Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross‐kingdom transcriptomic trends in the evolution of hybrid gene expression

Hybridization is a route to speciation that occurs widely across the eukaryote tree of life. The success of allopolyploids (hybrid species with increased ploidy) and homoploid hybrids (with unchanged ploidy) is well documented. However, their formation and establishment is not straightforward, with a suite of near‐instantaneous and longer term biological repercussions faced by the new species. Central to these challenges is the rewiring of gene regulatory networks following the merger of distinct genomes inherited from both parental species. Research on the evolution of hybrid gene expression has largely involved studies on a single hybrid species or a few gene families. Here, we present the first standardized transcriptome‐wide study exploring the fates of genes following hybridization across three kingdoms: animals, plants and fungi. Within each kingdom, we pair an allopolyploid system with a closely related homoploid hybrid to decouple the influence of increased ploidy from genome merger. Genome merger, not changes in ploidy, has the greatest effect on posthybridization expression patterns across all study systems. Strikingly, we find that differentially expressed genes in parent species preferentially switch to more similar expression in hybrids across all kingdoms, likely as a consequence of regulatory trans‐acting cross‐talk within the hybrid nucleus. We also highlight the prevalence of gene loss or silencing among extremely differentially expressed genes in hybrid species across all kingdoms. These shared patterns suggest that the evolutionary process of hybridization leads to common high‐level expression outcomes, regardless of the particular species or kingdom.
Comparison of Bone-Level and Tissue-Level Implants: A Pilot Study with a Histologic Analysis and a 4-Year Follow-up.

This study clinically and histologically evaluated the performance of implants with different crestal morphologies: tissue-level implants and bone-level implants. Nine patients received at least two adjacent implants in an edentulous area: one bone-level implant (EO) and one tissue-level implant (TG) (total: 23 implants), placed beside each other using a single-stage delayed loading protocol. The implants were rehabilitated with screw-retained fixed partial dentures. Plaque Index (PI), bleeding on probing (BOP), probing depth (PD), and peri-implant bone level were recorded at various postsurgical follow-ups, including 2 and 6 months as well as 1 and 4 years. At 3 months postsurgery, soft tissue biopsy samples were taken from all implant sites and histologically analyzed. Longitudinal assessment of the results (TG vs EO implants) was performed using a linear mixed model with random intercept and by using Spearman correlation or chi-square after visual inspection of the probability distribution. Student t test was used to compare means, and chi-square test was used for dichotomic variables. P < . 05 was considered statistically significant. All implants were functional at 4 years. Peri-implant bone resorption was limited, with means of 1.20 ± 0.71 mm and 1.24 ± 0.82 mm for TG and EO implants, respectively. No significant differences in clinical parameters were identified between EO and TG implants. Histologic analysis revealed normal peri-implant soft tissue healing with poor inflammatory infiltrate. Differences in the histologic appearance of soft tissues were more related to patients than implant type. Both implants appeared to be suitable for partial rehabilitation of edentulous arches without differences in the investigated clinical and histologic parameters. However, TG implants showed a greater risk of implant collar exposure.
Mixed population hypothesis of the active and inactive PSII complexes opens a new door for photoinhibition and fluorescence studies: an ecophysiological perspective.

The current hypotheses for the mechanisms of photosystem II (PSII) photodamage in vivo remain split on the primary damage site. However, most researchers have considered that PSII is inhibited by a sole mechanism and that the photoinhibited PSII consists of one population. In this perspective, we propose 'the mixed population hypothesis', in which there are four PSII populations: PSII with active/inactive Mn4CaO5 oxygen-evolving complex respectively with functional/damaged primary quinone (QA) reduction activity. This hypothesis provides a new insight into not only the PSII photoinhibition/photoprotection studies but also the repair process. We discuss our new data implying that the repair rate differs in the respective PSII populations.
Value of the Immunization Program for Children in the 2017 US Birth Cohort.

BACKGROUND AND OBJECTIVES We evaluated the economic impact of routine childhood immunization in the United States (US), reflecting updated vaccine recommendations and recent data on epidemiology and coverage rates. METHODS An economic model followed the 2017 US birth cohort from birth through death; impact was modeled via a decision tree for each of the vaccines recommended for children by the Advisory Committee on Immunization Practices as of 2017 (with annual influenza vaccine considered in scenario analysis). Using information on historic prevaccine and vaccine-era incidence and disease costs, we calculated disease cases, deaths, disease-related healthcare costs, and productivity losses without and with vaccination, as well as vaccination program costs. We estimated cases and deaths averted due to vaccination, life-years (LYs) and quality-adjusted life-years (QALYs) gained due to vaccination, incremental costs (2019 US dollars), and the overall benefit-cost ratio (BCR) of routine childhood immunization from the societal and healthcare payer perspectives. RESULTS Over the cohort's lifetime, routine childhood immunization prevented over 17 million cases of disease and 31,000 deaths; 853,000 LYs and 892,000 QALYs were gained. Estimated vaccination costs ($8.5 billion) were fully offset by the $63.6 billion disease-related averted costs. Routine childhood immunization was associated with $55.1 billion (BCR of 7.5) and $13.7 billion (BCR of 2.8) in averted costs from a societal and healthcare payer perspective, respectively. CONCLUSIONS In addition to preventing unnecessary morbidity and mortality, routine childhood immunization is cost-saving. Continued maintenance of high vaccination coverage is necessary to ensure sustained clinical and economic benefits of the vaccination program.
Preliminary Radio Continuum Maps of Three Spiral Galaxies

Abstract The Australia Telescope Compact Array has been used in two 6 km configurations to make 12 hour observations of the radio continuum structure of three spiral galaxies at 1380 MHz and 2378 MHz. Radio maps of NGC 1792, 6300 and 1097 are presented here, as part of a survey to find examples of anomalous radio structures in spiral galaxies.
Clinical and molecular features of patients with COL1 ‐related disorders: Implications for the wider spectrum and the risk of vascular complications

Abnormalities in type I procollagen genes (COL1A1 and COL1A2) are responsible for hereditary connective tissue disorders including osteogenesis imperfecta (OI), specific types of Ehlers‐Danlos syndrome (EDS), and COL1‐related overlapping disorder (C1ROD). C1ROD is a recently proposed disorder characterized by predominant EDS symptoms of joint and skin laxity and mild OI symptoms of bone fragility and blue sclera. Patients with C1ROD do not carry specific variants for COL1‐related EDS, including classical, vascular, cardiac‐valvular, and arthrochalasia types. We describe clinical and molecular findings of 23 Japanese patients with pathogenic or likely pathogenic variants of COL1A1 or COL1A2, who had either OI‐like or EDS‐like phenotypes. The final diagnoses were OI in 17 patients, classical EDS in one, and C1ROD in five. The OI group predominantly experienced recurrent bone fractures, and the EDS group primarily showed joint hypermobility and skin hyperextensibility, though various clinical and molecular overlaps between OI, COL1‐related EDS, and C1ROD as well as intrafamilial phenotypic variabilities were present. Notably, life‐threatening vascular complications (vascular dissections, arterial aneurysms, subarachnoidal hemorrhages) occurred in seven patients (41% of those aged >20 years) with OI or C1ROD. Careful lifelong surveillance and intervention regarding bone and vascular fragility could be required.
Investigating the active components of Huatan Tongjing decoction for the treatment of polycystic ovary syndrome via network pharmacology

Polycystic ovary syndrome (PCOS) is a common endocrine disease in women, potentially causing ovarian infertility for women at gestational age. Huatan Tongjing Decoction is commonly used to treat PCOS; however, the involved molecular mechanism has not been fully understood. In this study, the active components of Huatan Tongjing Decoction and potentially targeted proteins were downloaded from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. PCOS‐related genes were accessed from Malacards database. STRING database was utilized to construct a protein–protein interaction (PPI) network based on the PCOS‐related genes and the predicted targets. Subsequently, the PPI network was subjected to Random walk with restart (RWR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on top 50 genes with the high affinity scores to the drug targets. Subsequently, based on the predicted drug components and targets, a component–gene interaction network was constructed. Finally, the most central drug targets were selected, and the corresponding compounds were subjected to molecular docking and dynamic simulations to examine their bindings. The 122 main active components and 246 potential targets of Huatan Tongjing Decoction were obtained from TCMSP, and a total of 259 nodes and 1919 interactions were acquired from the PPI network. The top 50 genes were mainly enriched in response to peptide hormone function and PI3K‐Akt signaling pathway. Molecular docking and dynamic simulations predicted that MMP‐quercetin interaction played an important role in the treatment of PCOS using Huatan Tongjing Decoction. Luteolin and quercetin in Huatan Tongjing Decoction potentially bound MMP9 and served as active components. This study preliminarily suggested the efficacy of Huatan Tongjing Decoction against PCOS in molecular degree.
PPARgamma agonism inhibits progression of premalignant lesions in a murine lung squamous cell carcinoma model

The N‐nitroso‐trischloroethylurea (NTCU)‐induced mouse model of squamous lung carcinoma recapitulates human disease from premalignant dysplasia through invasive tumors, making it suitable for preclinical chemoprevention drug testing. Pioglitazone is a peroxisome proliferator‐activated receptor γ (PPARγ) agonist shown to prevent lung tumors in preclinical models. We investigated pioglitazone's effect on lesion development and markers of potential preventive mechanisms in the NTCU model. Female FVB/N mice were exposed to vehicle, NTCU or NTCU + oral pioglitazone for 32 weeks. NTCU induces the appearance of basal cells in murine airways while decreasing/changing their epithelial cell makeup, resulting in development of bronchial dysplasia. H&E and keratin 5 (KRT5) staining were used to detect and grade squamous lesions in formalin fixed lungs. mRNA expression of epithelial to mesenchymal transition (EMT) markers and basal cell markers were measured by qPCR. Dysplasia persistence markers desmoglein 3 and polo like kinase 1 were measured by immunohistochemistry. Basal cell markers KRT14 and p63, club cell specific protein and ciliated cell marker acetylated tubulin were measured by immunofluorescence. Pioglitazone treatment significantly reduced squamous lesions and the presence of airway basal cells, along with increasing normal epithelial cells in the airways of NTCU‐exposed mice. Pioglitazone also significantly influenced EMT gene expression to promote a more epithelial, and less mesenchymal, phenotype. Pioglitazone reduced the presence of squamous dysplasia and maintained normal airway cell composition. This work increases the knowledge of mechanistic pathways in PPARγ agonism for lung cancer interception and provides a basis for further investigation to advance this chemoprevention strategy.
Immune and Genetic Signatures of Breast Carcinomas Triggering Anti-Yo–Associated Paraneoplastic Cerebellar Degeneration

Background and Objectives Paraneoplastic cerebellar degeneration (PCD) with anti-Yo antibodies is a cancer-related autoimmune disease directed against neural antigens expressed by tumor cells. A putative trigger of the immune tolerance breakdown is genetic alteration of Yo antigens. We aimed to identify the tumors' genetic and immune specificities involved in Yo-PCD pathogenesis. Methods Using clinicopathologic data, immunofluorescence (IF) imaging, and whole-transcriptome analysis, 22 breast cancers (BCs) associated with Yo-PCD were characterized in terms of oncologic characteristics, genetic alteration of Yo antigens, differential gene expression profiles, and morphofunctional specificities of their in situ antitumor immunity by comparing them with matched control BCs. Results Yo-PCD BCs were invasive carcinoma of no special type, which early metastasized to lymph nodes. They overexpressed human epidermal growth factor receptor 2 (HER2) but were hormone receptor negative. All Yo-PCD BCs carried at least 1 genetic alteration (variation or gain in copy number) on CDR2L, encoding the main Yo antigen that was found aberrantly overexpressed in Yo-PCD BCs. Analysis of the differentially expressed genes found 615 upregulated and 54 downregulated genes in Yo-PCD BCs compared with HER2-driven control BCs without PCD. Ontology enrichment analysis found significantly upregulated adaptive immune response pathways in Yo-PCD BCs. IF imaging confirmed an intense immune infiltration with an overwhelming predominance of immunoglobulin G–plasma cells. Discussion These data confirm the role of genetic alterations of Yo antigens in triggering the immune tolerance breakdown but also outline a specific biomolecular profile in Yo-PCD BCs, suggesting a cancer-specific pathogenesis.
Influence of the angle between tibial and prosthesis mechanical axes on tibial bone remodeling in total knee arthroplasty

Osteoarthritis of the knee is one of the most common diseases that affect the quality of life in the elderly population, and Total Knee Arthroplasty is considered the only real treatment for it, and as with any other surgery, a suboptimal technique may lead to an undesirable outcome. This paper aims to investigate the effects of the angle between mechanical axes of the tibia and the implant on the bone remodeling process. A 3D model was reconstructed using CT images, which was then used in an ABAQUS model with a USDFLD subroutine to simulate bone remodeling post TKA. The USDFLD subroutine compares the strain energy density from each increment to that of the previous increment to determine how the bone density will change. Simulation results suggest that when the prosthesis is inclined to one side, stress and density distribution increase, whereas stress and bone density decrease substantially on the opposite side. This decrease in bone density can be as much as 35% in the coronal plane. Sagittal malalignment results suggest that the effect would be relatively localized to the vicinity of the cutting plane. Results suggest uniform load distribution may be achieved when the two mechanical axes are kept parallel, which in turn can lead to decreased prosthesis loosening and bone fractures.
Diet quality during pregnancy and its association with social factors: 3D Cohort Study (Design, Develop, Discover)

Abstract Good diet quality during pregnancy provides adequate nutrition to support both the mothers and the fetus. The objective of this study is to describe the distribution of diet quality during pregnancy and to study the association between social factors and diet quality during pregnancy in a Canadian population. This study was based on 1535 pregnant women who provided dietary information in the 3D Cohort Study in Quebec, Canada. A 3‐day food record was used to collect dietary intake in the second trimester of pregnancy. A Canadian adaption of the Healthy Eating Index (HEI‐C) 2010 was used to quantify diet quality. Univariate and multiple linear regression models were used to calculate unadjusted and adjusted effect estimates and confidence intervals for the association between social factors and HEI‐C. The mean HEI‐C 2010 score in this study was 62.9 (SD: 11.2). Only 4.5% and 8.3% of the pregnant women consumed the recommended amounts of whole grains and ‘greens and beans’, respectively. Diet quality was lower in some subgroups of pregnant women. After multivariable adjustment, lower diet quality was observed in participants who were less educated, younger, overweight or obese before pregnancy, or parous. There was an interaction between ethnicity and immigration status on diet quality in pregnancy. These findings could be useful for health practitioners and policymakers in developing strategies to improve the diet quality of pregnant women.
New insights in improving sustainability in meat production: opportunities and challenges

Abstract Treating livestock as senseless production machines has led to rampant depletion of natural resources, enhanced greenhouse gas emissions, gross animal welfare violations, and other ethical issues. It has essentially instigated constant scrutiny of conventional meat production by various experts and scientists. Sustainably in the meat sector is a big challenge which requires a multifaced and holistic approach. Novel tools like digitalization of the farming system and livestock market, precision livestock farming, application of remote sensing and artificial intelligence to manage production and environmental impact/GHG emission, can help in attaining sustainability in this sector. Further, improving nutrient use efficiency and recycling in feed and animal production through integration with agroecology and industrial ecology, improving individual animal and herd health by ensuring proper biosecurity measures and selective breeding, and welfare by mitigating animal stress during production are also key elements in achieving sustainability in meat production. In addition, sustainability bears a direct relationship with various social dimensions of meat production efficiency such as non-market attributes, balance between demand and consumption, market and policy failures. The present review critically examines the various aspects that significantly impact the efficiency and sustainability of meat production.
Competitive game motivation and trait aggression among Chinese adolescent players of Glory of the King: The mediating role of avatar identification and game aggression.

Previous studies have shown that competitive video gaming is associated with aggression; however, little is known about the relationship between personal competitive factors and aggression. Thus, we used structural equation modeling to examine the association between competitive game motivation and trait aggression, as well as the potential mediating roles of avatar identification and game aggression, among 1584 (59.66% male; Mage = 14.58 years, SD = 1.49, range = 12-19) Chinese adolescent players of Glory of the King. The results showed that the direct effect of competitive game motivation on trait aggression was statistically significant, as were the indirect effects of competitive motivation-via both avatar identification and game aggression-on the three indicators of aggressive behavioral tendencies in everyday life. These results support the General Aggression Model, suggesting that competitive motivation is a personal factor predicting trait aggression. It contributes to our understanding of the roles of competition in video gamers' real-life aggressive behavior from an individual perspective.
Machine learning-based estimation of riverine nutrient concentrations and associated uncertainties caused by sampling frequencies

Accurate and sufficient water quality data is essential for watershed management and sustainability. Machine learning models have shown great potentials for estimating water quality with the development of online sensors. However, accurate estimation is challenging because of uncertainties related to models used and data input. In this study, random forest (RF), support vector machine (SVM), and back-propagation neural network (BPNN) models are developed with three sampling frequency datasets (i.e., 4-hourly, daily, and weekly) and five conventional indicators (i.e., water temperature (WT), hydrogen ion concentration (pH), electrical conductivity (EC), dissolved oxygen (DO), and turbidity (TUR)) as surrogates to individually estimate riverine total phosphorus (TP), total nitrogen (TN), and ammonia nitrogen (NH4+-N) in a small-scale coastal watershed. The results show that the RF model outperforms the SVM and BPNN machine learning models in terms of estimative performance, which explains much of the variation in TP (79 ± 1.3%), TN (84 ± 0.9%), and NH4+-N (75 ± 1.3%), when using the 4-hourly sampling frequency dataset. The higher sampling frequency would help the RF obtain a significantly better performance for the three nutrient estimation measures (4-hourly > daily > weekly) for R2 and NSE values. WT, EC, and TUR were the three key input indicators for nutrient estimations in RF. Our study highlights the importance of high-frequency data as input to machine learning model development. The RF model is shown to be viable for riverine nutrient estimation in small-scale watersheds of important local water security.
Quasi-classical Ground States. I. Linearly Coupled Pauli-Fierz Hamiltonians

We consider a spinless, non-relativistic particle bound by an external potential and linearly coupled to a quantized radiation field. The energy $\mathcal{E}(u,f)$ of product states of the form $u\otimes \Psi_f$, where $u$ is a normalized state for the particle and $\Psi_f$ is a coherent state in Fock space for the field, gives the energy of a Klein-Gordon--Schr\''odinger system. We minimize the functional $\mathcal{E}(u,f)$ on its natural energy space. We prove the existence and uniqueness of a ground state under general conditions on the coupling function. In particular, neither an ultraviolet cutoff nor an infrared cutoff is imposed. Our results establish the convergence in the ultraviolet limit of both the ground state and ground state energy of the Klein-Gordon--Schr\''odinger energy functional, and provide the second-order asymptotic expansion of the ground state energy at small coupling.
Jets, Disks and Winds from Spinning Black Holes: Nature or Nurture?

A brief summary is given of an alternative interpretation of the Event Horizon Telescope observations of the massive black hole in the nucleus of the nearby galaxy M87. It is proposed that the flow is primarily powered by the black hole rotation, not the release of gravitational energy by the infalling gas. Consequently, the observed millimetre emission is produced by an “ergomagnetosphere” that connects the black hole horizon to an “ejection disk” from which most of the gas supplied at a remote “magnetopause” is lost through a magnetocentrifugal wind. It is argued that the boundary conditions at high latitude on the magnetopause play a crucial role in the collimation of the relativistic jets. The application of these ideas to other types of source is briefly discussed.