Miracle-dz/UniFAR-FTUs huggingface dataset:
Cancer stemness, intratumoral heterogeneity, and immune response across cancers

Significance The exclusion of immune cells from the tumor microenvironment has been associated with poor prognosis in the majority of cancers. We report that when considering 21 solid cancer types, immune cell exclusion is widely associated with the presence of a stem cell-like phenotype in tumors (“stemness”). Stemness positively correlates with higher intratumoral heterogeneity, possibly by protecting antigenic clones from elimination by the immune system. The activation of a stemness program appears to limit antitumor immune responses via tumor cell-intrinsic silencing of endogenous retrovirus expression, repression of type I interferon signaling, and up-regulation of immunosuppressive checkpoints. Our work suggests that targeting the stemness phenotype in cancer will promote T cell infiltration and render tumors more responsive to immune control. Regulatory programs that control the function of stem cells are active in cancer and confer properties that promote progression and therapy resistance. However, the impact of a stem cell-like tumor phenotype (“stemness”) on the immunological properties of cancer has not been systematically explored. Using gene-expression–based metrics, we evaluated the association of stemness with immune cell infiltration and genomic, transcriptomic, and clinical parameters across 21 solid cancers. We found pervasive negative associations between cancer stemness and anticancer immunity. This occurred despite high stemness cancers exhibiting increased mutation load, cancer-testis antigen expression, and intratumoral heterogeneity. Stemness was also strongly associated with cell-intrinsic suppression of endogenous retroviruses and type I IFN signaling, and increased expression of multiple therapeutically accessible immunosuppressive pathways. Thus, stemness is not only a fundamental process in cancer progression but may provide a mechanistic link between antigenicity, intratumoral heterogeneity, and immune suppression across cancers.
Indonesian Demand for Online Shopping: Revisited

Introduction/Main Objectives : This study aims to analyze the factors that influence online shopping. Data are aggregated at the national, island, and regional levels. The regions are categorized based on their level of demand for online shopping. Background Problems : The rapid development of information and communications technology contributes to the transformation of the digital economy. By using 281,185 internet users from the National Households Survey (Survei Sosial Ekonomi-Susenas) 2017 data, we found that the percentage of online shopping in Indonesia is 7.59%. Online shopping is concentrated on the island of Java, especially in the Greater Jakarta area (Jakarta, Bogor, Depok, Tangerang, and Bekasi). Novelty : This study analyzes online shopping from the point of view of economic development studies, especially related to the development of information technology and the digital economy. Research Methods : We used a binary logistic regression analysis to assess the effect of demographic, socio-economic, and spatial factors on an individual’s decision to shop online. Finding/Results : The results indicate that individuals who have a greater tendency to shop online are those who have a high income, are women, can access the internet using mobile phones, they are the spouses of the heads of households, are 25 to30 years old, live in urban areas, have graduated from college (especially with a diploma), and work in the tertiary sector. The higher that the share of online shopping is in an area, the more intense the influence of individual characteristics will be on the tendency to shop online, according to the demographic and socio-economic factors, while the spatial factors will fade away. Conclusion : Income, gender, internet access, and the shopper’s position in the household are factors that significantly influence individuals to shop online.
Analysis of cell signalling in dystrophin-deficient myoblasts

An absence of dystrophin in muscle has a massive impact throughout muscle development, and Duchene Muscular Dystrophy (DMD) is one of the consequences. The disruption of the dystrophin-glycoprotein complex (DGC) is caused by a mutation in the dmd gene, which effects muscle integrity, resulting in progressive muscle degeneration and weakness. In this study, dfd13 (dystrophin-deficient) and C2C12 (non-dystrophic) myoblasts were cultured in low mitogen conditions for 10 days to induce differentiation; however, dfdl3 myoblasts did not achieve terminal differentiation. It has been suggested that Pax7 may play a major role during myogenesis, therefore its expression pattern and transport protein were examined for any impairments. It was established that Pax7 localises in the cytoplasm of dystrophindeficient myoblasts and high expression is retained during differentiation. Colocalisation of Pax7 with subcellular markers analysis indicated that Pax7 is synthesised during the proliferative state. Pax7 was shown to possess a nuclear location signal and KPNA2 was suggested as escort protein for Pax7 translocation into the nucleus. The PTEN-PI3K/Akt signalling pathway was investigated and protein synthesis regulation and Fox03 was found to be impaired. Autophagy related genes were found to be highly expressed; however, LC3 lipidation and autophagy flux showed a reduction upon differentiation, indicating defective autophagy. The contribution of PTEN overexpression was assessed in relation to endoplasmic reticulum (ER) stress and activation of the unfolding protein response (UPR). It was established that a reduction in ER stress and changes to UPR activation lead to apoptosis. Finally, minidystrophintransfection of both types of myoblasts was utilised to examine the effect, especially in dystrophin-deficient myoblasts. Minidystrophin improved protein synthesis activation and increased autophagy (increased LC3 lipidation), suggesting that minidystrophin ameliorates dystrophic events at the level of autophagosome formation. To conclude, destabilisation of the plasma membrane owing to a dystrophin mutation causes cell signalling alterations which minidystrophin restoration can partly improve.
The biology of variation in anatomical brain asymmetries

24 Introduction . 25 Methods . 27 Study dataset . 27 Image acquisition . 28 Image processing . 28 Cortical correlates of handedness . 29 Power analysis . 29 Results . 30 Discussion. 33 Acknowledgements . 36 Appendix . 37 Supplementary material . 37 Asymmetry within and around the human planum temporale is sexually dimorphic and influenced by genes involved in steroid hormone receptor activity . 49 Abstract . 50. 50 Introduction . 51 Methods . 53 Study datasets . 53 Image acquisition . 53 Image processing . 54 Parcellation of cortical regions . 55 Regional asymmetry mapping by sex . 56
The Athlete Gratitude Group (TAGG): Effects of coach participation in a positive psychology intervention with youth athletes

Abstract Learning how to cultivate gratitude can be a valuable skill for life and sport, allowing one to reframe negative situations, enhance interpersonal relationships, and build resilience. While one-time gratitude interventions have demonstrated benefits for personal and social well-being, multi-session programs have the potential to strengthen these effects, as well as team dynamics. The purpose of this pilot study was to examine (1) the impact of a multi-session gratitude intervention among youth athletes and (2) the effect of coach participation on respective outcomes. Eighteen varsity members of a high school girls’ soccer team participated in The Athlete Gratitude Group (TAGG). To test the effect of coach participation, team members were randomly assigned to receive the intervention with or without the head coach present. Repeated measures analysis of variance tests and subsequent pairwise comparisons found significant improvements in athletes’ state gratitude, mental health, resilience, team cohesion, and coach-athlete relationship pre- to post-intervention. For the entire sample, lasting effects on mental health, resilience, and coach-athlete relationship were observed at 1-month and 3-month follow-ups. Moreover, positive effects on mental health were significantly maximized for athletes in the coach group. No significant group x time interaction effects were observed on state or trait gratitude, resilience, team cohesion, or quality of the coach-athlete relationship; all athletes derived positive benefits from the program, regardless of group membership. Strengths, limitations, practical implications, and future research recommendations are discussed. Lay summary: A high school soccer team participated in “The Athlete Gratitude Group,” a multi-session gratitude intervention. Half the team completed the program with the head coach present. All athletes exhibited enhanced gratitude, mental health, resilience, team cohesion, and coach-athlete relationship, with the coach group reporting even greater improvements in mental health. IMPLICATIONS FOR PRACTICE Intervention programs aimed toward cultivating gratitude in life and sport may enhance athlete mental health, resilience, team cohesion, and quality of the coach-athlete relationship. Coach participation in gratitude interventions at the team level may maximize positive effects on athlete mental health. Collectively engaging in gratitude practice as a team may increase resiliency and foster better quality relationships in sport.
Testing the effects of pathogen threat and sexual strategies on political ideology

Abstract. Disgust has been consistently associated with greater political conservatism. Two explanations have been proposed for this link. According to a pathogen threat model, disgust serves a pathogen-avoidance function, encouraging more conservative ideology, whereas a sexual strategies model suggests that this link is explained by variability in short-term versus long-term mating goals. In two preregistered studies using a college student and community sample (total N = 1,950), we examined whether experimentally manipulating pathogen threat and mate availability produced differences in political ideology and whether these differences were explained by disgust and sociosexual attitudes. Across both studies, we did not find evidence that manipulating pathogen threat or mate availability resulted in change in political ideology. In Study 1, manipulating mate availability was indirectly associated with greater political conservativism through stronger sociosexual attitudes that favor monogamy. These findings failed to replicate in Study 2. Implications for theory and future research are discussed.
Family-Specific Social Support at Work: The Role of Open and Trustworthy Communication

Family-friendly organizational policies are important for employees to manage work and family responsibilities. Besides formal policies, research has emphasized the importance of informal social support by organizational actors. The positive effects of organizational and supervisor support are already known, but findings are limited regarding family-specific support by coworkers. Taking a communicative perspective, this study tests the assumption that social support is contingent on trustworthy and open communication. To test this, 724 German employees participated in an online survey. Results confirm the relationship between family-specific support and the outcomes job satisfaction, policy use, and work-family conflict, through open and trustworthy communication. Additionally, the study illuminates the distinct roles of organizational actors’ (i.e., coworker, supervisor, organization) support on employee outcomes in the German context.
The Anatomic Connectome and Functional Dissection of the Caenorhabditis elegans First-stage Larvae (L1) Motor Circuit

During development, neural networks exhibits anatomic and functional modifications. Yet their activity patterns change remains poorly understood. The neural circuit controlling locomotion of C. elegans undergoes major reconstructions at the end of firstlarval (L1) stage. In adults, the ventral/dorsal body wall muscles are symmetrically innervated by cholinergic and GABAergic motor neurons (MNs). Cholinergic MNs innervating ventral muscles are not derived during early L1 stage, yet the animals can still generate undulation. This study addressed how L1 C. elegans produces undulation and the mechanism underlying muscle innervations. We demonstrated that the activities of dorsal cholinergic MNs are required for both dorsal and ventral muscle contraction, and the GABAergic MNs mediate only ventral muscle relaxation. This indicated a differential synaptic wiring between MNs and muscles in L1 to permit undulation. Through this comparative analysis between juvenile and adult locomotion, we hope to provide insights on principles of behavioral adaptation during sensorimotor development.
Defect Detection in Printed Circuit Boards Using You-Only-Look-Once Convolutional Neural Networks

In this study, a deep learning algorithm based on the you-only-look-once (YOLO) approach is proposed for the quality inspection of printed circuit boards (PCBs). The high accuracy and efficiency of deep learning algorithms has resulted in their increased adoption in every field. Similarly, accurate detection of defects in PCBs by using deep learning algorithms, such as convolutional neural networks (CNNs), has garnered considerable attention. In the proposed method, highly skilled quality inspection engineers first use an interface to record and label defective PCBs. The data are then used to train a YOLO/CNN model to detect defects in PCBs. In this study, 11,000 images and a network of 24 convolutional layers and 2 fully connected layers were used. The proposed model achieved a defect detection accuracy of 98.79% in PCBs with a batch size of 32.
Inside the Matrix: Immersive Live Coding for Architectural Design

Algorithmic Design (AD) uses computer programs to describe architectural models. These models are visual by nature and, thus, greatly benefit from immersive visualization. To allow architects to benefit from the advantages of Virtual Reality (VR) within an AD workflow, we propose a new design approach: Live Coding in Virtual Reality (LCVR). LCVR means that the architect programs the design while immersed in it, receiving immediate feedback on the changes applied to the program. In this paper, we discuss the benefits and impacts of such an approach, as well as the most pressing implementation issues, namely the projection of the programming environment onto VR, and the input mechanisms to change the program or parts of it. For each, we offer a critical analysis and comparison of the various solutions available in the context of two different programming paradigms: visual and textual.
Enabling the Development and Implementation of Digital Twins: Proceedings of the 20th International Conference on Construction Applications of Virtual Reality

Accidents resulting from poorly planned or set up work environments are a major concern within the construction industry. Even in a country like Denmark, which is known for its strict compliance with occupational safety, health and well-being, few to any of the educational concepts on construction safety and health education have focused on the use of advanced technologies that engage workers more actively in learning. While traditional education and training of personnel offer well known approaches for establishing safe work practices, Serious Games in Virtual Reality (VR) are increasingly being used as a complementary approach for active learning experiences. Their designs yet have to take full advantage of how a user can manipulate and interact with virtual imagery generated by the computer. In addition, little understanding exists in generating and analyzing the inherent synthetic data that can be collected about users in VR. This research presents a framework for the generation and automated assessment of such data in VR. The proposed approach is tested and evaluated in a virtual work environment consisting of, next to a user performing a realistic work task, multiple hazards that are consistent within today’s construction sites. While virtual sensors augment the immersion of the participant in the virtual scene, run time data analysis provides opportunities for rapid personalized feedback. Encouraging results on the experiences of the participants are presented and discussed based on real needs in the Danish construction industry. An outlook presents future avenues towards enhancing existing learning methods.
The impact of lifelong viral infection on development and maintenance of memory CD8+ T cells

Certain viruses are capable of establishing lifelong persistent infections within vertebrate hosts. Such infections can be chronic or latent, and accumulating evidence suggests that they provide ongoing antigenic stimulation to memory T cells throughout lifetime. In addition, infection with some persistent viruses were implicated in driving inflammation-driven expansions of bystander T cells. Both antigen-driven and bystander stimulation ofT cells can be expected to affect the composition and diversity of the T cell pool. These processes were suggested to drive the age-associated changes in maintenance of stable T cell pool, contributing to the process of immunosenescence. In this thesis I examined the impact of both lifelong viral infections as well as aging on the maintenance of systemic CD8+ T cells over lifetime in a mouse model of Herpes Simplex Virus type 1 (HSV -1) and murine cytomegalovirus (MCMV) infection. Both viruses establish latent infections, however recent evidence implies that infection with MCMV is characterized by frequent viral reactivation, as inferred from ongoing expansion of MCMV -specific CD8+ T cells over the timecourse of infection, a process termed memory inflation. Less is known about the effect of HSV -1 infection on maintenance of antiviral memory CD8+ T cell. Until recently, HSV -1 infection in mice was believed to be truly latent and not associated with ongoing antigen presentation. However, evidence gathered over the last decade implies that this may not be the case and that reactivation of HSV -1 from latency in mice is more frequent than previously thought. I investigated both primary and memory CD8+ T cell response to HSV-1, with special focus on involvement of antigen in maintenance of the memory population. I
Modeling of interactions between vascular endothelial growth factor family members and their receptors KDR and Flt-1.

The vascular endothelial growth factor (VEGF) family is prominently involved in angiogenesis, the formation of new vasculature. Overexpression has been linked to pathological conditions including solid tumor growth. Responses to VEGF are mediated by Flt-1 and KDR, two cell-surface receptors selectively expressed by vascular endothelial cells. A secreted form of Flt-1 (sFlt1) retains high affinity for VEGF and can compete for VEGF binding, thereby inhibiting angiogenic responses. In this study, a computational model of this ligand-receptor binding system is used to quantitatively describe the activation of KDR signaling by VEGF and its inhibition by sFlt-1. The model consists of a system of 12 ordinary differential equations, based on mass action kinetics, which describe, based on mass-action kinetics, the formation and disappearance of receptor-ligand complexes competent to transduce a VEGF signal. Cell-based assays were used to test predictions of the in silico model by measuring dynamics of 1) KDR tyrosine phosphorylation and 2) generation of intracellular second messengers in response to VEGF stimulation in the presence and absence of sFlt-1. Results indicate that the model predicts well the maximal activation in the presence of VEGF-A or the KDR-selective agonist VEGF-E. Subsequent characteristics of binding, such as time-to-peak activations, were less realistically modeled, suggesting that the mathematical descriptions of certain receptor fates (receptor internalization, sequestration or externalization) may need refinement. Also presented are the results of KDR activation experiments in the simultaneous presence of VEGF-A, sFlt1, and the Flt1-selective agonist placental growth factor (PlGF). Here, the model predicts accurately the percentage of inhibition of maximal activation when sFlt-1 is present in the system. Finally, a revised model that includes receptor heterodimerization is presented that suggests sFlt-1 can more effectively inhibit VEGF binding and activation when acting in a dominant negative fashion. Overall, the findings support the idea that the early events in VEGF signaling can be modeled successfully. A natural extension of the model, refined based on experimental testing, will be its application to normal physiological systems.
The Dynamic Maggot Mass Microbiome

Abstract Necrophagous insect studies have shown that decomposing vertebrate remains are an important ephemeral resource within an ecosystem. However, the microbes (e.g., bacteria and archaea) that were a part of the once living organism and the exogenous taxa that colonize this postmortem resource remain largely underexplored. Also, it is not well understood how these two kingdoms interact to recycle decaying biomass, an important mechanistic question for ecosystem function ecology. To better understand microbial community dynamics throughout decomposition, we used swine carcasses (N = 6) as models for mammalian postmortem decomposition to characterize epinecrotic microbial communities from: the abdominal skin of replicate carcasses; the internal microbiome of individual necrophagous dipteran larvae (maggots); and the microbiome of dipteran larval masses that had colonized the carcasses. Sampling occurred every 12 h for the duration of the decomposition process. We characterized these microbial communities over time using high-throughput 16S amplicon sequencing. The relative abundance of microbial taxa changed over decomposition as well as across sampling locations, suggesting significant interactions between the environment, microbes, and insect larvae. Maggot masses were represented by multiple blow fly species in each mass: Phormia regina (Meigen), Lucilia coeruleiviridis (Macquart), and Cochliomyia macellaria (F.). Relative abundance of these species within the mass also changed as decomposition progressed, suggesting the presence of certain Calliphoridae species within a mass may be associated with temporal shifts of the microbial communities. These results provide new insight into the community ecology of carrion decomposition by providing new data on interactions of microbes and dipteran larvae over time.
Nudging Timely Wage Reporting: Field Experimental Evidence from the United States Social Supplementary Income Program

We study a large-scale (n=50,000) natural field experiment implemented by the U.S. Social Security Administration that was aimed at increasing the timely and accurate self-reporting of wages by Supplemental Security Income (SSI) recipients. Sending a letter reminding SSI recipients of their wage reporting responsibilities significantly increased both the likelihood of reporting any earnings and the total amount of earnings reported, though this effect decays slightly over time. However, the specific letter content—providing social information or highlighting the salience of penalties—had no systematic effect. We develop a conservative estimate that the letters generated roughly $5.91 in savings on average per dollar spent for the U.S. government.
A description of the larva of Mesopodagrion tibetanum australe (Odonata: “Megapodagrionidae”)

The larva of the genus Mesopodagrion was identified with the help of DNA barcoding and described for the first time. The larvae have flat horizontal gills resembling those of Argiolestidae but the adults lack setae on the shaft of the genital ligula. Molecular data are shown to be useful and necessary in larval identification and should be adopted as a standard tool in future studies.