Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal Geostatistical Methods for Interpolation of the Ionosphere: A Case Study on the St Patrick’s Day Storm of 2015

Geostatistical Analyst is a set of advanced tools for analysing spatial data and generating surface models using statistical and deterministic methods available in ESRI ArcMap software. It enables interpolation models to be created on the basis of data measured at chosen points. The software also provides tools that enable analyses of the data variability, setting data limits and checking global trends, as well as creating forecast maps, estimating standard error and probability, making various surface visualisations, and analysing spatial autocorrelation and correlation between multiple data sets. The data can be interpolated using deterministic methods providing surface continuity, and also by stochastic techniques like kriging, based on a statistical model considering data autocorrelation and providing expected interpolation errors. These properties of Geostatistical Analyst make it a valuable tool for modelling and analysing the Earth’s ionosphere. Our research aims to test its applicability for studying the ionosphere, and ionospheric disturbances in particular. As raw source data, we use Global Navigation Satellite Systems (GNSS)-derived ionospheric total electron content. This paper compares ionosphere models (maps) developed using various interpolation methods available in Geostatistical Analyst. The comparison is based on several indicators that can provide the statistical characteristics of an interpolation error. In this contribution, we use our own method, the parametric assessment of the quality of estimation (MPQE). Here, we present analyses and a discussion of the modelling results for various states of the ionosphere: On the disturbed day of the St Patrick’s Day geomagnetic storm of 2015, one quiet day before the storm and one day after its occurrence, reflecting the ionosphere recovery phase. Finally, the optimal interpolation method is selected and presented.
Biomarkers of Muscle Metabolism in Peripheral Artery Disease: A Dynamic NIRS-Assisted Study to Detect Adaptations Following Revascularization and Exercise Training

We assessed whether muscle metabolism biomarkers (MMb) identified by near-infrared spectroscopy (NIRS) are valid for determining adaptations following revascularization or exercise training in peripheral artery disease (PAD). Eighteen patients (males n = 13; 69 ± 7 years) were randomized to receive revascularization (Rev = 6) or pain-free home-based exercise (Ex = 12). MMb were safely collected via a NIRS-assisted treadmill test as area-under-curve for the spectra of oxygenated (-oxy), deoxygenated (-deoxy), differential (-diff) and total (-tot) hemoglobin traces. MMb, ankle–brachial index (ABI), pain-free (PFWD) and 6-min (6MWD) walking distances were assessed at baseline and after four months. MMb were correlated at baseline with ABI (MMb-oxy r = 0.46) and 6MWD (MMb-tot r = 0.51). After treatments, MMb-oxy showed an expected increase, which was more relevant for Rev group than the Ex (56% vs. 20%), with trends towards normalization for the other MMb. These changes were significantly correlated with variations in ABI (MMb-oxy r = 0.71; p = 0.002) and 6MWD (MMb-tot r = 0.58; p = 0.003). The MMb-diff in Rev group and MMb-deoxy in Ex group at baseline predicted clinical outcomes being correlated with PFWD improvements after 4-month (r = −0.94; p = 0.005 and r = −0.57; p = 0.05, respectively). A noninvasive NIRS-based test, feasible in a clinical setting, identified muscle metabolism biomarkers in PAD. The novel MMb were associated with validated outcome measures, selectively modified after different interventions and able to predict long-term functional improvements after surgery or exercise training.
Plant Growth-promoting Fungus Penicillium oxalicum Enhances Plant Growth and Induces Resistance in Pearl Millet Against Downy Mildew Disease

Plant Growth-promoting Fungus (PGPF) Penicillium oxalicum was isolated from rhizosphere soil of pearl millet and was tested for its ability to promote growth and induce systemic resistance in pearl millet against downy mildew disease. The fungal isolate P. oxalicum UOM PGPF 16 was identified as P. oxalicum using ITS sequencing and morphological analysis and sequence was deposited at NCBI with accession number KF150220. Pearl millet susceptible seeds were treated with three different inducers (CS, CF and LCF) of PGPF P. oxalicum and all the inducers significantly reduced the downy mildew disease and enhanced plant growth. Among the inducers tested, CS treatment recorded highest seed germination of 91% and 1427 seedling vigour followed by LCF and CF treatments. The vegetative growth parameter and NPK uptake studies under greenhouse conditions revealed that the CS treatment of P. oxalicum remarkably enhanced the parameters tested when compared to control plants. A significant disease protection of 62% and 58% against downy mildew disease was observed in plants pretreated with CS of P. oxalicum under greenhouse and field conditions, respectively. The spatio-temporal studies revealed that inducers P. oxalicum required a minimum of 3 days for developing maximum disease resistance which was maintained thereafter. The maximum Peroxidase (POX) activity (62.7 U) was observed at 24 h in seedlings treated with CS of PGPF P. oxalicum and the activity gradually reduced at later time points after pathogen inoculation. Chitinase (CHT) activity was significantly higher in inducer treated seedlings when compared to control seedlings inoculated with pathogen after 48 h and remained constant at all time points.
Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-C

Abstract The complete sequence (37,609 bp) of the mitochondrial DNA (mtDNA) of the Saccharina sp. ye-C was determined using Illumina sequencing data. The genome contains 38 protein-coding genes (PCG), 3 ribosomal RNA (rRNA), 25 transfer RNA (tRNA) genes that are typical of Saccharina mtDNA. The phylogenetic analysis based on the mitochondrial genomes of brown algae showed that Saccharina sp. ye-C formed a robust clade with Saccharina coriacea, which strongly supports their close phylogenetic relationship.
Systemic Colonization by Metarhizium robertsii Enhances Cover Crop Growth

Fungi in the genus Metarhizium (Hypocreales: Clavicipitaceae) are insect pathogens that can establish as endophytes and can benefit their host plant. In field experiments, we observed a positive correlation between the prevalence of M. robertsii and legume cover crops, and a negative relationship with brassicaceous cover crops and with increasing proportion of cereal rye in mixtures. Here, we report the effects of endophytic M. robertsii on three cover crop species under greenhouse conditions. We inoculated seeds of Austrian winter pea (Pisum sativum L., AWP), cereal rye (Secale cereale L.), and winter canola (Brassica napus L.) with conidia of M. robertsii to assess the effects of endophytic colonization on cover crop growth. We recovered M. robertsii from 59%, 46%, and 39% of seed-inoculated AWP, cereal rye, and canola plants, respectively. Endophytic M. robertsii significantly increased height and above-ground biomass of AWP and cereal rye but did not affect chlorophyll content of any of the cover crop species. Among inoculated plants from which we recovered M. robertsii, above-ground biomass of AWP was positively correlated with the proportion of colonized root but not leaf tissue sections. Our results suggest that winter cover crops may help to conserve Metarhizium spp. in annual cropping systems.
Biomechanics and hemodynamics of stent-retrievers

In 2015, multiple randomized clinical trials showed an unparalleled treatment benefit of stent-retriever thrombectomy as compared to standard medical therapy for the treatment of a large artery occlusion causing acute ischemic stroke. A short time later, the HERMES collaborators presented the patient-level pooled analysis of five randomized clinical trials, establishing class 1, level of evidence A for stent-retriever thrombectomy, in combination with intravenous thrombolysis when indicated to treat ischemic stroke. In the years following, evidence continues to mount for expanded use of this therapy for a broader category of patients. The enabling technology that changed the tide to support endovascular treatment of acute ischemic stroke is the stent-retriever. This review summarizes the history of intra-arterial treatment of stroke, introduces the biomechanics of embolus extraction with stent-retrievers, describes technical aspects of the intervention, provides a description of hemodynamic implications of stent-retriever embolectomy, and proposes future directions for a more comprehensive, multi-modal endovascular approach for the treatment of acute ischemic stroke.
Quality of life, depression, and psychosocial mechanisms of suicide risk in prostate cancer.

INTRODUCTION Prostate cancer (PCa) is the most common non-cutaneous cancer in men and is usually identified at a stage at which prolonged survival is expected. Therefore, strategies to address survivorship and promote well-being are crucial. This study's aim was to better understand suicidal behavior in PCa patients by examining psychosocial mediators (i.e., depression, psychache, perceived burdensomeness [PB], thwarted belongingness [TB]) in the relationship between quality of life (PCa-QoL) and suicide risk. METHODS Four hundred and six men with PCa (Median age 69.35 years, standard deviation 7.79) completed an online survey on various psychosocial variables associated with suicide risk. A combined serial/parallel mediation model tested whether depression, in serial with both psychache and PB/TB, mediated the relationship between PCa-QoL and suicide risk. RESULTS Over 14% of participants' self-reports indicated clinically significant suicide risk. Poorer PCa-QoL was related to greater depression, which was related to both greater psychache and PB/TB, which was associated with greater suicide risk. The serial mediation effect of depression and psychache was significantly stronger than that of depression and PB/TB. PCa-QoL did not predict suicide risk through depression alone, showing that depressive symptoms affect suicide risk through psychache and PB/TB. CONCLUSIONS Given the alarming estimate of individuals at-risk for suicide in this study, clinicians should consider patients with poorer PCa-QoL and elevated depression for psychosocial referral or management. Psychache (i.e., psychological pain) and PB/TB (i.e., poor social fit) may be important targets for reducing suicide risk intervention beyond the impact of depression alone.
Supporting Online Material Materials and Methods Figs. S1 to S50 Tables S1 to S18 References Identification of Functional Elements and Regulatory Circuits by Drosophila Modencode

has an advisory role with DNANexus, a DNA sequence storage and analysis company. Transfer of GFP-tagged fosmids requires a Materials Transfer Agreement with the Max Planck Institute of Molecular Cell Biology and Genetics. Raw microarray data are available from the Gene Expression Omnibus archive, and raw sequencing data are available from the SRA archive (accessions are in table S18). We appreciate help from for sharing data on poly(A) sites before publication, WormBase curator G. Williams for assistance in quality checking and preparing the transcriptomics data sets for publication, as well as his fellow curator P. Davis for reviewing and hand-checking the list of pseudogenes. || To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage-and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation. S everal years after the complete genetic se-quencing of many species, it is still unclear how to translate genomic information into a functional map of cellular and developmental programs. The Encyclopedia of DNA Elements (ENCODE) (1) and model organism ENCODE (modENCODE) (2) projects use diverse genomic assays to comprehensively annotate the Homo sapiens (human), Drosophila melanogaster (fruit fly), and Caenorhabditis elegans (worm) genomes, through systematic generation and computational integration of functional genomic data sets. Previous genomic studies in flies have made seminal contributions to our understanding of basic biological mechanisms and genome functions , facilitated by genetic, experimental, computational , and manual annotation of the euchromatic and heterochromatic genome (3), small genome size, short life cycle, and a deep knowledge of development, gene function, and chromosome biology. The functions of ~40% of the protein-and nonprotein-coding genes [FlyBase 5.12 (4)] have been determined from cDNA collections (5, 6), manual curation of gene models (7), gene mutations and comprehensive genome-wide RNA interference …
On the Evolution of the Vertebrata, Progressive and Retrogressive (Continued)

consider ourselves as respectable and useful among man's companions, and in our habits we would show the generations of culture we have received. Leaving our plant and returning to human experience, we can summarize our view by saying that the problem of similarity of types with great structural diversity of kernel, is only soluble by influences which have had a very long period of time to work in; and the perfectness of the result attained is to be explained only upon the supposition of a very long period of intelligent selective action. It is very probable that a more intimate acquaintance with the facts concerning the development of a single domesticated plant, as gained from philological, physiological and recorded data will some time or other tend to throw some light upon the antiquity of man and the direction and extent of his migrations.
Biomarkers for Temporomandibular Disorders: Current Status and Future Directions

Numerous studies have been conducted in the previous years with an objective to determine the ideal biomarker or set of biomarkers in temporomandibular disorders (TMDs). It was recorded that tumour necrosis factor (TNF), interleukin 8 (IL-8), IL-6, and IL-1 were the most common biomarkers of TMDs. As of recently, although the research on TMDs biomarkers still aims to find more diagnostic agents, no recent study employs the biomarker as a targeting point of pharmacotherapy to suppress the inflammatory responses. This article represents an explicit review on the biomarkers of TMDs that have been discovered so far and provides possible future directions towards further research on these biomarkers. The potential implementation of the interactions of TNF with its receptor 2 (TNFR2) in the inflammatory process has been interpreted, and thus, this review presents a new hypothesis towards suppression of the inflammatory response using TNFR2-agonist. Subsequently, this hypothesis could be explored as a potential pain elimination approach in patients with TMDs.
Qiliqiangxin improves cardiac function and attenuates cardiac remodelling in doxorubicin-induced heart failure rats

Abstract Context Therapeutic doxorubicin administration is restricted as this anticancer drug may be cardiotoxic. The traditional Chinese medicine qiliqiangxin has been approved for clinical treatment of chronic heart failure. Objective To explore the protective effects and molecular mechanisms of qiliqiangxin on doxorubicin-induced congestive heart failure (CHF) in rats. Materials and methods A CHF rat model was established via intraperitoneal DOX injections (2.5 mg/kg/week) for 6 weeks. The rats were randomly assigned to control, CHF, CHF + QL (1.0 g/kg/d), or captopril (3.8 mg/kg/d) treatment groups (n = 10) for 4 weeks. MicroRNA sequencing elucidated the molecular mechanisms of qiliqiangxin on doxorubicin-induced CHF in rats. Results Unlike in the CHF group, QL significantly reduced Bax:Bcl-2 (2.05 ± 0.23 vs. 0.94 ± 0.09, p < 0.05) and the levels of collagen I (0.19 ± 0.02 vs. 0.15 ± 0.01, p < 0.05), collagen III (0.19 ± 0.02 vs. 0.14 ± 0.02, p < 0.05), TGF-β1 (5.28 ± 0.89 vs. 2.47 ± 0.51, p < 0.05), Smad3 (1.23 ± 0.12 vs. 0.78 ± 0.09, p < 0.05), MMP-2 (0.89 ± 0.01 vs. 0.53 ± 0.05, p < 0.05), and TIMP-2 (0.24 ± 0.03 vs. 0.44 ± 0.03, p < 0.05). QL also upregulated TGF-β3 (0.65 ± 0.06 vs. 0.96 ± 0.10, p < 0.05) and Smad7 (0.09 ± 0.01 vs. 0.19 ± 0.023, p < 0.05). Moreover, Smad3 was a target of miR-345-3p. Discussion and Conclusions The beneficial effects of QL on DOX-induced CHF in rats are mediated by reduction in myocardial fibrosis, promotion of TGF-β3/Smad7, and inhibition of TGF-β1/Smad3. QL may also modulate specific miRNAs. These results provide evidence that QL might be an effective treatment for DOX-induced CHF.
Association between Pet Ownership and Obesity: A Systematic Review and Meta-Analysis

Obesity is a major risk factor for lifestyle-related diseases, including cardiovascular disease, type 2 diabetes, and hypertension. Several studies have investigated the association between pet ownership and obesity, but the findings have been inconsistent. This systematic literature review and meta-analysis assessed the association between pet ownership and obesity. Using PubMed and Scopus, we overviewed the literature published until December 2019 and selected pertinent data for meta-analysis. Two independent reviewers extracted the data. Pooled relative risks (RRs) with 95% confidence intervals (CIs) for obesity were calculated using the random-effects model with inverse-variance weighting. The 21 included articles were cross-sectional studies. Five publications (nine analyses) that reported adjusted RRs for BMI ≥ 25 were included in the meta-analysis. No significant association existed between pet ownership and obesity (pooled RR = 1.038; 95% CI, 0.922–1.167; I2 = 51.8%). After stratification by age group (children vs. adults), no significant association was detected (pooled RR = 0.844; 95% CI, 0.604–1.179; I2 = 64.1% vs. pooled RR = 1.099; 95% CI, 0.997–1.212; I2 = 25.2%). Similarly, no significant association was observed between dog ownership and obesity, indicating no association between pet ownership and obesity. However, no infer causation can be reported because all studies included in this meta-analysis were cross-sectional. Therefore, further prospective studies are needed.
An Isolated Prairie Grove and Its Phytogeographical Significance

Probably less study has been given in recent times to the relation of prairie and forest than to any other general phytogeographical problem in the central states. Some of the large number of questions still awaiting satisfactory solution were briefly stated in a former paper, and in the following pages some evidence bearing on one of them is given and some conclusions of a more general nature are drawn. The present paper is not so much a description of modern conditions as an attempt to explain by existing distribution certain historical features of the relation of forest and prairie in central Illinois. It is probable that the conclusions drawn from the local area apply equally well to many other portions of the eastern extension of the Prairie Province. Early histories and maps show that the prairies of central Illinois were not continuous, but occupied chiefly the higher ground between the drainage systems. The latter were bordered in their lower courses by forests, which occupied the floodplain and bluffs and extended out a short distance on the uplands. The sources of the streams were usually in the prairie, and their margins were occupied by prairie vegetation for the first few miles. Scattered about on the prairie were a few isolated groves, far removed from the larger bodies of forest along the water courses. These groves were important to the Indians and early settlers as landmarks and camping grounds, and at a later period formed centers from which the settlement of the prairie proceeded. Bur Oak Grove is an example of such an isolated area of forest. It is situated in the east-central part of Champaign County, on the east side of the
Early life factors and their relevance to intima-media thickness of the common carotid artery in early adulthood

Abstract Introduction Early life factors may predispose an offspring to cardiovascular risk factors in later life. It is plausible a range of exposures in early life may be involved in this predisposition, which may extend to “healthy” populations in Western populations. We examined the association between a number of early life factors with the carotid intima-media thickness (IMT), a surrogate marker of atherosclerosis, in early adulthood of a healthy German population. Methods We studied term participants (n = 265) of the DONALD Study, with a bilateral sonographic measurement of the IMT in young adulthood (18–40 years) and data on early life factors (maternal and paternal age at child birth, birth weight (including appropriateness of birth weight- for gestational age), gestational weight gain and full breastfeeding (breastfeeding > 17weeks). Sonographic IMT measurements were performed on the left and right common carotid artery using a minimum of 4 measurements. Mean IMT values were obtained averaging the measurements from both sides, an overall average obtained from 8 and 16 measurement of both sides was used for this analysis. Information on gestation and birth were abstracted from the “Mutterpass”, maternal and paternal age at birth were inquired at study entry and breastfeeding information was assessed prospectively. Prospective association between early life factors and IMT were analyzed using multivariable linear regression models, considering age at IMT measurement, physician taking the measurement, in addition: birth year, first born status, maternal and paternal educational status, maternal overweight, presence of smokers in the household tested for potential confounding. Results Mean adult IMT was 0.56mm ± 0.03, range: 0.41mm-0.78 mm. Maternal age at child birth was of prospective relevance for IMT in young adulthood, however, this association was sex specific: Increased maternal age at child birth was independently associated with an increased IMT among female offspring during young adulthood (β 0.029, SE 0.009) mm/decade, P = 0.003) only, this was not mediated by adult waist circumference. None of the remaining early life factors showed relevance for adult IMT levels among males and females in early adulthood. Conclusion This study suggests that advanced maternal age at child birth is of prospective relevance for IMT levels in younger adulthood in a healthy Western population. This association appears to be sex specific, with maternal age at child birth positively associated with IMT in females in early adulthood only.