Miracle-dz/UniFAR-FTUs huggingface dataset:
scFed: federated learning for cell type classification with scRNA-seq

Abstract The advent of single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity and complexity in biological tissues. However, the nature of large, sparse scRNA-seq datasets and privacy regulations present challenges for efficient cell identification. Federated learning provides a solution, allowing efficient and private data use. Here, we introduce scFed, a unified federated learning framework that allows for benchmarking of four classification algorithms without violating data privacy, including single-cell-specific and general-purpose classifiers. We evaluated scFed using eight publicly available scRNA-seq datasets with diverse sizes, species and technologies, assessing its performance via intra-dataset and inter-dataset experimental setups. We find that scFed performs well on a variety of datasets with competitive accuracy to centralized models. Though Transformer-based model excels in centralized training, its performance slightly lags behind single-cell-specific model within the scFed framework, coupled with a notable time complexity concern. Our study not only helps select suitable cell identification methods but also highlights federated learning’s potential for privacy-preserving, collaborative biomedical research.
Cigarette Smoking and Atherosclerotic Cardiovascular Disease

The detrimental effects of cigarette smoking on cardiovascular health, particularly atherosclerosis and thrombosis, are well established, and more detailed mechanisms continue to emerge. As the fundamental pathophysiology of the adverse effects of smoking, endothelial dysfunction, inflammation, and thrombosis are considered to be particularly important. Cigarette smoke induces endothelial dysfunction, leading to impaired vascular dilation and hemostasis regulation. Factors contributing to endothelial dysfunction include reduced bioavailability of nitric oxide, increased levels of superoxide anion, and endothelin release. Chronic inflammation of the vascular wall is a central pathogenesis of smoking-induced atherosclerosis. Smoking systemically elevates inflammatory markers and induces the expression of adhesion molecules and cytokines in various tissues. Pattern recognition receptors and damage-associated molecular patterns play crucial roles in the mechanism underlying smoking-induced inflammation. Smoking-induced DNA damage and activation of innate immunity, such as the NLRP3 inflammasome, cyclic GMP–AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway, and Toll-like receptor 9, are shown to amplify inflammatory cytokine expression. Cigarette smoke-induced oxidative stress and inflammation influence platelet adhesion, aggregation, and coagulation via adhesion molecule upregulation. Furthermore, it affects the coagulation cascade and fibrinolysis balance, causing thrombus formation. Matrix metalloproteinases contribute to plaque vulnerability and atherothrombotic events. The impact of smoking on inflammatory cells and adhesion molecules further intensifies the risk of atherothrombosis. Collectively, exposure to cigarette smoke exerts profound effects on endothelial function, inflammation, and thrombosis, contributing to the development and progression of atherosclerosis and atherothrombotic cardiovascular diseases. Understanding these intricate mechanisms highlights the urgent need for smoking cessation to protect cardiovascular health. This comprehensive review investigates the multifaceted mechanisms through which smoking contributes to these life-threatening conditions.
Strengthening of alpha synchronization is a neural correlate of cognitive transfer

Abstract Cognitive training can lead to improvements in both task-specific strategies and general capacities, such as visuo-spatial working memory (VSWM). The latter emerge slowly and linearly throughout training, in contrast to strategy where changes typically occur within the first days of training. Changes in strategy and capacity have not been separated in prior neuroimaging studies. Here, we used a within-participants design with dense temporal sampling to capture the time dynamics of neural mechanisms associated with change in capacity. In four participants, neural activity was recorded with magnetoencephalography on seven occasions over two months of visuo-spatial working memory training. During scanning, the participants performed a trained visuo-spatial working memory task, a transfer task, and a control task. First, we extracted an individual visuo-spatial working memory-load-dependent synchronization network for each participant. Next, we identified linear changes over time in the network, congruent with the temporal dynamics of capacity change. Three out of four participants showed a gradual strengthening of alpha synchronization. Strengthening of the same connections was also found in the transfer task but not in the control task. This suggests that cognitive transfer occurs through slow, gradual strengthening of alpha synchronization between cortical regions that are vital for both the trained task and the transfer task.
Evaluación de la aceptabilidad del pan reducido en sodio en consumidores de la Región Metropolitana de Chile Acceptability assessment of bread reduced sodium in the Metropolitan Region of Chile

Introduction: Due to the disturbing increase in cardiovascular disease, in part associated with the consumption of salt, a pilot program was initiated in 2010 between the Ministry of Health, the Federation of Industrial Bakers and the Chilean Association of supermarkets to gradually reduce the amount of salt in bread. Aim: to evaluate the overall acceptability of salt-reduced bread in a pilot program compared with unmodifi ed bread in bakeries of Santiago. Methodology: A cross-sectional analytical study was performed. Random selection of 5 intervention bakeries and 5 control bakeries. A survey of 175 consumers per group was carried out in order to assess the acceptability of bread in relation to 5 sensory parameters, with a hedonic scale of 5 points. An index of overall acceptability (5-25 points) was developed qualifying as good acceptability a value ≥22 points. Results: Good acceptability was found in all parameters studied. A statistically signifi cant difference was found for the control group in the rating of the fl avor (p =0,01) and global acceptability of bread (p = 0, 02). Multivariate analysis showed better acceptability in persons over 60 years of age (p=0,02) and in control bakeries (p =0,01). Conclusions: Better acceptability was found in some parameters in the control group bread, although the sodium concentration is not the only factor to explain the acceptability.
So how special is special K? A systematic review and meta-analysis of ketamine for PTSD RCTs

ABSTRACT Background: PTSD is a significant mental health problem worldwide. Current evidence-based interventions suffer various limitations. Ketamine is a novel agent that is hoped to be incrementally better than extant interventions. Objective: Several randomized control trials (RCTs) of ketamine interventions for PTSD have now been published. We sought to systematically review and meta-analyse results from these trials to evaluate preliminary evidence for ketamine’s incremental benefit above-and-beyond control interventions in PTSD treatment. Results: Omnibus findings from 52 effect sizes extracted across six studies (n = 221) yielded a small advantage for ketamine over control conditions at reducing PTSD symptoms (g = 0.27, 95% CI = 0.03, 0.51). However, bias-correction estimates attenuated this effect (adjusted g = 0.20, 95%, CI = −0.08, 0.48). Bias estimates indicated smaller studies reported larger effect sizes favouring ketamine. The only consistent timepoint assessed across RCTs was 24-hours post-initial infusion. Effects at 24-hours post-initial infusion suggest ketamine has a small relative advantage over controls (g = 0.35, 95% CI = 0.06, 0.64). Post-hoc analyses at 24-hours post-initial infusion indicated that ketamine was significantly better than passive controls (g = 0.44, 95% CI = 0.03, 0.85), but not active controls (g = 0.24, 95% CI = −0.30, 0.78). Comparisons one-week into intervention suggested no meaningful group differences (g = 0.24, 95% CI = 0.00, 0.48). No significant differences were evident for RCTs that examined effects two-weeks post initial infusion (g = 0.17, 95% CI = −0.10, 0.44). Conclusions: Altogether, ketamine-for-PTSD RCTs reveal a nominal initial therapeutic advantage relative to controls. However, bias and heterogeneity appear problematic. While rapid acting effects were observed, all control agents (including saline) also evidenced rapid acting effects. We argue blind penetration to be a serious concern, and that placebo is the likely mechanism behind reported therapeutic effects.
Preservation of Intrinsically Photosensitive Retinal Ganglion Cells (ipRGCs) in Late Adult Mice: Implications as a Potential Biomarker for Early Onset Ocular Degenerative Diseases

Purpose Intrinsically photosensitive retinal ganglion cells (ipRGCs) play a crucial role in non–image-forming visual functions. Given their significant loss observed in various ocular degenerative diseases at early stages, this study aimed to assess changes in both the morphology and associated behavioral functions of ipRGCs in mice between 6 (mature) and 12 (late adult) months old. The findings contribute to understanding the preservation of ipRGCs in late adults and their potential as a biomarker for early ocular degenerative diseases. Methods Female and male C57BL/6J mice were used to assess the behavioral consequences of aging to mature and old adults, including pupillary light reflex, light aversion, visual acuity, and contrast sensitivity. Immunohistochemistry on retinal wholemounts from these mice was then conducted to evaluate ipRGC dendritic morphology in the ganglion cell layer (GCL) and inner nuclear layer (INL). Results Morphological analysis showed that ipRGC dendritic field complexity was remarkably stable through 12 months old of age. Similarly, the pupillary light reflex, visual acuity, and contrast sensitivity were stable in mature and old adults. Although alterations were observed in ipRGC-independent light aversion distinct from the pupillary light reflex, aged wild-type mice continuously showed enhanced light aversion with dilation. No effect of sex was observed in any tests. Conclusions The preservation of both ipRGC morphology and function highlights the potential of ipRGC-mediated function as a valuable biomarker for ocular diseases characterized by early ipRGC loss. The consistent stability of ipRGCs in mature and old adult mice suggests that detected changes in ipRGC-mediated functions could serve as early indicators or diagnostic tools for early-onset conditions such as Alzheimer's disease, Parkinson's disease, and diabetes, where ipRGC loss has been documented.
The effects of health-related food taxes on the environmental impact of consumer food purchases: secondary analysis of data from a randomised controlled trial in a virtual supermarket

Objective: To measure the effects of health-related food taxes on the environmental impact of consumer food purchases in a virtual supermarket. Design: This is a secondary analysis of data from a randomised controlled trial in which participants were randomly assigned to a control condition with regular food prices (n 152), an experimental condition with a sugar-sweetened beverage (SSB) tax (n 131) or an experimental condition with a nutrient profiling tax based on Nutri-Score (n 112). Participants were instructed to undertake their typical weekly grocery shopping for their households. Primary outcome measures were three environmental impact indicators: greenhouse gas (GHG) emissions, land use and blue water use per household per week. Data were analysed using linear regression analyses. Setting: Three-dimensional virtual supermarket. Participants: Dutch adults (≥ 18 years) who were responsible for grocery shopping in their household (n 395). Results: GHG emissions (–7·6 kg CO2-eq; 95 % CI –12·7, –2·5) and land use (–3·9 m2/year; 95 % CI –7·7, –0·2) were lower for the food purchases of participants in the nutrient profiling tax condition than for those in the control condition. Blue water use was not affected by the nutrient profiling tax. Moreover, the SSB tax had no significant effect on any of the environmental impact indicators. Conclusions: A nutrient profiling tax based on Nutri-Score reduced the environmental impact of consumer food purchases. An SSB tax did not affect the environmental impact in this study.
Survival-related risk score of lung adenocarcinoma identified by weight gene co-expression network analysis

The present study aimed to identify the novel biomarkers and underlying molecular mechanisms of lung adenocarcinoma (LAC) to aid in its diagnosis, prognosis, prediction, disease monitoring and emerging therapies. Data from a total of 498 LAC samples were collected from The Cancer Genome Atlas and divided into two sets by stratified randomization based on pathological Tumor-Node-Metastasis stage. The training set was comprised of 348 samples and the validation set was comprised of 150 samples. A total of 123 samples from the training set for patients who completed follow-up were analyzed by weighted gene co-expression network analysis. A module was identified that contained 113 protein-coding genes that were positively associated with overall survival (OS). A least absolute shrinkage and selection operator (LASSO) Cox regression model was constructed and four survival-associated genes (OPN3, GALNT2, FAM83A and KYNU) were retained. Risk score, calculated by the linear combination of each gene expression multiplied by the LASSO coefficient, could successfully discriminate between patients with LAC exhibiting low and high OS time in both sets. The results from the present study indicate that this risk score may contribute to potential diagnostic and therapeutic strategies for LAC management.
Climate Change Adaptation for Southern California Groundwater Managers: A Case Study of the Six Basins Aquifer

Groundwater has been very important to the economic development of Southern California, and will continue to be a crucial resource in the 21st century. However, Climate Change threatens to disrupt many of the physical and economic processes that control the flow of water in and out of aquifers. One groundwater manager, the Six Basins Watermaster in eastern Los Angeles and western San Bernardino Counties, has developed a long-term planning document called the Strategic Plan that mostly fails to address the implications of Climate Change, especially for local water supplies. This thesis presents an in-depth analysis of the Six Basin Watermaster’s Strategic Plan as a case-study of how groundwater managers can improve their planning assumptions to better prepare for Climate Change. It begins with a brief history of how Southern California’s environment influenced the development of the institutions that manage the Six Basins’ groundwater, then provides a physical description of the aquifer itself. The current scientific literature on Climate Change’s expected impacts on California water supplies are summarized, and the implications of these impacts for basin management are highlighted. The Strategic Plan’s projects are evaluated and critiqued in light of these insights, including a need for the Strategic Plan to: explicitly consider Climate Change in its planning assumptions, use decisionmaking frameworks that account for uncertainty, and prepare for more frequent droughts and floods in the future. Climate Change will have important effects on how Southern California’s groundwater is managed, and the Six Basins Strategic Plan should be revised to better account for these impacts.
A putative hepatitis B virus sequence motif associated with hepatocellular carcinoma in South African adults

Aim: Chronic hepatitis B virus (HBV) infection is a major risk factor for hepatocellular carcinoma (HCC) particularly in African populations, in whom malignancy frequently presents at an advanced stage with poor outcomes. We derived HBV whole genome sequences (WGS) from individuals with HCC and compared them to sequences from individuals without HCC. Methods: We identified adults with HBV infection, with and without complicating HCC, in Cape Town, South Africa and utilized pan-genotypic probe-based enrichment followed by Illumina sequencing to derive HBV WGS. Results: Compared to the non-HCC group, HCC patients were more likely to be male (p < 0.0001), older (p = 0.01), HIV-negative (p = 0.006), and to have higher HBV viral loads (p < 0.0001). Among 19 HCC and 12 non-HCC patients, genotype A dominated (74%), of which 96% were subtype A1. PreS2 deletions (delta 38-55) were enriched in HBV sequences from HCC patients (n = 7). The sequence motif most strongly associated with HCC comprised either deletion or polymorphism at site T53 in PreS2 (collectively coined non-T53) together with a basal core promoter (BCP) mutation G1764A (AUROC 0.79). Conclusions: In this setting, HBV sequence polymorphisms and deletions are associated with HCC, and non-T53 + G1764A represents a putative signature motif for HCC. Additional investigations are needed to disaggregate the impact of age, sex and HIV status, to ascertain the extent to which viral polymorphisms contribute to oncogenesis, and to determine whether HBV sequence is a useful biomarker for risk stratification.
Shifting Paradigms and Arising Concerns in Severe Hemophilia A Treatment

Abstract The management of hemophilia A has undergone a remarkable revolution, in line with technological advancement. In the recent past, the primary concern associated with Factor VIII (FVIII) concentrates was the risk of infections, which is now almost resolved by advanced blood screening and viral inactivation methods. Improving patients' compliance with prophylaxis has become a key focus, as it can lead to improved health outcomes and reduced health care costs in the long term. Recent bioengineering research is directed toward prolonging the recombinant FVIII (rFVIII) coagulant activity and synthesising higher FVIII yields. As an outcome, B-domain deleted, polyethylene glycolated, single-chain, Fc-fused rFVIII, and rFVIIIFc-von Willebrand Factor-XTEN are available for patients. Moreover, emicizumab, a bispecific antibody, is commercially available, whereas fitusiran and tissue factor pathway inhibitor are in clinical trial stages as alternative strategies for patients with inhibitors. With these advancements, noninfectious complications, such as inhibitor development, allergic reactions, and thrombosis, are emerging concerns requiring careful management. In addition, the recent approval of gene therapy is a major milestone toward a permanent cure for hemophilia A. The vast array of treatment options at our disposal today empowers patients and providers alike, to tailor therapeutic regimens to the unique needs of each individual. Despite significant progress in modern treatment options, these highly effective therapies are markedly more expensive than conventional replacement therapy, limiting their access for patients in developing countries.
Predicting Mobility of Cadmium (Cd) and Lead (Pb) in Contaminated Soil through a Mathematical Model

Indiscriminate discharge of industrial effluent particularly pharmaceutical effluent on agricultural soils poses serious health risk to plants, animals and ultimately humans. This study was carried out to predict the mobility of two of the most lethal soil pollutants (Cadmium and Lead). As such, the concentrations of Cadmium and Lead in soil at the initial point of effluent disposal and at subsequent points 4m, 8m, 12m, 16m and 20m away from the point source were determined. A simplified version of transport equation was used to simulate the mobility of Cadmium and Lead in the soil using polymath professional version 6.1. The simulated result showed a good level of agreement with the experimental data with correlation coefficients of 0.92 and 0.96 for Pb and 0.89 and 0.97 for Cd mobility respectively. Thus the model can be considered as a good representation of the phenomenon of mobility of heavy metals in the soil.
The effects of a progressive scaffolding approach on middle school students'computational thinking skills and self-efficacy

Computational thinking (CT) is considered a necessary skill for the 21st century. Researchers have increasingly focused on how to effectively enhance students’ CT in programming courses. This study proposes a progressive scaffolding approach with flowcharts and visual programming codes applied to a visual programming course based on an open-source hardware platform to improve CT skills and self-efficacy in middle school students. Forty-five middle school students in grades 7 and 8 participated in this study. Both quantitative and qualitative data were collected by using CT tests, scales, and semi-structured interviews. A repeated measures analysis of variance (ANOVA) examined differences in CT skills and self-efficacy on the pre-test, mid-test, and post-test. The results indicated that the progressive scaffolding approach significantly improved middle school students’ CT skills and self-efficacy. These results reveal the effectiveness of the progressive scaffolding approach in improving the computational thinking of middle school students in a visual programming course with an open-source hardware platform, which helps to extend the design of progressive scaffolding.
Once Upon a Time there was an Ozobot: Storytelling with Educational Robots

This paper shows a way to introduce computational thinking in early childhood teaching based on scientific results within Neurodidactics. This approach offers children to explore and develop their creativity. Aiming to raise the children's interest in STEAM and to prevent prejudices in this field, the educational Robots, Ozobots, can be used in elementary and primary school to tell fairy tales. In order to connect basic computer science concepts by means of Storytelling, a workshop for very young researchers was designed and presented.
CD14 Blockade Does Not Improve Outcomes of Deep Vein Thrombosis Following Inferior Vena Cava Stenosis in Mice

Background Neutrophil-mediated persistent inflammation and neutrophil extracellular trap formation (NETosis) promote deep vein thrombosis (DVT). CD14, a co-receptor for toll-like receptor 4 (TLR4), is actively synthesized by neutrophils, and the CD14/TLR4 signaling pathway has been implicated in proinflammatory cytokine overproduction and several aspects of thromboinflammation. The role of CD14 in the pathogenesis of DVT remains unclear. Objective To determine whether CD14 blockade improves DVT outcomes. Methods Bulk RNA sequencing and proteomic analyses were performed using isolated neutrophils following inferior vena cava (IVC) stenosis in mice. DVT outcomes (IVC thrombus weight and length, thrombosis incidence, neutrophil recruitment, and NETosis) were evaluated following IVC stenosis in mice treated with a specific anti-CD14 antibody, 4C1, or control antibody. Results Mice with IVC stenosis exhibited increased plasma levels of granulocyte colony-stimulating factor (G-CSF) along with a higher neutrophil-to-lymphocyte ratio and increased plasma levels of cell-free DNA, elastase, and myeloperoxidase. Quantitative measurement of total neutrophil mRNA and protein expression revealed distinct profiles in mice with IVC stenosis compared to mice with sham surgery. Neutrophils of mice with IVC stenosis exhibited increased inflammatory transcriptional and proteomic responses, along with increased expression of CD14. Treatment with a specific anti-CD14 antibody, 4C1, did not result in any significant changes in the IVC thrombus weight, thrombosis incidence, or neutrophil recruitment to the thrombus. Conclusion The results of the current study are important for understanding the role of CD14 in the regulation of DVT and suggest that CD14 lacks an essential role in the pathogenesis of DVT following IVC stenosis.