Miracle-dz/UniFAR-FTUs huggingface dataset:
Music Discovery as Differentiation Strategy for Streaming Providers

Music discovery presents itself in an instant and in a multitude of possible ways. When comparing the user personas of streaming services in the dimension of music discovery, two main differentiation criteria become apparent, namely the degree of intention and the control one wants to exert when discovering new music. Against this background, this paper proposes a framework which categorises the possible ways of music discovery in a streaming provider with the help of those two criteria into active, semi-active, semi-passive and passive ways in order to analyse them separately, outline success factors and current research.
Influence of Humic Substances on the Sorption Interactions between Lanthanide and Actinide Ions and Clay Minerals

Lanthanide (Eu, Nd, Gd) and actinide (Th, U) adsorption in a system consisting of fulvic acid, metal ions and clay minerals (montmorillonite, kaolinite, illite) was studied as a function of pH, metal ion concentration and fulvic acid concentration using spectrophotometric analysis and 152Eu tracer methods. Increasing metal ion adsorption on to the clay minerals was observed when humic substances were present in the system. The bridging of polyvalent metal ions between clay minerals and humic substance complexes was proposed as the possible adsorption mechanism.
Effect of organic Nitrogen Management on Yield, Quality, Economicsand Nutrient Uptake of onion (Allium cepa L.).

A field experiment was conducted during summer season of 2004 and 2005 to find out the effect of various sources (FYM, VC and PM) and rates of organic manures (100%, 125%, 150% RND) on yield, quality and economics of onion (Pusa Red) on a sandy clay-loam soil low in available N and medium in available phosphorus and potassium. Pooled data analysis revealed that the application of organic manure significantly influenced the yield attributes and bulb yield of onion over 100% RND as urea (control). Progressive increase in dose of all the organic manures significantly increased the bulb yield, haulm yield, pungency (%) and nutrient uptake (NPK). The application of 150% RND as poultry manure gave higher bulb (270.84 q ha-1) and haulm yields (35.13 q ha-1) than other sources and levels of organic manures. Soil physical parameters viz. bulk density and water stable aggregates did not showed any profound effect due to addition of organic materials. The maximum organic carbon build up was accured (0.54%) when 150% RND was supplied through PM (T4). Soil biological properties showed improvement in the soil microbial counts over its initial values at the end of 2-years due to supplementation of organic sources. All the organic treatments recorded higher economic returns over control and the highest net returns (Rs. 74,233 ha-1) was obtained due to 100% as poultry manure followed by 125% RND as poultry manure (Rs. 72,195ha-1) which was 105.05 per cent higher than control (Rs. 36,202 ha-1). The net benefit-cost ratio was also highest with 100% RND applied as poultry manure (2.33).
METHYLOME DYNAMICS UPON PROTEASOME INHIBITION BY THE PSEUDOMONAS VIRULENCE FACTOR SYRINGOLIN A

DNA methylation is an important epigenetic mark required for proper gene expression and silencing of transposable elements. DNA methylation patterns can be modified by environmental factors such as pathogen infection, where modification of DNA methylation can be associated with plant resistance. To counter the plant defense pathways, pathogens produce effectors molecule, several of which act as proteasome inhibitors. Here we investigated the effect of proteasome inhibition by the bacterial virulence factor Syringolin A on genome-wide DNA methylation. We show that Syringolin A treatment results in an increase of DNA methylation at centromeric and pericentromeric regions of Arabidopsis chromosomes. We identify several CHH DMRs that are enriched in the proximity of transcriptional start sites. Syringolin A treatment does not result in significant changes in small RNA composition. However, significant changes in genome transcriptional activity can be observed, including a strong upregulation of resistance genes that are located on chromosomal arms. We hypothesize that DNA methylation changes could be linked to the upregulation of some atypical members of the de novo DNA methylation pathway: AGO3, AGO9 and DRM1. Our data suggests that modification of genome-wide DNA methylation resulting from an inhibition of the proteasome by bacterial effectors could be part of a epi-genomic arms race against pathogens.
Chromatin dynamics controls epigenetic domain formation

In multicellular organisms, nucleosomes carry epigenetic information that defines distinct patterns of gene expression, which are inherited over multiple generations. The enhanced capacity for information storage arises by nucleosome modifications, triggered by enzymes. Modified nucleosomes can transfer the mark to others that are in proximity by a positive feedback (modification begets modification) mechanism. We created a polymer model in which each bead, representing a nucleosome, stochastically switches between unmodified (U) and modified (M) states depending on the states of the neighbors. Spreading is initiated at a specific nucleation site (NS) that is permanently in the M state. Modifications spread among the non-nucleation loci probabilistically. If the spreading rate is higher than the chromatin relaxation rate, domains containing the modified nucleosomes form without bound. In the opposite biologically relevant limit, finite-sized domains form, driven by contacts between nucleosomes through a three-dimensional looping mechanism, with chromatin remaining in an expanded state, as is appropriate for fission yeast. Surprisingly, finite bounded domains arise without the need for any boundary elements as long as the spreading is slow. Maintenance of spatially and temporally stable domains require the presence of the NS whose removal eliminates finite-sized modified domains. By varying the solvent quality we show that finite heterochromatin domains form as long as initially chromatin is not fully condensed. The predictions compare well with experimental data for H3K9me3 spreading in Mouse Embryonic Stem cell.
Construction of an RNA-Binding Protein-Related Prognostic Model for Pancreatic Adenocarcinoma Based on TCGA and GTEx Databases

Background: Recently, RNA-binding proteins (RBPs) were reported to interact with target mRNA to regulate gene posttranscriptional expression, and RBP-mediated RNA modification can regulate the expression and function of proto-oncogenes and tumor suppressor genes. We systematically analyzed the expression of RBPs in pancreatic adenocarcinoma (PAAD) and constructed an RBP-associated prognostic risk model. Methods: Gene expression data of normal pancreatic samples as well as PAAD samples were downloaded from TCGA-PAAD and GTEx databases. Wilcoxon test and univariate Cox analysis were, respectively, applied to screen differential expression RBPs (DE-RBPs) and prognostic-associated RBPs (pRBPs). Functional enrichment was analyzed by GO, KEGG, and GSEA. Protein–protein interaction (PPI) network was constructed by STRING online database. Modeling RBPs were selected by multivariate Cox analysis. Kaplan–Meier survival and Cox analysis were applied to evaluate the effects of risk score on the overall survival of PAAD patients. ROC curves and validation cohort were applied to verify the accuracy of the model. Nomogram was applied for predicting 1-, 3-, and 5-year overall survival (OS) of PAAD patients. At last, modeling RBPs were further analyzed to explore their differential expression, prognostic value, as well as enrichment pathways in PAAD. Results: RBPs (453) were differentially expressed in normal and tumor samples, besides, 28 of which were prognostic associated. DE-RBPs (453) are functionally associated with ribosome, ribonuclease, spliceosome, etc. Eight RBPs (PABPC1, PRPF6, OAS1, RBM5, LSM12, IPO7, FXR1, and RBM6) were identified to construct a prognostic risk model. Higher risk score not only predicted poor prognosis but also was an independent poor prognostic indicator, which was verified by ROC curves and validation cohort. Eight modeling RBPs were confirmed to be significantly differentially expressed between normal and tumor samples from RNA and protein level. Besides, all of eight RBPs were related with overall survival of PAAD patients. Conclusions: We successfully constructed an RBP-associated prognostic risk model in PAAD, which has a potential clinical application prospect.
Effects of Banana Resistant Starch on the Biochemical Indexes and Intestinal Flora of Obese Rats Induced by a High-Fat Diet and Their Correlation Analysis

The effects of banana resistant starch (BRS) on obesity-related metabolic and intestinal flora were investigated in a high-fat diet-induced obesity model. After 6 weeks of intervention, the glucolipid metabolism index [blood glucose (GLU), total cholesterol (TC), triacylglycerol (TG), low density lipoprotein-cholesterol (LDL-C), and high density lipoprotein-cholesterol (HDL-C)], hormone index [leptin (LEP), insulin (INS), ghrelin, adiponectin (ADP), and thyroxine (T4)], and 16S rRNA sequencing analyses were performed for each group to explore the regulating effect of intestinal flora and the mechanism of weight loss in obese rats. The results showed that (1) BRS intervention significantly reduced the levels of GLU, TG, TC, LDL-C, LEP, and INS (p < 0.01) and increased the contents of ghrelin (p < 0.05) and ADP (p < 0.01). (2) BRS could improve the diversity of intestinal flora and regulate the overall structure of intestinal microorganisms, mainly by upregulating the Bacteroides/Firmicutes ratio and the relative abundance of Cyanobacteria and downregulating the relative abundances of Deferribacteres and Tenericutes (at the phylum level). BRS could inhibit the proliferation of Turicibacter, Romboutsia, and Oligella and increase the abundances of Bacteroides, Ruminococcaceae, and Lachnospiraceae (at the genus level). (3) Some significant correlations were observed between the gut microbiota and biomarkers. Turicibacter, Romboutsia, and Oligella were positively correlated with GLU, TG, TC, LEP, and INS and negatively correlated with ghrelin and ADP. Bacteroides, Parabacteroides, and Akkermansia were negatively correlated with GLU, TG, and TC. Conclusion: BRS had promising effects on weight loss, which could be associated with the improvement in host metabolism by regulating intestinal flora.
Architecture of the Neuro-Glia-Vascular System

Astrocytes connect the vasculature to neurons and mediate the supply of nutrients and biochemicals. They also remove metabolites from the neurons and extracellular environment. They are involved in a growing number of physiological and pathophysiological processes. Understanding the biophysical, physiological, and molecular interactions in this neuro-glia-vascular ensemble (NGV) and how they support brain function is severely restricted by the lack of detailed cytoarchitecture. To address this problem, we used data from multiple sources to create a data-driven digital reconstruction of the NGV at micrometer anatomical resolution. We reconstructed 0.2 mm3 of rat somatosensory cortical tissue with approximately 16000 morphologically detailed neurons, its microvasculature, and approximately 2500 morphologically detailed protoplasmic astrocytes. The consistency of the reconstruction with a wide array of experimental measurements allows novel predictions of the numbers and locations of astrocytes and astrocytic processes that support different types of neurons. This allows anatomical reconstruction of the spatial microdomains of astrocytes and their overlapping regions. The number and locations of end-feet connecting each astrocyte to the vasculature can be determined as well as the extent to which they cover the microvasculature. The structural analysis of the NGV circuit showed that astrocytic shape and numbers are constrained by vasculature’s spatial occupancy and their functional role to form NGV connections. The digital reconstruction of the NGV is a resource that will enable a better understanding of the anatomical principles and geometric constraints which govern how astrocytes support brain function. Table of contents Main points The Blue Brain Project digitally reconstructs a part of neocortical Neuro-Glia-Vascular organization Interdependencies and topological methods allow dense in silico reconstruction from sparse experimental data The polarized role of protoplasmic astrocytes constrains their shapes and numbers Table of contents image
Analgesics for Dental Implants: A Systematic Review

Postsurgical pain is commonly associated with dental and oral surgery, and the use of analgesics has been investigated in the management of postoperative pain. This systematic review summarizes available evidence on analgesics used to manage dental implant surgery postoperative pain, to identify best therapeutic protocols and knowledge gap. A comprehensive search was conducted including MEDLINE/Pubmed, EMBASE, SCOPUS, clinicaltrials.gov, and the Cochrane Database of Systematic Reviews through May 2020. Only randomized controlled trials were included. PRISMA guidelines were followed, and risk of bias was appraised using Cochrane RoB2 tool. Eleven trials (762 patients overall) were included. Some aspects limited the feasibility of a meaningful meta-analysis; thus, a narrative synthesis was conducted. Risk of bias was low in four studies and high in two studies, while five studies raised some concerns due to the randomization process. Analgesic use seemed to be associated with improved postoperative outcomes (pain, patient’s satisfaction, and need for rescue medication) when compared to placebo. Overall, this review suggests that the administration of analgesics may provide some advantages in the management of postoperative outcomes after dental implant placement, while indications about the best analgesics cannot be provided.
Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems

Mycoplasmas are minute bacteria controlled by very small genomes ranging from 0.6 to 1.4 Mbp. They lack a cell wall and have been suggested to have progressed through reductive evolution from phylogenetically closely related Clostridia. They are known to colonize the respiratory tract or the urogenital tract among other organs and can cause chronic and subclinical diseases associated with long persistence of the causative agent. Toxin-antitoxin systems (TAS) are genetic elements that have been described for several respiratory and urogenital pathogens as well as for Clostridia, but never for pathogenic mycoplasmas. Here we describe for the first-time different types of TAS in a Mycoplasma pathogen, namely M. mycoides subsp. capri. We identified candidate TAS in silico via TASmania database. Two candidate TAS identified in silico and another candidate TAS suggested in a minimal cell based on transposon mutagenesis were systematically tested for their functionality in hosts with different phylogenetic distance using heterologous expression. Phylogenetic distance of the host used for heterologous expression influenced the outcome of the functional testing. We corroborated functionality of the three candidate TAS in Mycoplasma capricolum subsp. capricolum. Moreover, we confirmed transcription and translation of molecules of the TAS investigated during in vitro growth. We sequence analyzed 15 genomes of M. mycoides subsp. capri and revealed an unequal distribution of the TAS studied pointing towards dynamic gain and loss of TAS within the species. Author summary Mycoplasmas have a minimal genome and have never been shown to possess TAS. In this work we showed the presence of different functional TAS systems in Mycoplasma mycoides subsp. capri, a caprine pathogen for the first time. Sequence analysis of a number of Mycoplasma mycoides subsp. capri strains revealed a plasticity of the genome with respect to TAS carriage. This work paves the way to investigate the biological role of TAS (e.g. persistence, stress tolerance) during infection using mycoplasmas as a simple model organism. Since most mycoplasmas lack classical virulence factors such as exotoxins and go into a kind of stealth mode to evade the immune system, TAS are likely to contribute to the parasitic lifestyle of mycoplasmas and should be investigated in that respect. The availability of synthetic genomics tools to modify a range of Mycoplasma pathogens and well-established challenge models for the latter mycoplasmas will foster future research on TAS in mycoplasmas.
FOD-Net: A Deep Learning Method for Fiber Orientation Distribution Angular Super Resolution

Mapping the human connectome using fibre-tracking permits the study of brain connectivity and yields new insights into neuroscience. However, reliable connectome reconstruction using diffusion magnetic resonance imaging (dMRI) data acquired by widely available clinical protocols remains challenging, thus limiting the connectome/tractography clinical applications. Here we develop fibre orientation distribution (FOD) network (FOD-Net), a deep-learning-based framework for FOD angular super-resolution. Our method enhances the angular resolution of FOD images computed from common clinical-quality dMRI data, to obtain FODs with quality comparable to those produced from advanced research scanners. Super-resolved FOD images enable superior tractography and structural connectome reconstruction from clinical protocols. The method was trained and tested with high-quality data from the Human Connectome Project (HCP) and further validated with a local clinical 3.0T scanner. Using this method, we improve the angular resolution of FOD images acquired with typical single-shell low-angular-resolution dMRI data (e.g., 32 directions, b=1000 s/mm2) to approximate the quality of FODs derived from time-consuming, multi-shell high-angular-resolution dMRI research protocols. We also demonstrate tractography improvement, removing spurious connections and bridging missing connections. We further demonstrate that connectomes reconstructed by super-resolved FOD achieve comparable results to those obtained with more advanced dMRI acquisition protocols, on both HCP and clinical 3T data. Advances in deep-learning approaches used in FOD-Net facilitate the generation of high quality tractography/connectome analysis from existing clinical MRI environments.
Stress and corticotropin releasing factor (CRF) promote necrotizing enterocolitis in a formula-fed neonatal rat model

The etiology of necrotizing enterocolitis (NEC) is not known. Alterations in gut microbiome, mucosal barrier function, immune cell activation, and blood flow are characterized events in its development, with stress as a contributing factor. The hormone corticotropin-releasing factor (CRF) is a key mediator of stress responses and influences these aforementioned processes. CRF signaling is modulated by NEC’s main risk factors of prematurity and formula feeding. Using an established neonatal rat model of NEC, we tested hypotheses that: (i) increased CRF levels—as seen during stress—promote NEC in formula-fed newborn rats, and (ii) antagonism of CRF action ameliorates NEC. Newborn pups were formula-fed to initiate gut inflammation and randomized to: no stress, no stress with subcutaneous CRF administration, stress (acute hypoxia followed by cold exposure—NEC model), or stress after pretreatment with the CRF peptide antagonist Astressin. Dam-fed unstressed and stressed littermates served as controls. NEC incidence and severity in the terminal ileum were determined using a histologic scoring system. Changes in CRF, CRF receptor (CRFRs), and toll-like receptor 4 (TLR4) expression levels were determined by immunofluorescence and immunoblotting, respectively. Stress exposure in FF neonates resulted in 40.0% NEC incidence, whereas exogenous CRF administration resulted in 51.7% NEC incidence compared to 8.7% in FF non-stressed neonates (p<0.001). Astressin prevented development of NEC in FF-stressed neonates (7.7% vs. 40.0%; p=0.003). CRF and CRFR immunoreactivity increased in the ileum of neonates with NEC compared to dam-fed controls or FF unstressed pups. Immunoblotting confirmed increased TLR4 protein levels in FF stressed (NEC model) animals vs. controls, and Astressin treatment restored TLR4 to control levels. Peripheral CRF may serve as specific pharmacologic target for the prevention and treatment of NEC.
Influence of the Mechanical Environment on the Regeneration of Osteochondral Defects

Articular cartilage is a highly specialised connective tissue of diarthrodial joints which provides a smooth, lubricated surface for joint articulation and plays a crucial role in the transmission of loads. In vivo cartilage is subjected to mechanical stimuli that are essential for cartilage development and the maintenance of a chondrocytic phenotype. Cartilage damage caused by traumatic injuries, ageing, or degradative diseases leads to impaired loading resistance and progressive degeneration of both the articular cartilage and the underlying subchondral bone. Since the tissue has limited self-repairing capacity due its avascular nature, restoration of its mechanical properties is still a major challenge. Tissue engineering techniques have the potential to heal osteochondral defects using a combination of stem cells, growth factors, and biomaterials that could produce a biomechanically functional tissue, representative of native hyaline cartilage. However, current clinical approaches fail to repair full-thickness defects that include the underlying subchondral bone. Moreover, when tested in vivo, current tissue-engineered grafts show limited capacity to regenerate the damaged tissue due to poor integration with host cartilage and the failure to retain structural integrity after insertion, resulting in reduced mechanical function. The aim of this review is to examine the optimal characteristics of osteochondral scaffolds. Additionally, an overview on the latest biomaterials potentially able to replicate the natural mechanical environment of articular cartilage and their role in maintaining mechanical cues to drive chondrogenesis will be detailed, as well as the overall mechanical performance of grafts engineered using different technologies.
Variability of Lipids and Fatty Acids in Pacific Walrus Blubber

The variability of lipid content and fatty acid (FA) composition across blubber depth and body sites are important considerations for condition and diet studies of marine mammals. We investigated lipid and FA variability among inner and outer blubber layers, three body sites, four study years, and lactation status of adult female Pacific walruses (Odobenus rosmarus divergens) using blubber samples collected from subsistence-harvested walruses in spring 2007–2010. Percent lipid content did not differ between the inner and outer blubber layers at the rump, flank, or sternum of walruses. Although FA composition differed between the inner and outer blubber layers, the difference was consistent across body sites, and differences between layers within individual FAs were small (<2%). Lipid content at the sternum of lactating females was 6% higher than non-lactating females, consistent with known variation in body condition among these reproductive classes. Across study years, lipid content varied 18% and individual FAs varied 6%, likely reflecting population-level interannual variability in energy budgets and small differences in diet among years. Consistency in blubber lipid content across blubber depth and body sites and detectable variation in blubber lipid content among reproductive classes and years suggests the potential for lipid content to be a useful indicator of walrus body condition. In addition to information on condition, FA composition of blubber samples could potentially provide insights into changes in walrus diet that may be expected to occur from changes in their access to prey resources resulting from continued sea ice loss.