Miracle-dz/UniFAR-FTUs huggingface dataset:
Pre-diagnostic predictors of mortality in patients with heart failure: The multi-ethnic study of atherosclerosis

Background There are multiple predictive factors for cardiovascular (CV) mortality measured at, or after heart failure (HF) diagnosis. However, the predictive role of long-term exposure to these predictors prior to HF diagnosis is unknown. Objectives We aim to identify predictive factors of CV mortality in participants with HF, using cumulative exposure to risk factors before HF development. Methods Participants of Multi-Ethnic Study of Atherosclerosis (MESA) with incident HF were included. We used stepwise Akaike Information Criterion to select CV mortality predictors among clinical, biochemical, and imaging markers collected prior to HF. Using the AUC of B-spline-corrected curves, we estimated cumulative exposure to predictive factors from baseline to the last exam before HF. The prognostic performance for CV mortality after HF was evaluated using competing risk regression with non-CV mortality as the competing risk. Results Overall, 375 participants had new HF events (42.9% female, mean age: 74). Over an average follow-up of 4.7 years, there was no difference in the hazard of CV death for HF with reduced versus preserved ejection fraction (HR = 1.27, p = 0.23). The selected predictors of CV mortality in models with the least prediction error were age, cardiac arrest, myocardial infarction, and diabetes, QRS duration, HDL, cumulative exposure to total cholesterol and glucose, NT-proBNP, left ventricular mass, and statin use. The AUC of the models were 0.72 when including the latest exposure to predictive factors and 0.79 when including cumulative prior exposure to predictive factors (p = 0.20). Conclusion In HF patients, besides age and diagnosed diabetes or CVD, prior lipid profile, NT-proBNP, LV mass, and QRS duration available at the diagnosis time strongly predict CV mortality. Implementing cumulative exposure to cholesterol and glucose, instead of latest measures, improves predictive accuracy for HF mortality, though not reaching statistical significance.
Elevated VCAM-1, MCP-1 and ADMA serum levels related to pulmonary fibrosis of interstitial lung disease associated with rheumatoid arthritis

Introduction: Early diagnosis of interstitial lung disease (ILD) associated with rheumatoid arthritis (RA) constitutes a challenge for the clinicians. Pulmonary vasculopathy is relevant in the development of interstitial lung disease. Accordingly, we aimed to explore the role of vascular cell adhesion molecule-1 (VCAM-1), monocyte chemoattractant protein-1 (MCP-1) and asymmetric dimethylarginine (ADMA), key molecules in the vasculopathy, as potential biomarkers of pulmonary fibrosis in RA-ILD+. Methods: We included 21 RA-ILD+ patients and two comparative groups: 25 RA-ILD- patients and 21 idiopathic pulmonary fibrosis (IPF) patients. Serum levels of the molecules were determined by ELISA, and mRNA expression was quantified by qPCR. Results: VCAM-1, MCP-1 and ADMA serum levels were increased in RA-ILD+ patients in relation to RA-ILD- and IPF patients. Additionally, RA-ILD+ patients exhibited increased CCL2 (gene encoding MCP-1) and decreased PRMT1 (gene related to ADMA synthesis) mRNA expression in relation to RA-ILD- patients. A lower expression of VCAM1, CCL2, and PRMT1 was observed in RA-ILD+ patients when compared with those with IPF. Furthermore, MCP-1 serum levels and PRMT1 mRNA expression were positively correlated with RA duration, and ADMA serum levels were positively associated with C-reactive protein in RA-ILD+ patients. Conclusion: Our study suggests that VCAM-1, MCP-1 and ADMA could be considered as useful biomarkers to identify ILD in RA patients, as well as to discriminate RA-ILD+ from IPF, contributing to the early diagnosis of RA-ILD+.
Cloning of TaeRF1 gene from Caucasian clover and its functional analysis responding to low-temperature stress

Low temperature (LT) is an important threat to the normal growth of plants. In this study, based on the full-length transcriptome sequencing results, the cold resistance genes were cloned from Caucasian clover with strong cold resistance. We cloned the CDS of TaeRF1, which is 1311 bp in length and encodes 436 amino acids. The molecular weight of the protein is 48.97 kDa, which had no transmembrane structure, and its isoelectric point (pI) was 5.42. We predicted the structure of TaeRF1 and found 29 phosphorylation sites. Subcellular localization showed that TaeRF1 was localized and expressed in cell membrane and chloroplasts. The TaeRF1 gene was induced by stress due to cold, salt, alkali and drought and its expression level was higher in roots and it was more sensitive to LT. Analysis of transgenic A. thaliana plants before and after LT treatment showed that the TaeRF1 gene enhanced the removal of excess H2O2, and increased the activity of antioxidant enzymes, thus improving the plant’s ability to resist stress. Additionally, the OE lines showed increased cold tolerance by upregulating the transcription level of cold-responsive genes (CBF1, CBF2, COR15B, COR47, ICE1, and RD29A). This study demonstrates that TaeRF1 is actively involved in the responses of plants to LT stress. We also provide a theoretical basis for breeding and a potential mechanism underlying the responses of Caucasian clover to abiotic stress.
Global transcriptomic analysis reveals candidate genes associated with different phosphorus acquisition strategies among soybean varieties

Introduction Soybean adapts to phosphorus-deficient soils through three important phosphorus acquisition strategies, namely altered root conformation, exudation of carboxylic acids, and symbiosis with clumping mycorrhizal fungi. However, the trade-offs and regulatory mechanisms of these three phosphorus acquisition strategies in soybean have not been researched. Methods In this study, we investigated the responses of ten different soybean varieties to low soil phosphorus availability by determining biomass, phosphorus accumulation, root morphology, exudation, and mycorrhizal colonization rate. Furthermore, the molecular regulatory mechanisms underlying root phosphorus acquisition strategies were examined among varieties with different low-phosphorus tolerance using transcriptome sequencing and weighted gene co-expression network analysis. Results and discussion The results showed that two types of phosphorus acquisition strategies—“outsourcing” and “do-it-yourself”—were employed by soybean varieties under low phosphorus availability. The “do-it-yourself” varieties, represented by QD11, Zh30, and Sd, obtained sufficient phosphorus by increasing their root surface area and secreting carboxylic acids. In contrast, the “outsourcing” varieties, represented by Zh301, Zh13, and Hc6, used increased symbiosis with mycorrhizae to obtain phosphorus owing to their large root diameters. Transcriptome analysis showed that the direction of acetyl-CoA metabolism could be the dividing line between the two strategies of soybean selection. ERF1 and WRKY1 may be involved in the regulation of phosphorus acquisition strategies for soybeans grown under low P environments. These findings will enhance our understanding of phosphorus acquisition strategies in soybeans. In addition, they will facilitate the development of breeding strategies that are more flexible to accommodate a variety of production scenarios in agriculture under low phosphorus environments. Background Association of gastric atrophy or cancer with levels of serum pepsinogens, gastrin-17 and anti-Helicobacter pylori IgG antibody have been extensively studied. However, the association of serum pepsinogen and gastrin-17 with H. pylori infection has not been studied in a large population.
The value of stereotactic biopsy of primary and recurrent brain metastases in the era of precision medicine

Background Brain metastases (BM) represent the most frequent intracranial tumors with increasing incidence. Many primary tumors are currently treated in protocols that incorporate targeted therapies either upfront or for progressive metastatic disease. Hence, molecular markers are gaining increasing importance in the diagnostic framework of BM. In cases with diagnostic uncertainty, both in newly diagnosed or recurrent BM, stereotactic biopsy serves as an alternative to microsurgical resection particularly whenever resection is not deemed to be safe or feasible. This retrospective study aimed to analyze both diagnostic yield and safety of an image-guided frame based stereotactic biopsy technique (STX). Material and methods Our institutional neurosurgical data base was searched for any surgical procedure for suspected brain metastases between January 2016 and March 2021. Of these, only patients with STX were included. Clinical parameters, procedural complications, and tissue histology and concomitant molecular signature were assessed. Results Overall, 467 patients were identified including 234 (50%) with STX. Median age at biopsy was 64 years (range 29 – 87 years). MRI was used for frame-based trajectory planning in every case with additional PET-guidance in 38 cases (16%). In total, serial tumor probes provided a definite diagnosis in 230 procedures (98%). In 4 cases (1.7%), the pathological tissue did not allow a definitive neuropathological diagnosis. 24 cases had to be excluded due to non-metastatic histology, leaving 206 cases for further analyses. 114 patients (49%) exhibited newly diagnosed BM, while 46 patients (20%) displayed progressive BM. Pseudoprogression was seen in 46 patients, a median of 12 months after prior therapy. Pseudoprogression was always confirmed by clinical course. Metastatic tissue was found most frequently from lung cancer (40%), followed by breast cancer (9%), and malignant melanoma (7%). Other entities included gastrointestinal cancer, squamous cell cancer, renal cell carcinoma, and thyroid cancer, respectively. In 9 cases (4%), the tumor origin could not be identified (cancer of unknown primary). Molecular genetic analyses were successful in 137 out of 144 analyzed cases (95%). Additional next-generation sequencing revealed conclusive results in 12/18 (67%) cases. Relevant peri-procedural complications were observed in 5 cases (2.4%), which were all transient. No permanent morbidity or mortality was noted. Conclusion In patients with BM, frame-based stereotactic biopsy constitutes a safe procedure with a high diagnostic yield. Importantly, this extended to discerning pseudoprogression from tumor relapse after prior therapy. Thus, comprehensive molecular characterization based on minimal-invasive stereotactic biopsies lays the foundation for precision medicine approaches in the treatment of primary and recurrent BM.
Frank's family of bivariate distributions

SUMMARY This paper examines the properties of a new class of bivariate distributions whose members are stochastically ordered and likelihood ratio dependent. The proposed class can be used to construct bivariate families of distributions whose marginals are arbitrary and which include the Frechet bounds as well as the distribution corresponding to independent variables. Three nonparametric estimators of the association parameter are suggested and Monte Carlo experiments are used to compare their small-sample behaviour to that of the maximum likelihood estimate.
Dublin’s saltmarshes contain climate-relevant carbon pools

Wetland ecosystems, particularly coastal vegetated ecosystems, play a vital role in climate mitigation and adaptation. Coastal vegetated habitats (including coastal wetlands such as seagrass meadows, saltmarshes, and mangroves) are some of the most efficient ecosystems for storing carbon on a per hectare basis, retaining organic carbon for centuries to millennia. We conducted carbon stock assessments, to a depth of 1 m, across four young saltmarsh sites and the adjacent mudflats in Dublin, Ireland. Soil cores and vegetation samples were taken across each site in order to analyze the carbon content of each carbon pool. The carbon density of Dublin’s saltmarshes was 112.1 ± 10.1 Mg C org ha− 1 . The dominant plant species were Spartina anglica, Plantago maritima, and Atriplex portulacoides. The soil carbon pool of these saltmarshes contributes 87% to the total carbon stock, with living plant biomass contributing the remaining 13%. Saltmarshes are important ecosystems for climate mitigation and can provide nature-based solutions to reduce net carbon emissions; however, their degradation will lead to the loss of climate-relevant carbon pools.
Divergent taxonomic responses of below-ground microbial communities to silicate fertilizer and biofertilizer amendments in two rice ecotypes

Using silicate fertilizer and bacterial inoculum as biofertilizer is significant for increasing soil silicon (Si) availability and rice agronomic performance. To use microbial technology for sustainable agriculture, it is crucial to have a deeper knowledge of how microbial populations shift among the plant hosts and related compartments, as well as how they respond to various fertilization models. In this study, the effects of silicate fertilizer, a single bacterial strain Bacillus mucilagniosis as biofertilizer, and their integrated application on soil physiochemical properties and soil microbiota structure, composition, and diversity in two eco-geographically diverse races (Indica and Japonica rice) were evaluated. Plant compartment, cultivar type, and fertilizer treatments contributed to microbiome variation. Indica and Japonica harbor different root microbiota; notably, taxa enriched in the rhizosphere soil were more diverse than in the root. Bacterial genera Leptonema, Azospira, Aquabacterium, Fluviicola, Aquabacterium, Leptonema, and fungal genera Metarhizium, Malassezia, and Cladosporium all were found in the rice core microbiome. Both silicate and biofertilizer applications increase the relative abundance of Betaproteobacteria, Deltaproteobacteria, and Actinobacteria, while suppressing fungal pathogens Alternaria and Fusarium. Silicate and bacterial inoculum applications increased the soil pH, available silicon content (ASi), available phosphorous (AP), available potassium (AK), and organic carbon (OC), while reduced the total nitrogen (N). These changes were also associated with major bacterial phyla Spirochaetes, Bacteroidetes, Actinobacteria, and Proteobacteria, except for Acidobacteria, and fungal phyla Ascomycota, Mortierellomycota and unassigned fungi. Several treatment-specific biomarkers were revealed through Linear discriminant analysis effect size (LEfSe) analysis. In conclusion, the change in the structure of root-associated communities driven by plant compartment and genetics suggests dynamic interactions in the host plant microbiome. Short-term silicate and biofertilizer amendments improved soil physiochemical status and altered bacterial and saprotrophic fungal communities, which have important implications for sustainable rice production.
Effects of varying types and amounts of herbivory and nutrient enrichment on a tropicalizing seagrass meadow

Climate change is impacting marine ecosystem community dynamics on a global scale. While many have assessed direct effects of climate change, indirect effects on marine ecosystems produced by biotic interactions remain poorly understood. For example, warming-induced range expansions and increased consumption rates of herbivores can lead to significant and unexpected changes in seagrass-dominated ecosystems. To better understand the threats tropicalization presents for the functioning of turtlegrass (Thalassia testudinum) meadows, we focused on the extensive turtlegrass beds of St. Joseph Bay, Florida in the northern Gulf of Mexico, a location with increasing numbers of tropically-associated green turtles. Our goals were to investigate experimentally how different grazing rates (natural and simulated),including high levels reflective of green turtle herbivory, coupled with nutrient supply, might alter turtlegrass structure and functioning in a higher latitude, subtropical turtlegrass meadow. We found that 4 months of varying levels of herbivory did not affect turtlegrass productivity, while 7 months of herbivory reduced percent cover, and 10 months reduced shoot density. Nutrient additions had few important effects. Ten months into the study, a massive recruitment of the herbivorous sea urchin (Lytechinus variegatus), whose densities reached 19 urchins/m2 completely overgrazed our study area and a large portion of the lush turtlegrass meadows of St. Joseph Bay. While local turtlegrass overgrazing had been previously noted at these urchin densities, a total loss of seagrass in such a large area has rarely ever been recorded. Overgrazing of the kind we observed, likely a result of both urchin and increasing green turtle grazing, can result in the loss of many key ecosystem services. As tropicalization continues, understanding how changes in biotic interactions, such as increased herbivory, affect higher latitude seagrass meadows will be necessary for their proper management and conservation.
Diet supplemented with olive cake as a model of circular economy: Metabolic and endocrine responses of beef cattle

Introduction Integrating by-products into livestock diet represents a great opportunity for implementing the concept of circular economy while reducing feed costs. Olive cake (OC) is considered an agro-industrial waste, but the high content of valuable metabolites makes it a promising feed integration. Therefore, this study investigated the effect of OC integration in beef cattle diet on different blood parameters. Methods Forty-eight young growing fattening Limousines-−24 bulls (body weight 350 ± 15 kg) and 24 heifers (280 ± 10 kg)—, aged 240 ± 20 days, were randomly allocated to 1 of 3 dietary treatments: concentrate at 0% (Control group: CTR), 10% (Low-olive cake group: L-OC), or 15% (High-olive cake group: H-OC) of OC inclusion. Blood samples and body weights were collected before administrating the supplemented diet (0 d), at the end of the stocker growing phase (56 d), and at the end of the fattening (147 d). After being slaughtered, animal carcasses were weighted. A linear regression model was fitted for each blood parameter with the 0 d as covariate and diet, time, sex, diet × time, and diet × sex as fixed effects. Results In males, body weight was highest in CTR, but carcass weight was similar in all the groups. All the blood parameters were within physiological ranges, independently from the animal diet. CTR group showed the highest alanine aminotransferase (ALT, P = 0.0027) and creatine kinase (P = 0.0119), whereas total bilirubin (P = 0.0023) was higher in H-OC than in CTR. Moreover, ALT was highest in CTR at 56 d, becoming similar in all the groups at 147 d (P = 0.0280). Instead, the increase observed in total cholesterol from 56 to 147 d was lower in H-OC compared with CTR and L-OC (P = 0.0451). A significant effect of diet × sex interaction was observed on triglycerides, urea, liver enzymes, and insulin. These data support the OC inclusion of up to 15% of the concentrate with no detrimental effect on beef cattle metabolic status. Discussion In conclusion, OC can be considered as a component in beef diet giving an opportunity to improve agriculture sustainability.
Complex sexual-social environments produce high boldness and low aggression behavioral syndromes

Introduction Evidence of animal personality and behavioral syndromes is widespread across animals, yet the development of these traits remains poorly understood. Previous research has shown that exposure to predators, heterospecifics, and urbanized environments can influence personality and behavioral syndromes. Yet, to date, the influence of early social experiences with conspecifics on the development of adult behavioral traits is far less known. We use swordtail fish (Xiphophorus nigrensis), a species with three genetically-determined male mating strategies (courtship display, coercion, or mixed strategy) to assess how different early-life social experiences shape adult behavioral development. Methods We raised female swordtails from birth to adulthood in density-controlled sexual-social treatments that varied in the presence of the type of male mating tactics (coercers only, displayers only, coercers and displayers, and mixed-strategists only). At adulthood, we tested females’ boldness, shyness, aggression, sociality, and activity. Results We found that the number of different mating strategies females were raised with (social complexity) shaped behavioral development more than any individual mating strategy. Females reared in complex environments with two male mating tactics were bolder, less shy, and less aggressive than females reared with a single male mating tactic (either courtship only or coercion only). Complex sexual-social environments produced females with behavioral syndromes (correlations between aggression and activity, shyness and aggression, and social interaction and activity), whereas simple environments did not. Discussion Importantly, the characteristics of these socially-induced behavioral syndromes differ from those driven by predation, but converge on characteristics emerging from animals found in urban environments. Our findings suggest that complexity of the sexual-social environment shapes the development of personality and behavioral syndromes to facilitate social information gathering. Furthermore, our research highlights the previously overlooked influence of sexual selection as a significant contributing factor to diverse behavioral development.
The contextual cogs of “migrant jobs”: A comparative study of the institutional determinants of migrant marginalization in European labor markets

Migrants play a significant role in European labor markets and are used as sources of “cheap labor”; often being disproportionately represented in low-wage, poor conditions, or otherwise precarious positions. Past research has suggested that the process of migrants being filtered into these low-end occupations is linked to institutional factors in receiving countries such as immigration policy, the welfare state and employment regulation. This paper calculates the extent of migrant marginalization in 17 European countries and uses qualitative comparative analysis (QCA) and regression modeling to understand how institutional factors operate and interact, leading to migrant marginalization. The QCA showed that when a country with a prominent low skills sector and restrictive immigration policy is combined with either strong employment protection legislation or a developed welfare state, migrants will be more strongly marginalized on the labor market. The results of the statistical analysis largely aligned with the idea that restrictive immigrant policy by itself and in combination with other factors can increase marginalization.