Miracle-dz/UniFAR-FTUs huggingface dataset:
Analyzing biomarker discovery: Estimating the reproducibility of biomarker sets

Many researchers try to understand a biological condition by identifying biomarkers. This is typically done using univariate hypothesis testing over a labeled dataset, declaring a feature to be a biomarker if there is a significant statistical difference between its values for the subjects with different outcomes. However, such sets of proposed biomarkers are often not reproducible – subsequent studies often fail to identify the same sets. Indeed, there is often a very small overlap between the biomarkers proposed in pairs of related studies that explore the same phenotypes over the same distribution of subjects. This paper first defines the Reproducibility Score for a labeled dataset as a measure (taking values between 0 and 1) of the reproducibility of the results produced by an arbitrary fixed biomarker discovery process for a given distribution of subjects. We then provide ways to reliably estimate this score by defining algorithms that produce an over-bound and an under-bound for this score for a given dataset and biomarker discovery process, for the case of univariate hypothesis testing on dichotomous groups. We confirm that these approximations are meaningful by providing empirical results on a large number of datasets and show that these predictions match known reproducibility results. We have also created a publicly available website, hosted at https://biomarker.shinyapps. io/BiomarkerReprod/, that produces these Reproducibility Score approximations for any given dataset (with continuous or discrete features and binary class labels).
Large-scale field phenotyping using backpack LiDAR and GUI-based CropQuant-3D to measure structural responses to different nitrogen treatments in wheat

Plant phenomics is widely recognised as a key area to bridge the gap between traits of agricultural importance and genomic information. A wide range of field-based phenotyping solutions have been developed, from aerial-based to ground-based fixed gantry platforms and handheld devices. Nevertheless, several disadvantages of these current systems have been identified by the research community concerning mobility, affordability, throughput, accuracy, scalability, as well as the ability to analyse big data collected. Here, we present a novel phenotyping solution that combines a commercial backpack LiDAR device and our graphical user interface (GUI) based software called CropQuant-3D, which has been applied to phenotyping of wheat and associated 3D trait analysis. To our knowledge, this is the first use of backpack LiDAR for field-based plant research, which can acquire millions of 3D points to represent spatial features of crops. A key feature of the innovation is the GUI software that can extract plot-based traits from large, complex point clouds with limited computing time and power. We describe how we combined backpack LiDAR and CropQuant-3D to accurately quantify crop height and complex 3D traits such as variation in canopy structure, which was not possible to measure through other approaches. Also, we demonstrate the methodological advance and biological relevance of our work in a case study that examines the response of wheat varieties to three different levels of nitrogen fertilisation in field experiments. The results indicate that the combined solution can differentiate significant genotype and treatment effects on key morphological traits, with strong correlations with conventional manual measurements. Hence, we believe that the combined solution presented here could consistently quantify key traits at a larger scale and more quickly than heretofore possible, indicating the system could be used as a reliable research tool in large-scale and multi-location field phenotyping for crop research and breeding activities. We exhibit the system’s capability in addressing challenges in mobility, throughput, and scalability, contributing to the resolution of the phenotyping bottleneck. Furthermore, with the fast maturity of LiDAR technologies, technical advances in image analysis, and open software solutions, it is likely that the solution presented here has the potential for further development in accuracy and affordability, helping us fully exploit available genomic resources.
Preface

When you think about thinking, what images come to mind? Perhaps Rodin’s statueThe Thinker, a genius like Einstein, or an old oil painting like that of the philosopher Kierkegaard, bent in concentration over his candlelit desk. In the popular imagination, thinking is almost always conceived of as a solitary pursuit, an act of deep engagement with one’s own thoughts. But if you think about, this is weird. Today, we might in fact say it is WEIRD: a strange quirk of Western, educated, industrialised, rich and democratic (WEIRD) societies (Henrich et al., 2010). In many other parts of the world and times in history, reasoning has widely been assumed to have been much more socially embedded. Confucius, for instance, described himself as ‘a transmitter, not a maker, believing in and loving the ancients’. He saw his task as preserving the accumulated wisdom of the past, not making a great, new original contribution. Even naming the school he figureheads ‘Confucianism’ is misleading since in China it has never been known by an individual’s name but as Rujia, or the school of the ru (a scholar or learned man). ‘Confucianism’was a 16th century Jesuit missionary coinage, the work of the proto-WEIRDS. Indian philosophy is also characterised by adherence to schools rooted in deep traditions rather than in individuals. For example, the 8th-9th century thinker Śaṅkara (or Śaṅkarācārya) is indubitably a foundational figure in Advaita Vedanta, but its adherents trace its roots much further back than this and grant no individual the status of a founder. To them it would perhaps be like insisting on referring to transcendental idealism rather than Kantianism on the grounds that Kant’s philosophy built on many before him and so should not bear his name alone. In oral traditions, the role of the individual is even less important. Usually no one has any idea who, if anyone, came up with the core ideas that comprise their philosophies. In any case, what matters is that generations have found them to be true.
Epigenomics in Hurthle Cell Neoplasms: Filling in the Gaps Towards Clinical Application

It has been widely described that cancer genomes have frequent alterations to the epigenome, including epigenetic silencing of various tumor suppressor genes with functions in almost all cancer-relevant signalling pathways, such as apoptosis, cell proliferation, cell migration and DNA repair. Epigenetic alterations comprise DNA methylation, histone modification, and microRNAs dysregulated expression and they play a significant role in the differentiation and proliferation properties of TC. In this review, our group assessed the published evidence on the tumorigenic role of epigenomics in Hurthle cell neoplasms (HCN), highlighting the yet limited, heteregeneous and non-validated data preventing its current use in clinical practice, despite the well developed assessment techniques available. The identified evidence gaps call for a joint endeavour by the medical community towards a deeper and more systematic study of HCN, aiming at defining epigenetic markers in early diagnose, allowing for accurate stratification of maligancy and disease risk and for effective systemic treatment.
Single Cell RNA-Seq Analysis Identifies Differentially Expressed Genes of Treg Cell in Early Treatment-Naive Rheumatoid Arthritis By Arsenic Trioxide

Objective: Early treatment-naïve rheumatoid arthritis (RA) has defective regulatory T (Treg) cells and increased inflammation response. In this study, we aim to illustrate the regulation of Treg cells in pathogenesis of early rheumatoid arthritis by arsenic trioxide (As2O3). Methods: We studied the effects of As2O3 on gene expression in early treatment-naïve RA Treg cells with single cell RNA-seq (scRNA-seq). Treg cells were sorted from peripheral blood mononuclear cells (PBMCs) and purified by fluorescence-activated cell sorting (FACS) and cultured with or without As2O3 (at 0.1 µM) for 24 h. Total RNA was isolated and sequenced, and functional analysis was performed against the Gene Ontology (GO) database. Results for selected genes were confirmed with RT-qPCR. Results: As2O3 exerts no significant effect on CD4+ T-cell apoptosis under physical condition, and selectively modulate CD4+ T cells toward Treg cells not Th17 cells under special polarizing stimulators. As2O3 increased the expression of 200 and reduced that of 272 genes with fold change (FC) 2.0 or greater. Several genes associated with inflammation, Treg-cell activation and differentiation as well as glucose and amino acids metabolism were among the most strongly affected genes. GO function analysis identified top ten ranked significant biological process (BPs), molecular functions (MFs), and cell components (CCs) in treatment and nontreatment Treg cells. In GO analysis, genes involved in the immunoregulation, cell apoptosis and cycle, inflammation, and cellular metabolism were enriched among the significantly affected genes. The KEGG pathway enrichment analysis identified the forkhead box O (FoxO) signal pathway, apoptosis, cytokine–cytokine receptor interaction, cell cycle, nuclear factor-kappa B (NF-κB) signaling pathway, tumor necrosis factor α (TNF-α), p53 signaling pathway, and phosphatidylinositol 3′-kinase (PI3K)-Akt signaling pathway were involved in the pathogenesis of early treatment-naïve RA. Conclusion: This is the first study investigating the genome-wide effects of As2O3 on the gene expression of treatment-naïve Treg cells. In addition to clear anti-inflammatory and immunoregulation effects, As2O3 affect amino acids and glucose metabolism in Treg cells, an observation that might be particularly important in the metabolic phenotype of treatment-naïve RA.
A Scoping Review of Evidence-Informed Recommendations for Designing Inclusive Playgrounds

Background: Playgrounds provide children with many sensory, motor, and socioemotional experiences that are critical to child development. Unfortunately, playgrounds also represent an environment where children with disabilities experience barriers to accessing play. Structures and materials that are prominently found in almost all playground designs (e.g., swings, slides, sand) can present as obstacles for many children with disabilities to engage in independent play. Aims: This scoping review engaged in the empirical literature to address the research question, “What are the evidence-informed recommendations for designing inclusive playgrounds to enable participation for children with disabilities? ” Consideration was given not only to the physical design of playgrounds, but also the playgrounds' surrounding built and social environments. Methods: A systematic search of Medline, PsycINFO, CINAHL, EMBase, ERIC and Scopus was conducted. Only peer-reviewed literature published in English between January 1990 and January 2021, with a primary focus on inclusive playground structure design related to any type of disability were included. Data extraction included the study author(s), year of publication, country of origin, purpose, disability types considered, methods, sample characteristics and key findings. Key findings were synthesized into evidence-informed recommendations, which were later collated, using inductive content analysis, into five broader thematically congruent groups. Results: Thirty-five studies were included using case study (n = 17); observational (n = 6); survey (n = 5); experimental (n = 4); and multiple study (n = 3) designs. Thirteen evidence-based recommendations and one promising practice were categorized into five broad playground elements: entry points; surfacing and paths; features to foster inclusive play; staffing/supervision; and design process. Conclusion: These recommendations build upon previous design-based best-practices that focused exclusively on the physical design of the playground. Our recommendations have implications for how future playgrounds should be designed to maximize usability and inclusiveness and the overall playground experiences for children with disabilities.
Alexithymia and Sensory Processing Sensitivity: Areas of Overlap and Links to Sensory Processing Styles

Alexithymia is a dimensional trait characterized by difficulties identifying and describing feelings and an externally oriented thinking (EOT) style. Here, we explored interrelationships between alexithymia and measures assessing how individuals process and regulate their responses to environmental and body-based cues. Young adults (N = 201) completed self-report questionnaires assessing alexithymia, sensory processing sensitivity (SPS), interoceptive accuracy (IA), sensory processing styles, and current levels of depression, anxiety, and stress. Whereas EOT was related to low orienting sensitivity, problems with emotional appraisal (difficulties identifying feelings/difficulties describing feelings) were related to heightened sensory sensitivity. In addition, features of SPS improved the prediction of alexithymia above and beyond that accounted for by IA. We suggest that EOT is linked to problems maintaining a representation of one’s emotions in working memory and that low IA and problems with emotional appraisal are linked to atypicalities in sensory processing that may impact embodiment. A latent profile analysis revealed five classes of individuals distinguished by the relative strength of different alexithymic traits and by differences in IA and sensory processing styles. The classes identified included two lexithymic, one modal, and two alexithymic groups, showing different susceptibilities to SPS. Overall, our findings lend support to the view that alexithymia is associated with atypicalities in both bottom–up and top–down processes that impact emotion processing and regulation. They also raise the possibility that individuals with different alexithymia subtypes may differ with regard to a range of factors, including not only SPS but also early life experiences, mental health outcomes, and susceptibility to various personality disorders.
Evolving Interplay Between Dietary Polyphenols and Gut Microbiota—An Emerging Importance in Healthcare

Polyphenols are natural plant compounds and are the most abundant antioxidants in the human diet. As the gastrointestinal tract is the primary organ provided to diet sections, the diet may be regarded as one of the essential factors in the functionality, integrity, and composition of intestinal microbiota. In the gastrointestinal tract, many polyphenols remain unabsorbed and may accumulate in the large intestine, where the intestinal microbiota are most widely metabolized. When assuming primary roles for promoting host well-being, this intestinal health environment is presented to the effect of external influences, including dietary patterns. A few different methodologies have been developed to increase solvency and transport across the gastrointestinal tract and move it to targeted intestinal regions to resolve dietary polyphenols at the low bioavailability. Polyphenols form a fascinating community among the different nutritional substances, as some of them have been found to have critical biological activities that include antioxidant, antimicrobial, or anticarcinogenic activities. Besides, it affects metabolism and immunity of the intestines and has anti-inflammatory properties. The well-being status of subjects can also benefit from the development of bioactive polyphenol-determined metabolites, although the mechanisms have not been identified. Even though the incredible variety of health-advancing activities of dietary polyphenols has been widely studied, their effect on intestinal biology adaptation, and two-way relationship between polyphenols and microbiota is still poorly understood. We focused on results of polyphenols in diet with biological activities, gut ecology, and the influence of their proportional links on human well-being and disease in this study.
Candida albicans Biofilm Inhibition by Ethnobotanicals and Ethnobotanically-Synthesized Gold Nanoparticles

The virulence and drug resistance of globally prevalent Candida albicans has presented complications toward its control while advances in effective antivirulence drugs remain critical. Emerging methods are now being evaluated to facilitate development of novel therapeutic approaches against this pathogen. This study focuses on the biofilm formation inhibition of ethnobotanical crude extracts and the use of nanotechnology through the ethnobotanically-synthesized gold nanoparticles to control C. albicans. Control on biofilm formation was compared using crude extracts (CEs) and biologically synthesized gold nanoparticles (CEs + AuNPs). Significantly lower biofilm formation was exhibited in thirteen (13) CEs and fourteen (14) CEs + AuNPs. Biofilm-linked genes Bcr1 and HSP90 expression were consequently downregulated. Higher biofilm inhibition activity was noted in some CEs + AuNPs compared to its counterpart CEs. This study emphasizes the biofilm inhibition activity of ethnobotanicals and the use of nanoparticles to enhance delivery of compounds, and points to its prospects for developing anti-pathogenic drugs without evolving resistance.
Validation and Psychometric Properties of the Persian Version of the 21-Item Game Addiction Scale With a Sample of Adolescents and Young Adults

Background: Excessive gaming has become a psychological health issue for both gamers and their social environments. This observation holds true for western but also non-western countries such as Iran. The aim of the present study was to translate and validate a Persian version of the Game Addiction Scale 21 (GAS 21) using a sample of adolescents and adults. Methods: A total of 412 participants (mean age: 22.16 years; 55.3% females) took part in the study. They completed questionnaires covering sociodemographic information and gaming-related information, as well as the Persian version of the GAS 21, the GAS 7, the Internet Addiction Test, and the Generalized Self-Efficacy Scale. Results: Of the initial 21 items of the Persian version of the GAS 21, five proved redundant and were eliminated. Factors analyses yielded four factors explaining 66.35% of the variance: 1. Withdrawal; 2. Feelings of guilt and addiction; 3. Mood modification; 4. Issues of time budget. Cronbach's alphas were satisfactory (alphas > 0.87). To validate the results, scores on the translated version were compared with the well-established Young Internet Addiction test. Factors correlated positively (rs between 0.21 and 0.31) with overall score on this latter test but, against expectations, positively with the generalized self-efficacy scale. Conclusions: A Persian version of the Game Addiction Scale-21 proved to be a useful tool for assessing the risk of game addiction behavior. Further, the solution with 16 items loading on four factors appears respond to the ecological need of parsimony.
Analysis and Design of Social Presence in a Computer-Mediated Communication System

Social presence, or the subjective experience of being present with another existing person, varies with the interaction medium. In general, social presence research has mainly focused on uni-directional aspects of each exchanged message, not on bidirectional interactions. Our primary purpose is to introduce such bidirectional evaluation by quantifying the degree of social presence with a few statistical measures. To this end, we developed a software called “TypeTrace” that records all keystrokes of online chat interactants and reenacts their typing actions and analyzed the results from different chat conditions, mainly focusing on the characterization of bi-directional interactions. We also compared the chat interaction patterns with the patterns from phone call datasets to investigate the difference of live communication in different media. The hypothesis of the experiment was that either richness or concurrency of communication is important for organizing social presence. Richness is defined by the variety of information at a time in communication and the concurrency is the number of temporal thread being processed at the same time. Our results show that when we merely increase the richness of information by presenting the typing process, the cognition of others' presence does not significantly increase. However, when the information concurrency is augmented by introducing the transmission of realtime text, we found that the transfer entropy between the interactants becomes considerably higher, and the social presence and emotional arousal, intimacy increased. High transfer entropy was also observed in the phone call dataset. This result shows that the mere augmentation of information richness does not necessarily lead to increased social presence, and concurrent communication is another critical factor for fostering vivid conversation in digital environments.
Broad-Spectrum Photo-Antimicrobial Polymers Based on Cationic Polystyrene and Rose Bengal

New strategies to fight bacteria and fungi are necessary in view of the problem of iatrogenic and nosocomial infections combined with the growing threat of increased antimicrobial resistance. Recently, our group has prepared and described two new readily available materials based on the combination of Rose Bengal (singlet oxygen photosensitizer) and commercially available cationic polystyrene (macroporous resin Amberlite® IRA 900 or gel-type resin IRA 400). These materials showed high efficacy in the antimicrobial photodynamic inactivation (aPDI) of Pseudomonas aeruginosa. Here, we present the photobactericidal effect of these polymers against an extended group of pathogens like Escherichia coli, Enterococcus faecalis, Staphylococcus aureus, and the opportunistic yeast Candida albicans using green light. The most interesting finding is that the studied materials are able to reduce the population of both Gram-positive and Gram-negative bacteria with good activity, although, for C. albicans, in a moderate manner. In view of the results achieved and especially considering the inexpensiveness of these two types of photoactive polymers, we believe that they could be used as the starting point for the development of coatings for self-disinfecting surfaces.