Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and genetics of red coloration in the zebrafish relative Danio albolineatus

Animal pigment patterns play important roles in behavior and, in many species, red coloration serves as an honest signal of individual quality in mate choice. Among Danio fishes, some species develop erythrophores, pigment cells that contain red ketocarotenoids, whereas other species, like zebrafish (D. rerio) only have yellow xanthophores. Here, we use pearl danio (D. albolineatus) to assess the developmental origin of erythrophores and their mechanisms of differentiation. We show that erythrophores in the fin of D. albolineatus share a common progenitor with xanthophores and maintain plasticity in cell fate even after differentiation. We further identify the predominant ketocarotenoids that confer red coloration to erythrophores and use reverse genetics to pinpoint genes required for the differentiation and maintenance of these cells. Our analyses are a first step towards defining the mechanisms underlying the development of erythrophore-mediated red coloration in Danio and reveal striking parallels with the mechanism of red coloration in birds.
High-Stability Polyimide-based Flexible Electrodes with IrOx to Interface the Mouse Vagus Nerve

Objective We developed robust and cost-effective cuff Flex electrodes to facilitate bioelectronic medicine research in mouse models. They utilize polyimide (PI) as a dielectric insulation and iridium oxide (IrOx) for the electrodes, and are designed to interface small autonomic and somatic nerves (e.g. mouse vagus nerve). Approach Flex electrodes were made using micro-fabrication technology, and innovative integration processes were developed to enable reliable acute and chronic vagus nerve interfaces. The electrochemical properties of Flex electrodes were characterized. Moreover, accelerated aging at 57 °C and stimulation-stability (Stim-Stab) testing (109 pulses at ∼ 1.59 mC/cm2/phase) were performed to evaluate the lifetime of the PI encapsulation and IrOx electrodes, respectively. Flex electrodes efficacy was demonstrated by stimulating the mouse vagus nerve (∼100 µm) and measuring heart and respiratory rate changes as biomarkers. Results Cost effective and robust lead and connector integration strategies were demonstrated, including small helical leads that improved the lead elongation by > 7x. PI encapsulation had stable impedance spectra for at least 336 days for interdigitated electrodes. Stim-Stab testing using an aggressive paradigm and rigorous optical and electrical characterization, revealed that half of electrodes showed less than minor damage at the endpoints. A trend of decreasing respiratory rate with stimulation current reached statistical significance at 500 µA, demonstrating efficacy for Flex electrodes. Significance Flex electrodes offer demonstrated efficacy, low impedance (443 ± 32 Ω at 103 Hz), excellent bench test stability, and cost-effective fabrication. Acute devices are easy to integrate, and mechanically robust chronic devices will be investigated in vivo in future studies. These characteristics make the electrodes well-positioned to advance bioelectronics medicine research by 1) enabling reliable studies with statistically relevant populations of acute mouse models, and 2) offering the potential for a technology that can be used in chronic studies, which scales to very small nerves.
Heart Rate Fluctuation and Mortality in Critically Ill Myocardial Infarction Patients: A Retrospective Cohort Study

Background: Whether heart rate (HR) fluctuation after admission has an impact on the outcomes of critically ill myocardial infarction (MI) patients in intensive care unit remains unknown. Methods: A total of 2,031 MI patients were enrolled from the Medical Information Mart for Intensive Care (MIMIC-III) database. HR fluctuation was calculated as the maximum HR minus the minimum HR in the initial 24 h after admission. Participants were divided into 3 groups, namely, low HR fluctuation [<30 beats per minute (bpm)], medium HR fluctuation (30–49 bpm), and high HR fluctuation (≥ 50 bpm). The main outcomes were 30–day and 1-year mortality. Cox regression and restricted cubic spline model were used. Results: Each 10-bpm increase in HR fluctuation was associated with a higher risk of 30-day mortality and 1-year mortality, with adjusted hazard ratios of 1.122 (95% CI, 1.083–1.162) and 1.107 (95% CI, 1.074–1.140), respectively. Compared with the low HR fluctuation group, the high HR fluctuation group suffered a significantly higher risk of mortality after adjustment, with hazard ratios of 2.156 (95% CI, 1.483–3.134) for 30-day mortality and 1.796 (95% CI, 1.354–2.381) for 1-year mortality. A typical J-type curve was observed in restricted cubic splines for the association between HR fluctuation and 30-day or 1-year mortality of MI patients, with the lowest risk on the HR fluctuation of 30 bpm. Sensitivity analyses emphasized the robustness of our results. Conclusions: This retrospective cohort study revealed an independent positive association between HR fluctuation and 30-day and 1-year mortality in critically ill MI patients, which warrants further investigation.
Avian Use of Agricultural Areas as Migration Stopover Sites: A Review of Crop Management Practices and Ecological Correlates

An estimated 17% of migratory bird species are threatened or near threatened with extinction. This represents an enormous potential loss of biodiversity and cost to human societies due to the economic benefits that birds provide through ecosystem services and ecotourism. Conservation of migratory bird species presents many unique challenges, as these birds rely on multiple geographically distinct habitats, including breeding grounds, non-breeding grounds, and stopover sites during migration. In particular, stopover habitats are seldom studied relative to breeding and non-breeding habitats, despite their importance as refueling stations for migratory birds. In this study, we summarize the current research on the use of temporary primary crops by birds during migration and we assess the species characteristics and agricultural practices most often associated with the use of cropland as stopover habitat. First, we conducted a systematic review of the literature to document the effects various farming practices and crop types have on the abundance and diversity of migratory birds using agricultural areas for stopovers. Second, we analyzed the ecological correlates of bird species in the Northern Hemisphere that predict which species may use these areas while migrating. We ran a GLMM to test whether primary diet, diet breadth, primary habitat, habitat breadth, or realm predicted stopover use of agricultural areas. Our review suggests that particular crop types (principally rice, corn, and sunflower), as well as farming practices that result in higher non-cultivated plant diversity, encourage the use of agricultural areas by migrating birds. We found that cropland is used as stopover habitat by bird species that can utilize a large breadth of habitats, as well as species with preferences for habitat similar in structure to agricultural areas.
Frequency of Participation in a Return-to-Work Program Predicts Successful Work Restoration but Not Maintenance

Several predictors for work restoration and maintenance of restoration have been examined among employees with mood and/or anxiety disorders, but whether frequency of participation in a return-to-work (RTW) program can predict successful work restoration and maintenance remains unclear. In the present study, we attempted to investigate the hypothesis that the frequency of RTW program participation can predict successful work restoration and maintenance. Among seventy-seven patients attending an RTW program, the frequency of participation was positively associated with work restoration but not with maintenance. The result was in partial agreement (restoration) and partial disagreement (maintenance of restoration) with our hypothesis. Thus, the present study suggests that the frequency of participation in an RTW program can predict successful work restoration but not maintenance.
Screening of Reference Genes for RT-qPCR in Chicken Adipose Tissue and Adipocytes

Reverse transcription quantitative real-time PCR is the most commonly used method to detect gene expression levels. In experiments, it is often necessary to correct and standardize the expression level of target genes with reference genes. Therefore, it is very important to select stable reference genes to obtain accurate quantitative results. Although application examples of reference genes in mammals have been reported, no studies have investigated the use of reference genes in studying the growth and development of adipose tissue and the proliferation and differentiation of preadipocytes in chickens. In this study, GeNorm, a reference gene stability statistical algorithm, was used to analyze the expression stability of 14 candidate reference genes in the abdominal adipose tissue of broilers at 1, 4, and 7 weeks of age, the proliferation and differentiation of primary preadipocytes, as well as directly isolated preadipocytes and mature adipocytes. The results showed that the expression of the TATA box binding protein (TBP) and hydroxymethylbilane synthase (HMBS) genes was most stable during the growth and development of abdominal adipose tissue of broilers, the expression of the peptidylprolyl isomerase A (PPIA) and HMBS genes was most stable during the proliferation of primary preadipocytes, the expression of the TBP and RPL13 genes was most stable during the differentiation of primary preadipocytes, and the expression of the TBP and HMBS genes was most stable in directly isolated preadipocytes and mature adipocytes. These results provide reference bases for accurately detecting the mRNA expression of functional genes in adipose tissue and adipocytes of chickens.
Comparative Proteomics Analysis for Elucidating the Interaction Between Host Cells and Toxoplasma gondii

Toxoplasma gondii, a representative model organism belonging to the phylum Apicomplexa, can infect almost all warm-blooded organisms, including humans. The invasion of host cells via host–parasite interaction is the key step for T. gondii to complete its life cycle. Herein we performed tandem mass tag analysis to investigate global proteomic changes in host cells (human foreskin fibroblasts, HFFs) [HFFs infected with T. gondii (HT) vs. HFFs (H)] and T. gondii [HT vs. T. gondii (T)] during intracellular infection. Overall, 3477 and 1434 proteins were quantified, of which 375 and 1099 proteins were differentially expressed (adjusted p-value < 0.05 and >1.5 or <0.67-fold change) in host cells and T. gondii, respectively. T. gondii invasion relies on the secretion of numerous secretory proteins, which originate from three secretory organelles: micronemes, rhoptries, and dense granules. In the HT vs. T group, few secretory proteins were upregulated, such as microneme proteins (MICs: MIC6, MIC10), rhoptry bulb proteins (ROPs: ROP5, ROP17), and dense granule proteins (GRAs: GRA4, GRA5, GRA12). In contrast, dozens of known secretory proteins were significantly downregulated in T. gondii-infected HFFs. In HFFs, gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed a large number of differentially expressed proteins (DEPs) enriched in metabolic processes and immune-associated signaling pathways, such as NF-κB, cAMP, and Rap1 signaling pathways. Further, in case of T. gondii, DEPs were involved in ribosome biogenesis, citrate cycle, and galactose metabolism, indicating that cell biosynthesis and metabolism of T. gondii were altered after host cell invasion. These findings reveal novel modifications in the proteome of host cells as well as T. gondii, helping us better understand the mechanisms underlying host–parasite interaction.
Interpretability Versus Accuracy: A Comparison of Machine Learning Models Built Using Different Algorithms, Performance Measures, and Features to Predict E. coli Levels in Agricultural Water

Since E. coli is considered a fecal indicator in surface water, government water quality standards and industry guidance often rely on E. coli monitoring to identify when there is an increased risk of pathogen contamination of water used for produce production (e.g., for irrigation). However, studies have indicated that E. coli testing can present an economic burden to growers and that time lags between sampling and obtaining results may reduce the utility of these data. Models that predict E. coli levels in agricultural water may provide a mechanism for overcoming these obstacles. Thus, this proof-of-concept study uses previously published datasets to train, test, and compare E. coli predictive models using multiple algorithms and performance measures. Since the collection of different feature data carries specific costs for growers, predictive performance was compared for models built using different feature types [geospatial, water quality, stream traits, and/or weather features]. Model performance was assessed against baseline regression models. Model performance varied considerably with root-mean-squared errors and Kendall’s Tau ranging between 0.37 and 1.03, and 0.07 and 0.55, respectively. Overall, models that included turbidity, rain, and temperature outperformed all other models regardless of the algorithm used. Turbidity and weather factors were also found to drive model accuracy even when other feature types were included in the model. These findings confirm previous conclusions that machine learning models may be useful for predicting when, where, and at what level E. coli (and associated hazards) are likely to be present in preharvest agricultural water sources. This study also identifies specific algorithm-predictor combinations that should be the foci of future efforts to develop deployable models (i.e., models that can be used to guide on-farm decision-making and risk mitigation). When deploying E. coli predictive models in the field, it is important to note that past research indicates an inconsistent relationship between E. coli levels and foodborne pathogen presence. Thus, models that predict E. coli levels in agricultural water may be useful for assessing fecal contamination status and ensuring compliance with regulations but should not be used to assess the risk that specific pathogens of concern (e.g., Salmonella, Listeria) are present.
Self-Sacrifice Is Not the Only Way to Practice Filial Piety for Chinese Adolescents in Conflict With Their Parents

We applied the theoretical perspective of the dual filial piety model to consider the diversity of parent–child conflict resolution strategies in order to determine whether Chinese adolescents use strategies other than self-sacrifice to practice filial piety when in conflict with their parents. Study 1 utilized a cross-sectional design with 247 valid responses. The structural equation modeling analysis indicated that Taiwanese adolescents’ authoritarian filial piety (AFP) beliefs are positively related to use of a self-sacrifice strategy, and reciprocal filial piety (RFP) beliefs are positively related to use of compatibility and compromise strategies. Adolescents’ AFP and RFP beliefs are negatively related to use of utility and escape strategies. Study 2 applied a temporal separation procedure with a 1-year lag to remedy common method variance bias. Analysis of 1,063 valid responses replicated the findings of Study 1 and indicated that adolescents’ function-oriented appraisal of conflict can play a mediating role between RFP and the use of the compatibility and compromise strategies. These findings broaden the understanding of filial piety in modern Chinese societies and have implications for adolescents’ well-being and family life.
Battling for Consumer's Positive Purchase Intention: A Comparative Study Between Two Psychological Techniques to Achieve Success and Sustainability for Digital Entrepreneurships

This research focuses on students' online purchase intentions in Pakistan toward different products available for sale on numerous e-business websites. This study's main objective is to determine which methodology is better to enhance customer online purchase intention. It also aims to discover how to improve perceived benefits and lower perceived risks associated with any available online product and entrepreneurship. AMOS 24 has been used to deal with the mediation in study design with bootstrap methodology. The study was conducted on 250 students from different educational institutes in Pakistan using a simple random sampling technique. A finding of this study suggests that both methods positively impact online purchase intention of consumers and sustainable digital economy. But social media advertisement is more effective through enhancing the perceived benefits of products. In contrast, product content factors are more effective at lowering the perceived risks associated with available online products.
Characterization of BoaCRTISO Reveals Its Role in Carotenoid Biosynthesis in Chinese Kale

Carotenoids are organic pigments that play an important role in both plant coloration and human health; they are a critical subject in molecular breeding due to growing demand for natural molecules in both food and medicine. In this study, we focus upon characterizing BoaCRTISO, the carotenoid isomerase gene before the branch of the carotenoid biosynthetic pathway, which is expressed in all organs and developmental stages of Chinese kale, and BoaCRTISO, which is located in the chloroplast. The expression of BoaCRTISO is induced by strong light, red and blue combined light, and gibberellic acid treatment, but it is suppressed by darkness and abscisic acid treatment. We obtained BoaCRTISO-silenced plants via virus-induced gene silencing technology, and the silence efficiencies ranged from 52 to 77%. The expressions of most carotenoid and chlorophyll biosynthetic genes in BoaCRTISO-silenced plants were downregulated, and the contents of carotenoids and chlorophyll were reduced. Meanwhile, BoaCRTISO-silenced plants exhibited phenotypes of yellowing leaves and inhibited growth. This functional characterization of BoaCRTISO provides insight for the biosynthesis and regulation of carotenoid in Chinese kale.
Integrated Analysis of ceRNA Network Reveals Prognostic and Metastasis Associated Biomarkers in Breast Cancer

Background Breast cancer is a malignancy and lethal tumor in women. Metastasis of breast cancer is one of the causes of poor prognosis. Increasing evidences have suggested that the competing endogenous RNAs (ceRNAs) were associated with the metastasis of breast cancer. Nonetheless, potential roles of ceRNAs in regulating the metastasis of breast cancer remain unclear. Methods The RNA expression (3 levels) and follow-up data of breast cancer and noncancerous tissue samples were downloaded from the Cancer Genome Atlas (TCGA). Differentially expressed and metastasis associated RNAs were identified for functional analysis and constructing the metastasis associated ceRNA network by comprehensively bioinformatic analysis. The Kaplan-Meier (K-M) survival curve was utilized to screen the prognostic RNAs in metastasis associated ceRNA network. Moreover, we further identified the metastasis associated biomarkers with operating characteristic (ROC) curve. Ultimately, the data of Cancer Cell Line Encyclopedia (CCLE, https://portals.broadinstitute.org/ccle) website were selected to obtained the reliable metastasis associated biomarkers. Results 1005 mRNAs, 22 miRNAs and 164 lncRNAs were screened as differentially expressed and metastasis associated RNAs. The results of GO function and KEGG pathway enrichment analysis showed that these RNAs are mainly associated with the metabolic processes and stress responses. Next, a metastasis associated ceRNA (including 104 mRNAs, 19 miRNAs, and 16 lncRNAs) network was established, and 12 RNAs were found to be related to the overall survival (OS) of patients. In addition, 3 RNAs (hsa-miR-105-5p, BCAR1, and PANX2) were identified to serve as reliable metastasis associated biomarkers. Eventually, the results of mechanism analysis suggested that BCAR1 might promote the metastasis of breast cancer by facilitating Rap 1 signaling pathway. Conclusion In the present research, we identified 3 RNAs (hsa-miR-105-5p, BCAR1 and PANX2) might associated with prognosis and metastasis of breast cancer, which might be provide a new perspective for metastasis of breast cancer and contributed to the treatment of breast cancer.
Whole-Body Prolyl Hydroxylase Domain (PHD) 3 Deficiency Increased Plasma Lipids and Hematocrit Without Impacting Plaque Size in Low-Density Lipoprotein Receptor Knockout Mice

Background and aims: Atherosclerosis is an important cause of clinical cardiovascular events. Atherosclerotic plaques are hypoxic, and reoxygenation improves plaque phenotype. Central players in hypoxia are hypoxia inducible factors (HIF) and their regulators, HIF-prolyl hydroxylase (PHD) isoforms 1, 2, and 3. PHD inhibitors, targeting all three isoforms, are used to alleviate anemia in chronic kidney disease. Likewise, whole-body PHD1 and PHD2ko ameliorate hypercholesterolemia and atherogenesis. As the effect of whole-body PHD3 is unknown, we investigated the effects of germline whole-body PHD3ko on atherosclerosis. Approach and Results: To initiate hypercholesterolemia and atherosclerosis low-density lipoprotein receptor knockout (LDLrko) and PHD3/LDLr double knockout (PHD3dko), mice were fed a high-cholesterol diet. Atherosclerosis and hypoxia marker pimonidazole were analyzed in aortic roots and brachiocephalic arteries. In contrast to earlier reports on PHD1- and PHD2-deficient mice, a small elevation in the body weight and an increase in the plasma cholesterol and triglyceride levels were observed after 10 weeks of diet. Dyslipidemia might be explained by an increase in hepatic mRNA expression of Cyp7a1 and fatty acid synthase, while lipid efflux of PHD3dko macrophages was comparable to controls. Despite dyslipidemia, plaque size, hypoxia, and phenotype were not altered in the aortic root or in the brachiocephalic artery of PHD3dko mice. Additionally, PHD3dko mice showed enhanced blood hematocrit levels, but no changes in circulating, splenic or lymphoid immune cell subsets. Conclusion: Here, we report that whole-body PHD3dko instigated an unfavorable lipid profile and increased hematocrit, in contrast to other PHD isoforms, yet without altering atherosclerotic plaque development.