Miracle-dz/UniFAR-FTUs huggingface dataset:
Algorithmically Deduced FREM2 Molecular Pathway Is a Potent Grade and Survival Biomarker of Human Gliomas

Simple Summary Gliomas are the most common malignant brain tumors with high mortality rates. Recently the role of the FREM2 gene has been shown in glioblastoma progression. Here we reconstructed the FREM2 molecular pathway. We assessed the biomarker capacity of FREM2 expression and its pathway as the overall survival (OS) and progression-free survival (PFS) biomarkers. We used 566 glioblastomas (GBM) and 1097 low-grade gliomas (LGG) to test these biomarkers. FREM2 molecular pathway was a better biomarker than FREM2 gene expression. It could robustly discriminate between GBM and LGG. High FREM2 pathway activation level was associated with poor overall survival (OS) in LGG, and low progression-free survival in LGG and GBM. FREM2 pathway activation level was also a poor prognosis biomarker for OS and PFS in LGG with IDH mutation, for PFS in LGG with wild type IDH and mutant IDH with 1p/19q codeletion, in GBM with unmethylated MGMT, and in GBM with wild type IDH. Abstract Gliomas are the most common malignant brain tumors with high mortality rates. Recently we showed that the FREM2 gene has a role in glioblastoma progression. Here we reconstructed the FREM2 molecular pathway using the human interactome model. We assessed the biomarker capacity of FREM2 expression and its pathway as the overall survival (OS) and progression-free survival (PFS) biomarkers. To this end, we used three literature and one experimental RNA sequencing datasets collectively covering 566 glioblastomas (GBM) and 1097 low-grade gliomas (LGG). The activation level of deduced FREM2 pathway showed strong biomarker characteristics and significantly outperformed the FREM2 expression level itself. For all relevant datasets, it could robustly discriminate GBM and LGG (p < 1.63 × 10−13, AUC > 0.74). High FREM2 pathway activation level was associated with poor OS in LGG (p < 0.001), and low PFS in LGG (p < 0.001) and GBM (p < 0.05). FREM2 pathway activation level was poor prognosis biomarker for OS (p < 0.05) and PFS (p < 0.05) in LGG with IDH mutation, for PFS in LGG with wild type IDH (p < 0.001) and mutant IDH with 1p/19q codeletion(p < 0.05), in GBM with unmethylated MGMT (p < 0.05), and in GBM with wild type IDH (p < 0.05). Thus, we conclude that the activation level of the FREM2 pathway is a potent new-generation diagnostic and prognostic biomarker for multiple molecular subtypes of GBM and LGG.
The Identification of Zinc-Finger Protein 433 as a Possible Prognostic Biomarker for Clear-Cell Renal Cell Carcinoma

Clear-cell renal cell carcinoma (ccRCC) is the most common and aggressive form of all urological cancers, with poor prognosis and high mortality. At late stages, ccRCC is known to be mainly resistant to chemotherapy and radiotherapy. Therefore, it is urgent and necessary to identify biomarkers that can facilitate the early detection of ccRCC in patients. In this study, the levels of transcripts of ccRCC from The Cancer Genome Atlas (TCGA) dataset were used to identify prognostic biomarkers in this disease. Analyzing the data obtained indicated that the KRAB-ZNF protein is significantly suppressed in clear-cell carcinomas. Furthermore, ZNF433 is differentially expressed in ccRCC in a stage- and histological-grade-specific manner. In addition, ZNF433 expression was correlated with metastasis, with greater node involvement associated with lower ZNF433 expression (p < 0.01) and with a more unsatisfactory overall survival outcome (HR, 0.45; 95% CI, 0.33–0.6; p = 8.5 × 10−8). Since ccRCC is characterized by mutations in proteins that alter epigenetic modifications and /or chromatin remodeling, we examined the expression of ZNF433 transcripts in ccRCC with wildtype and mutated forms of BAP1, KDMC5, MTOR, PBRM1, SETD2, and VHL. Analysis revealed that ZNF433 expression was significantly reduced in ccRCC with mutations in the BAP1, SETD2, and KDM5C genes (p < 0.05). In addition, the ZNF433 promoter region was highly methylated, and hypermethylation was significantly associated with mRNA suppression (p < 2.2 × 10−16). In silico analysis of potential ZNF target genes found that the largest group of target genes are involved in cellular metabolic processes, which incidentally are particularly impaired in ccRCC. It was concluded from this study that gene expression of ZNF433 is associated with cancer progression and poorer prognosis, and that ZNF433 behaves in a manner that suggests that it is a prognostic marker and a possible tumor-suppressor gene in clear-cell renal cell carcinoma.
The Importance of Biological Maturation and Years of Practice in Kayaking Performance

Previous canoe sprint studies evaluated the best paddlers of their categories. This investigation aimed to identify the importance of biological maturation and athletes’ experience in kayaking performance and observe possible differences regarding anthropometry, years of practice, and performance. Eighty under 14 years of age (U14) and fifty under 16 years of age (U16) kayakers aged 13.40 ± 0.54 and 15.25 ± 0.61 years were evaluated. Kayakers were assessed for anthropometry (body mass (kg); stretch stature (cm); and sitting height (cm)), performance (time at 3000 m for U14 and 5000 m for U16 kayakers), and somatic maturation (predicted adult height (PAH) and maturity offset). In the U14 kayakers, years of practice, sitting height, and maturity offset showed significant differences (p < 0.05) between the Top10 and Middle, and Middle and Bottom10 performance times. Significantly higher (p < 0.05) sitting heights were identified between the Top10 and Middle U16 kayakers. Significant differences (p < 0.05) were observed for maturity offset and PAH% between the Top10 and Middle groups compared to the Bottom10 group. In conclusion, this research shows differences in the maturity status of young U14 and U16 kayakers, identifying that the more biologically mature individuals, with more years of specific practice, achieved better performances.
Activity Profiles among Older Adults: Latent Class Analysis Using the Korean Time Use Survey

This study empirically explored the activity profiles of Korean older adults by considering a wide range of activities simultaneously and further investigated the socioeconomic factors associated with activity profiles. Gender differences in activity profiles were examined in-depth. Latent class analysis (LCA) was used to identify activity profiles based on a nationally representative sample of older adults from the most recent two waves of the Korean Time Use Survey (n = 3034 for 2014 and n = 3960 for 2019). Multinomial logistic regression analysis was employed to further examine the factors associated with the activity profiles. The findings revealed four distinct activity groups, although there were differences in activity profiles between the two waves. Several sociodemographic factors, such as gender, age, assets and income, were significantly associated with the activity profiles. Findings from this study can inform policy makers seeking interventions that enhance the overall well-being of older adults through activity engagement.
Integral Membrane Protein 2A Is a Negative Regulator of Canonical and Non-Canonical Hedgehog Signalling

The Hedgehog (Hh) receptor PTCH1 and the integral membrane protein 2A (ITM2A) inhibit autophagy by reducing autolysosome formation. In this study, we demonstrate that ITM2A physically interacts with PTCH1; however, the two proteins inhibit autophagic flux independently, since silencing of ITM2A did not prevent the accumulation of LC3BII and p62 in PTCH1-overexpressing cells, suggesting that they provide alternative modes to limit autophagy. Knockdown of ITM2A potentiated PTCH1-induced autophagic flux blockade and increased PTCH1 expression, while ITM2A overexpression reduced PTCH1 protein levels, indicating that it is a negative regulator of PTCH1 non-canonical signalling. Our study also revealed that endogenous ITM2A is necessary for timely induction of myogenic differentiation markers in C2C12 cells since partial knockdown delays the timing of differentiation. We also found that basal autophagic flux decreases during myogenic differentiation at the same time that ITM2A expression increases. Given that canonical Hh signalling prevents myogenic differentiation, we investigated the effect of ITM2A on canonical Hh signalling using GLI-luciferase assays. Our findings demonstrate that ITM2A is a strong negative regulator of GLI transcriptional activity and of GLI1 stability. In summary, ITM2A negatively regulates canonical and non-canonical Hh signalling.
Visualization of Local Concentration and Viscosity Distribution during Glycerol-Water Mixing in a Y-Shape Minichannel: A Proof-of-Concept-Study

The work presents an efficient and non-invasive method to visualize the local concentration and viscosity distribution of two miscible and non-reacting substances with a significant viscosity difference in a microchannel with a Y-shape cell. The proof-of-concept setup consists of a near-infrared (NIR) camera and cost-effective dome lighting with NIR light-emitting diodes (LED) covering the wavelength range of 1050 to 1650 nm. Absorption differences of glycerol and water and their mixtures with a mass fraction of glycerol from 0 to 0.95 gGlycgtotal−1 were analyzed in the NIR spectral area. The resulting measurement images were converted in a concentration profile by using absorbance calculated with Lambert–Beer law. A linear behavior between the concentration and the absorption coefficient is demonstrated. The result of local concentration in mass fraction was used to determine the local viscosity and illustrated as distribution images. By variating the fluid parameters, the influences of the highly different original viscosities in the mixing procedure were investigated and visualized.
Bioactive Hydrogels: Design and Characterization of Cellulose-Derived Injectable Composites

Cellulose represents a low cost, abundant, and renewable polysaccharide with great versatility; it has a hierarchical structure composed of nanofibers with high aspect ratio (3–4 nm wide, hundreds of μm long). TEMPO-mediated oxidation represents one of the most diffused methods to obtain cellulose nanofibers (CNFs): It is possible to obtain physically crosslinked hydrogels by means of divalent cation addition. The presence of inorganic components, such as calcium phosphates (CaP), can improve not only their mechanical properties but also the bioactivity of the gels. The aim of this work is to design and characterize a TEMPO-oxidized cellulose nanofibers (TOCNFs) injectable hydrogel embedded with inorganic particles, CaP and CaP-GO, for bone tissue regeneration. Inorganic particles act as physical crosslinkers, as proven by rheological characterization, which reported an increase in mechanical properties. The average load value registered in injection tests was in the range of 1.5–4.4 N, far below 30 N, considered a reasonable injection force upper limit. Samples were stable for up to 28 days and both CaP and CaP-GO accelerate mineralization as suggested by SEM and XRD analysis. No cytotoxic effects were shown on SAOS-2 cells cultured with eluates. This work demonstrated that the physicochemical properties of TOCNFs-based dispersions could be enhanced and modulated through the addition of the inorganic phases, maintaining the injectability and bioactivity of the hydrogels.
L-myc Gene Expression in Canine Fetal Fibroblasts Promotes Self-Renewal Capacity but Not Tumor Formation

Canines are useful in mammalian preclinical studies because they are larger than rodents and share many diseases with humans. Canine fetal fibroblast cells (CFFs) are an easily accessible source of somatic cells. However, they are easily driven to senescence and become unusable with continuous in vitro culture. Therefore, to overcome these deficiencies, we investigated whether tetracycline-inducible L-myc gene expression promotes self-renewal activity and tumorigenicity in the production of induced conditional self-renewing fibroblast cells (iCSFCs). Here, we describe the characterization of a new iCSFC line immortalized by transduction with L-myc that displays in vitro self-renewal ability without tumorigenic capacity. We established conditionally inducible self-renewing fibroblast cells by transducing CFF-3 cells with L-myc under the tetracycline-inducible gene expression system. In the absence of doxycycline, the cells did not express L-myc or undergo self-renewal. The iCSFCs had a fibroblast-like morphology, normal chromosome pattern, and expressed fibroblast-specific genes and markers. However, the iCSFCs did not form tumors in a soft agar colony-forming assay. We observed higher expression of three ES modules (core pluripotency genes, polycomb repressive complex genes (PRC), and MYC-related genes) in the iCSFCs than in the CFF-3 cells; in particular, the core pluripotency genes (OCT4, SOX2, and NANOG) were markedly up-regulated compared with the PRC and MYC module genes. These results demonstrated that, in canine fetal fibroblasts, L-myc tetracycline-inducible promoter-driven gene expression induces self-renewal capacity but not tumor formation. This study suggests that L-myc gene-induced conditional self-renewing fibroblast cells can be used as an in vitro tool in a variety of biomedical studies related to drug screening.
The Window Matters: A Systematic Review of Time Restricted Eating Strategies in Relation to Cortisol and Melatonin Secretion

Time-Restricted Eating is an eating pattern based on the circadian rhythm which limits daily food intake (usually to ≤12 h/day), unique in that no overt restriction is imposed on the quality, nor quantity, of food intake. This paper aimed to examine the effects of two patterns of TRE, traditional TRE, and Ramadan fasting, on two markers of circadian rhythm, cortisol and melatonin. PubMed and Web of Science were searched up to December 2020 for studies examining the effects of time restricted eating on cortisol and melatonin. Fourteen studies met our inclusion criteria. All Ramadan papers found statistically significant decrease in melatonin (p < 0.05) during Ramadan. Two out of the three Ramadan papers noted an abolishing of the circadian rhythm of cortisol (p < 0.05). The non-Ramadan TRE papers did not examine melatonin, and cortisol changes were mixed. In studies comparing TRE to control diets, Stratton et al. found increased cortisol levels in the non-TRE fasting group (p = 0.0018) and McAllister et al. noted no difference. Dinner-skipping resulted in significantly reduced evening cortisol and non-significantly raised morning cortisol. Conversely, breakfast skipping resulted in significantly reduced morning cortisol. This blunting indicates a dysfunctional HPA axis, and may be associated with poor cardio-metabolic outcomes. There is a paucity of research examining the effects of TRE on cortisol and melatonin. The contrasting effect of dinner and breakfast-skipping should be further examined to ascertain whether timing the feeding window indeed has an impact on circadian rhythmicity.
Effect of SGLT2-Inhibitors on Epicardial Adipose Tissue: A Meta-Analysis

(1) Sodium–glucose cotransporter-2 inhibitors (SGLT2-i) reduce adipose tissue and cardiovascular events in patients with type 2 diabetes (T2D). Accumulation of epicardial adipose tissue (EAT) is associated with increased cardio-metabolic risks and obstructive coronary disease events in patients with T2D. (2) We performed a systematic review and meta-analysis of SGLT2-i therapy on T2D patients, reporting data on changes in EAT after searching the PubMed/MEDLINE, Embase, Science Direct, Scopus, Google Scholar, and Cochrane databases. A random effects or fixed effects model meta-analysis was then applied. (3) Results: A total of three studies (n = 64 patients with SGLT2-i, n = 62 with standard therapy) were included in the final analysis. SGLT2 inhibitors reduced EAT (SMD: −0.82 (−1.49; −0.15); p < 0.0001). An exploratory analysis showed that HbA1c was significantly reduced with SGLT2-i use, while body mass index was not significantly reduced with this drug. (4) Conclusions: This meta-analysis suggests that the amount of EAT is significantly reduced in T2D patients with SGLT2-i treatment.
High-throughput screening and genome-wide analyses of 44 anticancer drugs in the 1000 Genomes cell lines reveals an association of the NQO1 gene with the response of multiple anticancer drugs

Cancer patients exhibit a broad range of inter-individual variability in response and toxicity to widely used anticancer drugs, and genetic variation is a major contributor to this variability. To identify new genes that influence the response of 44 FDA-approved anticancer drug treatments widely used to treat various types of cancer, we conducted high-throughput screening and genome-wide association mapping using 680 lymphoblastoid cell lines from the 1000 Genomes Project. The drug treatments considered in this study represent nine drug classes widely used in the treatment of cancer in addition to the paclitaxel + epirubicin combination therapy commonly used for breast cancer patients. Our genome-wide association study (GWAS) found several significant and suggestive associations. We prioritized consistent associations for functional follow-up using gene-expression analyses. The NAD(P)H quinone dehydrogenase 1 (NQO1) gene was found to be associated with the dose-response of arsenic trioxide, erlotinib, trametinib, and a combination treatment of paclitaxel + epirubicin. NQO1 has previously been shown as a biomarker of epirubicin response, but our results reveal novel associations with these additional treatments. Baseline gene expression of NQO1 was positively correlated with response for 43 of the 44 treatments surveyed. By interrogating the functional mechanisms of this association, the results demonstrate differences in both baseline and drug-exposed induction.
Neurobiological correlates of antisociality across adolescence and young adulthood: a multi-sample, multi-method study

Abstract Background Antisociality across adolescence and young adulthood puts individuals at high risk of developing a variety of problems. Prior research has linked antisociality to autonomic nervous system and endocrinological functioning. However, there is large heterogeneity in antisocial behaviors, and these neurobiological measures are rarely studied conjointly, limited to small specific studies with narrow age ranges, and yield mixed findings due to the type of behavior examined. Methods We harmonized data from 1489 participants (9–27 years, 67% male), from six heterogeneous samples. In the resulting dataset, we tested relations between distinct dimensions of antisociality and heart rate, pre-ejection period (PEP), respiratory sinus arrhythmia, respiration rate, skin conductance levels, testosterone, basal cortisol, and the cortisol awakening response (CAR), and test the role of age throughout adolescence and young adulthood. Results Three dimensions of antisociality were uncovered: ‘callous-unemotional (CU)/manipulative traits’, ‘intentional aggression/conduct’, and ‘reactivity/impulsivity/irritability’. Shorter PEPs and higher testosterone were related to CU/manipulative traits, and a higher CAR is related to both CU/manipulative traits and intentional aggression/conduct. These effects were stable across age. Conclusions Across a heterogeneous sample and consistent across development, the CAR may be a valuable measure to link to CU/manipulative traits and intentional aggression, while sympathetic arousal and testosterone are additionally valuable to understand CU/manipulative traits. Together, these findings deepen our understanding of the fundamental mechanisms underlying different components of antisociality. Finally, we illustrate the potential of using current statistical techniques for combining multiple datasets to draw robust conclusions about biobehavioral associations.
Produits, en particulier laitiers, comprenant des fractions selectionnees de globules gras, obtention et applications

Procede pour separer de maniere selective, selon leur taille, les globules gras presents dans un milieu alimentaire ou biologique, consistant a soumettre le milieu a traiter a au moins une microfiltration tangentielle sur membrane ayant un seuil de coupure compris entre 1,8 et 10 νm dans des conditions de pression transmembranaire substantiellement uniforme et a recuperer le retentat et le permeat obtenus.
Integrating the Roles for Cytokinin and Auxin in De Novo Shoot Organogenesis: From Hormone Uptake to Signaling Outputs

De novo shoot organogenesis (DNSO) is a procedure commonly used for the in vitro regeneration of shoots from a variety of plant tissues. Shoot regeneration occurs on nutrient media supplemented with the plant hormones cytokinin (CK) and auxin, which play essential roles in this process, and genes involved in their signaling cascades act as master regulators of the different phases of shoot regeneration. In the last 20 years, the genetic regulation of DNSO has been characterized in detail. However, as of today, the CK and auxin signaling events associated with shoot regeneration are often interpreted as a consequence of these hormones simply being present in the regeneration media, whereas the roles for their prior uptake and transport into the cultivated plant tissues are generally overlooked. Additionally, sucrose, commonly added to the regeneration media as a carbon source, plays a signaling role and has been recently shown to interact with CK and auxin and to affect the efficiency of shoot regeneration. In this review, we provide an integrative interpretation of the roles for CK and auxin in the process of DNSO, adding emphasis on their uptake from the regeneration media and their interaction with sucrose present in the media to their complex signaling outputs that mediate shoot regeneration.
Developing an Agnostic Risk Prediction Model for Early AKI Detection in Cancer Patients

Acute kidney injury (AKI) is a common complication among oncology patients associated with lower remission rates and higher mortality. To reduce the impact of this condition, we aimed to predict AKI earlier than existing tools, to allow clinical intervention before occurrence. We trained a random forest model on 597,403 routinely collected blood test results from 48,865 patients undergoing cancer treatment at The Christie NHS Foundation Trust between January 2017 and May 2020, to identify AKI events upcoming in the next 30 days. AKI risk levels were assigned to upcoming AKI events and tested through a prospective analysis between June and August 2020. The trained model gave an AUROC of 0.881 (95% CI 0.878–0.883), when assessing predictions per blood test for AKI occurrences within 30 days. Assigning risk levels and testing the model through prospective validation from the 1st June to the 31st August identified 73.8% of patients with an AKI event before at least one AKI occurrence, 61.2% of AKI occurrences. Our results suggest that around 60% of AKI occurrences experienced by patients undergoing cancer treatment could be identified using routinely collected blood results, allowing clinical remedial action to be taken and disruption to treatment by AKI to be minimised.