. Here, we report the results of a candidate gene association study of sporadic breast cancer in 176 cases and 183 controls in the Uruguayan population. We analyzed 141 variants from 98 loci that have been associated with overall breast cancer risk in European populations. We found weak evidence for the association of risk variants rs294174 (ESR1), rs16886165 (MAP3K1), rs2214681 (CNTNAP2), rs4237855 (VDR), rs9594579 (RANKL), rs8183919 (PTGIS), rs2981582 (FGFR2), and rs1799950 (BRCA1) with sporadic breast cancer. These results provide useful insight into the genetic susceptibility to sporadic breast cancer in the Uruguayan population and support the use of genetic risk scores for individualized screening and prevention.
Prediction of Chromatographic Separation of Eugenolby the Fast Fourier Transform Method

The switching time to change from adsorption to desorption in liquid chromatography, which is the time at which the concentration of the effluent reaches the breakthrough value, is important in the operation, scale-up, and optimisation of chromatographic separation. The switching time can be estimated by computer simulation of the chromatographic adsorption column. In this paper, the theoretical simulation of the chromatographic column of Chen and Hsu (1987) based on the Fast Fourier Transform (FFT) method originally proposed for chromatographic systems by Hsu using estimated axial diffusivity, film mass transfer coefficient and pore diffusivity obtained from analytical scale separation, is compared with experimental data of chromatographic separation of eugenol. The use of FIT over more sophisticated techniques such as finite difference or orthogonal collocation methods was dictated by the simpler computation and the availability of better inverting techniques. The model was validated by experimental data on chromatographic separation of eugenol on IBondapak CIS analytical column, mobile phase methanol-water (80:20), and flow rate 0.5 ml/min, at different solution concentration injection at equilibrium condition. Physical property data required for validation such as equilibrium adsorption isotherm data was determined experimentally, and mass transfer data was calculated from normal correlations and from analytical scale separation. The simulation agreed with experimental data at a Peclet number of 6000, a bed length parameter of 3.0 and number of samples 90.
Surveillance of Zoonotic Parasites in Animals Involved in Animal-Assisted Interventions (AAIs)

Animal-assisted interventions (AAIs) are based on the establishment of a therapeutic relationship between animals and beneficiaries that is certain to provide positive effects, while currently, it reads as if AAIs aim at exposing stakeholders to potential risk of infection. The surveillance of zoonotic pathogens is necessary for guaranteeing common health. This study investigated the presence of potentially zoonotic parasites, including dermatophytes, in animals involved in AAIs. Between 2015 and 2017, 190 animals (equids, dogs, cats, birds, rabbits, rodents, and goats) were investigated. Anamnestic and management data were recorded. Individual faecal samples were analysed using a copromicroscopic procedure. Fur and skin were examined for ectoparasites during clinical examinations, and samples for mycological investigation were collected by brushing. Parasites were described in 60 (31.6%) investigated animals. Thirteen out of the 60 (21.7%) animals harboured potentially zoonotic parasites, mainly recovered in dogs (Ancylostomatidae, Eucoleus aerophilus, Toxocara canis, and Giardia duodenalis) and a cat (G. duodenalis). Nannizzia gypsea and Paraphyton mirabile, potential agents of cutaneous mycosis, were isolated in a dog and a horse, respectively. No ectoparasites were found. AAIs might represent a source of infections either directly or via environmental contamination. Thus, active surveillance is necessary and animal screenings should be planned and scheduled according to the risk of exposure.
Effects of the Dietary Inclusion of Buriti Oil on Lamb Performance, Carcass Traits, Digestibility, Nitrogen Balance, Ingestive Behavior and Blood Metabolites

Simple Summary Dietary fat is important for animals, not only because it supplies essential fatty acids and fat-soluble vitamins, but also because of its high energy content, approximately twice as many calories per gram of carbohydrates. Thus, it induces a caloric increase, in addition to modulating the fatty acid (FA) profile of meat. Vegetable oils inclusion in the diet of lambs improves the lipid quality of meat. Among them, buriti oil (Mauritia flexuosa L.F.) is an example that stands out; it can represent an important alternative to meet the energy demands of lambs, particularly because of its easy availability, especially in the northern and northeast states of Brazil. In addition, as a consequence of the high cost of protein supplements in feed concentrates, unconventional alternatives have been exploited in recent years. Thus, this research proposes the use of a byproduct of the biofuel industry. This study was conducted to enhance our knowledge of interesting opportunities for farmers in terms of lamb meat production. Its use could promote activity in the livestock sector by reducing feed costs and becoming an alternative to producers without easy access to more expensive supplements. Abstract Buriti (Mauritia flexuosa L.) oil (BO) is a byproduct that can be incorporated into the diet of lambs, thus increasing the energy density. The study aimed to evaluate the optimum BO inclusion level in lamb diets. Sixty-five Santa Ines lambs were distributed in two completely randomized experiments with five treatments each (BO inclusion at 0 (control), 12, 24, 36 and 48 g/kg dry matter (DM) total). The BO supplementation to partially replace ground corn linearly decreased the nutrient intake and digestibility of DM, ether extract and neutral detergent fiber (NDF), N° chews/bolus, DM and NDF rumination or eating efficiencies, the N intake and N balance, carcass weights and yields, and dressing content of lamb carcasses (p < 0.05). The addition of BO responded quadratically to DM eating efficiency and N-fecal and N-urinary excretion (p < 0.05). The linear response plateau (LRP) analysis demonstrated that the levels of 0 and 12 g/kg of BO were similar, and improved intake and digestibility and consequently performance (p < 0.001). There was a linear increase in feed efficiency and shrinkage after chilling with the BO inclusion replacing ground corn. The inclusion of 12 g/kg BO in the total DM of diet is recommended, because it improves feeding intake, digestibility and performance of lambs.