Miracle-dz/UniFAR-FTUs huggingface dataset:
Reclassification of TCGA Diffuse Glioma Profiles Linked to Transcriptomic, Epigenetic, Genomic and Clinical Data, According to the 2021 WHO CNS Tumor Classification

In 2021, the fifth edition of the WHO classification of tumors of the central nervous system (WHO CNS5) was published. Molecular features of tumors were directly incorporated into the diagnostic decision tree, thus affecting both the typing and staging of the tumor. It has changed the traditional approach, based solely on histopathological classification. The Cancer Genome Atlas project (TCGA) is one of the main sources of molecular information about gliomas, including clinically annotated transcriptomic and genomic profiles. Although TCGA itself has played a pivotal role in developing the WHO CNS5 classification, its proprietary databases still retain outdated diagnoses which frequently appear incorrect and misleading according to the WHO CNS5 standards. We aimed to define the up-to-date annotations for gliomas from TCGA’s database that other scientists can use in their research. Based on WHO CNS5 guidelines, we developed an algorithm for the reclassification of TCGA glioma samples by molecular features. We updated tumor type and diagnosis for 828 out of a total of 1122 TCGA glioma cases, after which available transcriptomic and methylation data showed clustering features more consistent with the updated grouping. We also observed better stratification by overall survival for the updated diagnoses, yet WHO grade 3 IDH-mutant oligodendrogliomas and astrocytomas are still indistinguishable. We also detected altered performance in the previous diagnostic transcriptomic molecular biomarkers (expression of SPRY1, CRNDE and FREM2 genes and FREM2 molecular pathway) and prognostic gene signature (FN1, ITGA5, OSMR, and NGFR) after reclassification. Thus, we conclude that further efforts are needed to reconsider glioma molecular biomarkers.
Preclinical in vivo animal models of intervertebral disc degeneration. Part 1: A systematic review

Intervertebral disc degeneration (IVDD), a widely recognized cause of lower back pain, is the leading cause of disability worldwide. A myriad of preclinical in vivo animal models of IVDD have been described in the literature. There is a need for critical evaluation of these models to better inform researchers and clinicians to optimize study design and ultimately, enhance experimental outcomes. The purpose of this study was to conduct an extensive systematic literature review to report the variability of animal species, IVDD induction method, and experimental timepoints and endpoints used in in vivo IVDD preclinical research. A systematic literature review of peer‐reviewed manuscripts featured on PubMed and EMBASE databases was conducted in accordance with PRISMA guidelines. Studies were included if they reported an in vivo animal model of IVDD and included details of the species used, how disc degeneration was induced, and the experimental endpoints used for analysis. Two‐hundred and fifty‐nine (259) studies were reviewed. The most common species, IVDD induction method and experimental endpoint used was rodents(140/259, 54.05%), surgery (168/259, 64.86%) and histology (217/259, 83.78%), respectively. Experimental timepoint varied greatly between studies, ranging from 1 week (dog and rodent models), to >104 weeks in dog, horse, monkey, rabbit, and sheep models. The two most common timepoints used across all species were 4 weeks (49 manuscripts) and 12 weeks (44 manuscripts). A comprehensive discussion of the species, methods of IVDD induction and experimental endpoints is presented. There was great variability across all categories: animal species, method of IVDD induction, timepoints and experimental endpoints. While no animal model can replicate the human scenario, the most appropriate model should be selected in line with the study objectives to optimize experimental design, outcomes and improve comparisons between studies.
Optimal Investment and Consumption with Transaction Costs

An agent can invest in a high—yield bond and a low—yield bond, holding either long or short positions in either asset. Any movement of money between these two assets incurs a transaction cost proportional to the size of the transaction. The low—yield bond is liquid in the sense that wealth invested in this bond can be consumed directly without a transaction cost; wealth invested in the high—yield bond can be consumed only by first moving it into the low—yield bond. The problem of optimal consumption and investment on an infinite planning horizon is solved for a class of utility functions larger than the class of power functions.
Improvement of Kernel Type Density Estimators

Abstract Estimation of the value of a density function at a point of continuity using a kernel-type estimator is discussed and improvements of the technique are presented. The generalized jackknife method is employed to reduce the asymptotic and small sample mean square error and bias of these estimators. The procedure presented has the flexibility to afford the user a choice between bias reduction, variance reduction, or both.
Impact of Chronic Kidney Disease on Corneal Neuroimmune Features in Type 2 Diabetes

Aim: To determine the impact of chronic kidney disease on corneal nerve measures and dendritic cell counts in type 2 diabetes. Methods: In vivo corneal confocal microscopy images were used to estimate corneal nerve parameters and compared in people with type 2 diabetes with chronic kidney disease (T2DM-CKD) (n = 29) and those with type 2 diabetes without chronic kidney disease (T2DM-no CKD) (n = 29), along with 30 healthy controls. Corneal dendritic cell densities were compared between people with T2DM-CKD and those with T2DM-no CKD. The groups were matched for neuropathy status. Results: There was a significant difference in corneal nerve fiber density (p < 0.01) and corneal nerve fiber length (p = 0.04) between T2DM-CKD and T2DM-no CKD groups. The two diabetes groups had reduced corneal nerve parameters compared to healthy controls (all parameters: p < 0.01). Immature central dendritic cell density was significantly higher in the T2DM-CKD group compared to the T2DM-no CKD group ((7.0 (3.8–12.8) and 3.5 (1.4–13.4) cells/mm2, respectively, p < 0.05). Likewise, central mature dendritic cell density was significantly higher in the T2DM-CKD group compared to the T2DM-no CKD group (0.8 (0.4–2.2) and 0.4 (0.6–1.1) cells/mm2, respectively, p = 0.02). Additionally, total central dendritic cell density was increased in the T2DM-CKD group compared to T2DM-no CKD group (10.4 (4.3–16.1) and 3.9 (2.1–21.0) cells/mm2, respectively, p = 0.03). Conclusion: The study showed that central corneal dendritic cell density is increased in T2DM-CKD compared to T2DM-no CKD, with groups matched for peripheral neuropathy severity. This is accompanied by a loss of central corneal nerve fibers. The findings raise the possibility of additional local factors exacerbating central corneal nerve injury in people with diabetic chronic kidney disease.
A facile and practical p-toluenesulfonic acid catalyzed route to dicoumarols and their biological evaluation

ABSTRACT New Dicoumarols 2a-g efficiently synthesized employing p-TSA as a catalyst from the reaction of 4-hydroxycoumarin with aryl aldehydes in water. This method offers direct access to structurally diverse Dicoumarols derivatives in a good yields (65-94%). Upon heating 3,3' -arylidenebis-4-hydroxycoumarins derivative in acetic anhydride, the epoxydicoumarins were formed. 1H, 13C{1H}-NMR, elemental analysis, and infrared spectroscopic techniques were used for the characterization of the obtained compounds. A possible relationship between such hydrogen-bonded structures and the antimicrobial and the antioxidant activities of compounds is suggested. The synthetized compounds 2a-g and 3a-g were subjected to in vitro antimicrobial and antifungal activities against DNA gyrase and Mycobacterium tuberculosis-CYP51 target proteins at the active sites. Compound 3d shows effective inhibitory effect in terms of MIC = 15 µg mL-1. against Salmonella typhimuriumATCC 14028. Compounds 2b, 2c, 3b, 3c, 3e and 3g have recorded an important scavenging activity against the radical DPPH. The EC50 of these compounds was 47.17, 46.90, 50.55,48.27 , 46.55 and 47.54 µg mL-1 respectively. Investigation of the anti-inflammatory activity of the synthesized compounds showed that compounds 2b,2c, 3f, 3b and 3c are the most potent inflammatory activities. GRAPHICAL ABSTRACT
Effect of Dietary Inclusion of Riboflavin on Growth, Nutrient Digestibility and Ruminal Fermentation in Hu Lambs

Simple Summary Riboflavin (RF), in the form of flavin mononucleotides and flavin adenine dinucleotides, is involved in the transfer of electrons during redox reactions and plays an important role in animal metabolism and growth. Dietary RF supply has the potential to improve growth performance and nutrient digestion in lambs, and this might be associated with the stimulatory impacts of RF on ruminal microbial growth. The effects of RF on lamb growth performance and rumen fermentation were evaluated. The results showed that RF supplementation improved the growth performance, nutrient digestion and rumen fermentation in lambs. Abstract The study evaluated the influences of riboflavin (RF) supply on the growth performance, nutrient digestibility and ruminal fermentation in lambs. Forty-eight Hu lambs were randomly assigned into four groups receiving RF of 0, 15, 30 and 45 mg/kg dry mater (DM), respectively. Increasing RF supply did not affect the DM intake, but quadratically increased the average daily gain and linearly decreased feed conversion ratio. Total-tract DM, neutral detergent fibre, acid detergent fibre and crude protein digestibility increased quadratically. Rumen pH and propionate molar percentage decreased linearly, total volatile fatty acids concentration, acetate proportion and the ratio of acetate to propionate increased linearly, but ammonia nitrogen concentration was unchanged with increasing RF supply. Linear increases were observed on the activities of carboxymethyl-cellulase, xylanase, pectinase and protease, and the populations of bacteria, fungi, protozoa, dominant cellulolytic bacteria, Ruminobacter amylophilus and Prevotella ruminicola. Methanogens population was not affected by RF supplementation. The microbial protein amount and urinary total purine derivatives excretion increased quadratically. The results indicated that 30 mg/kg DM RF supply improved growth performance, rumen fermentation and nutrient digestion in lambs.
Dye Degradation and Sulfur Oxidation of Methyl Orange and Thiophenol via Newly Designed Nanocomposite GQDs/NiSe‐NiO Photocatalyst Under Homemade LED Light

Photocatalytic processes triggered by graphene‐based photocatalysts under solar light have sparked interest as a new sort of instrument for solar chemical synthesis. Herein we investigated self‐assembled graphene quantum dots (GQDs)/NiSe‐NiO composite photocatalyst for organic transformation as well as dye degradation. The synthesized GQDs/NiSe‐NiO composite photocatalyst has an excellent suitable band gap, high molar extinction coefficient, low toxicity and chemical/thermal stability. The GQDs/NiSe‐NiO composite photocatalyst emerges as a new standard for sulfur oxidation and dye degradation reactions under homemade LED light with high yield.
Global Evaluation of Runoff Simulation From Climate, Hydrological and Land Surface Models

Recent advances in global hydrological modeling yield many global runoff data sets that are extensively used in global hydrological analyses. Here, we provide a comprehensive evaluation of simulated runoff from 21 global models, including 12 climate models from CMIP6, six global hydrological models from the Inter‐Sectoral Impact Model Inter‐Comparison Project (ISMIP2a) and three land surface models from the Global Land Data Assimilation System (GLDAS), against observed streamflow in 840 unimpaired catchments globally. Our results show that (a) no model performs consistently better in estimating runoff from all aspects, and all models tend to perform better in more humid regions and non‐cold areas; (b) the interannual runoff variability is well represented in ISIMIP2a and GLDAS models, and no model performs satisfactorily in capturing the annual runoff trend; (c) the runoff intra‐annual cycle is reasonably captured by all models yet an overestimation of intra‐annual variability and an early bias in peak flow timing are commonly found; and (d) model uncertainty leads to a larger uncertainty in runoff estimates than that induced by forcing uncertainty in ISIMIP2a, and model uncertainty in GLDAS is larger than that in ISIMIP2a. Finally, we confirm that the multi‐model ensemble is an effective way to reduce uncertainty in individual models except for CMIP6 regarding mean annual magnitude and annual runoff trend. Overall, our findings suggest that assessments/projections of runoff changes based on these global outputs contain great uncertainties and should be interpreted with caution, and call for more advanced, observation‐guided ensemble techniques for better large‐scale hydrological applications.
Feasibility Assessment of a School Nurse-Led Approach Using Chronic Absenteeism to Establish the School-Based Active Surveillance Process

This article shares what was learned from the feasibility assessment of a nurse-led school-based active surveillance (SBAS) pilot to track chronic absenteeism using myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) as an exemplar. This pilot encompassed a 3-year period with training and feedback from school nurses (SNs) on data collection and ME/CFS. SNs found that the SBAS process helped them effectively identifying undiagnosed conditions. The assessment revealed the importance of focusing outreach efforts and establishing relationships with the school leadership in developing health policies and programs in the school setting. The pilot data were used to develop a manual to guide SNs for the SBAS process. This can be viewed as a model for SNs in establishing a surveillance to identify and track conditions like ME/CFS. With overlapping symptoms of Long COVID to ME/CFS, this assessment may provide insights for additional efforts to understand the impact of Long COVID on students’ education.
Pl@ntNet Crops: merging citizen science observations and structured survey data to improve crop recognition for agri-food-environment applications

We present a new application to recognize 218 species of cultivated crops on geo-tagged photos, ‘Pl@ntNet Crops’. The application and underlying algorithms are developed using more than 750k photos voluntarily collected by Pl@ntNet users. The app is then enriched by data and photos coming from the European Union’s (EU) Land Use and Coverage Area frame Survey (LUCAS). During five tri-annual LUCAS campaigns from 2006 to 2018, 242 476 close-up ‘cover’ photos of crops were collected. The survey protocol for these photos specified that ‘the picture should be taken at a close distance, so that the structure of leaves can be clearly seen, as well as flowers or fruits’. This unique labelled data provides an opportunity to further generalize the Pl@ntNet computer vision algorithms to recognize crops and enlarge their geographic representivity across the EU. To include LUCAS cover photos, we semantically match Pl@ntNet species and LUCAS legends, predict the species on LUCAS cover photos with the existing Pl@ntNet algorithm, and consider the accuracy of the classification and the number of species enriched by the photos. By setting a threshold of > 0.5 on the Pl@ntNet prediction probabilities, 70 170 LUCAS photos representing 101 species classified with an accuracy of 0.9 were added to the ‘Crops’ app. The thematic accuracy of the legacy LUCAS data was improved by distinguishing 218 species, opposed to the original 36 LUCAS levels. Official and publicly financed LUCAS datastreams can now be improved because of Pl@ntNet citizen science, photo collection, and deep learning model development. Further use of the app and policy-relevant workflows in the agri-food-environment domain are discussed.
Seeking Better Life Chances by Crossing Borders: The Existential Paradox and Strategic Use of Italian Citizenship by Migrant Women

Based on long-term ethnographic fieldwork carried out in Naples (Italy) in the period 2014 to 2020, this article focuses on the rearticulation of the migration–citizenship nexus through a gender perspective. The article questions how migrant women exercise their agency despite the structural constraints that prevent their full inclusion and how they are able to cross and transgress the boundaries of citizenship and national belonging in search of better life opportunities. The data analyzed show the existential paradox linked to the migration–citizenship nexus that affects the lives of migrant women in Italy and their use of citizenship as a strategy to react to a blocked destiny, to follow one’s aspirations, and to rebalance gender relations. The article refines an integrated approach that considers the relationship between agency, aspiration, and capability as a broader theoretical framework within which to jointly study the dynamics of gender, migration, and citizenship as closely related, beyond the boundaries of fixed and opposite categories.
Risk of thyroid cancer in a lung cancer screening population of the National Lung Screening Trial according to the presence of incidental thyroid nodules detected on low-dose chest CT

Purpose This study evaluated thyroid cancer risk in a lung cancer screening population according to the presence of an incidental thyroid nodule (ITN) detected on low-dose chest computed tomography (LDCT). Methods Of 47,837 subjects who underwent LDCT, a lung cancer screening population according to the National Lung Screening Trial results was retrospectively enrolled. The prevalence of ITN on LDCT was calculated, and the ultrasonography (US)/fine-needle aspiration (FNA)–based risk of thyroid cancer according to the presence of ITN on LDCT was compared using the Fisher exact or Student t-test as appropriate. Results Of the 2,329 subjects (female:male=44:2,285; mean age, 60.9±4.9 years), the prevalence of ITN on LDCT was 4.8% (111/2,329). The incidence of thyroid cancer was 0.8% (18/2,329, papillary thyroid microcarcinomas [PTMCs]) and was higher in the ITN-positive group than in the ITN-negative group (3.6% [4/111] vs. 0.6% [14/2,218], P=0.009). Among the 2,011 subjects who underwent both LDCT and thyroid US, all risks were higher (P<0.001) in the ITNpositive group than in the ITN-negative group: presence of thyroid nodule on US, 94.1% (95/101) vs. 48.6% (928/1,910); recommendation of FNA according to the American Thyroid Association guideline and Korean Thyroid Imaging Reporting and Data System guideline, 41.2% (42/101) vs. 2.4% (46/1,910) and 39.6% (40/101) vs. 1.9% (37/1,910), respectively. Conclusion Despite a higher risk of thyroid cancer in the LDCT ITN-positive group than in the ITN-negative group in a lung cancer screening population, all cancers were PTMCs. A heavy smoking history may not necessitate thorough screening US for thyroid incidentalomas.
Putting a Price on Temperature *

Abstract. This paper analyzes the weather derivatives traded at the Chicago Mercantile Exchange (CME), with futures and options written on different temperature indices. We propose to model the temperature dynamics as a continuous‐time autoregressive process with lag p and seasonal variation. The choice p=3 turns out to be sufficient to explain the temperature dynamics observed in Stockholm, Sweden, where we fit the model to more than 40 years of daily observations. The main finding is a clear seasonal variation in the regression residuals, where temperature shows high variability in winter, low in autumn and spring, and increasing variability towards the early summer. Our model allows for derivations of explicit prices for several futures and options. Note that the volatility term structure of futures written on the cumulative average temperature has a modified Samuelson effect, where the volatility prior to the measurement period increases, except for the last part, where it may decrease.
Characterization of sound enamel and natural white spot lesions

Objective: To compare optical, morphological, chemical, and physical aspects of the sound enamel and white spot lesions (WSL) classified as ICDAS 2. Material and Methods: Seventeen human molars with one surface presenting WSL and a sound surface (2 x 2 mm window) were characterized by Quantitative light-induced fluorescence (QLF ® ), Optical coherence tomography (OCT), microhardness, and Raman spectroscopy. The ANOVA and Tukey’s test were used at 5% significance level. Results: The QLF comparison between distinct substrates yielded decreased ∆ Q (integrated fluorescence loss) of -15,37%mm 2 and -11,68% ∆ F (fluorescence loss) for WSL. The OCT detected mean lesion depth of 174,43 µm. ANOVA could not detect differences in the optical attenuation coefficient between the substrates (p>0.05). Lower microhardness measures were observed in WSL than on sound enamel (p<0.05). The Raman spectra showed four vibrational phosphate bands (v1, v2, v3, v4), where the highest peak was at 960.3 cm -1 (v1) for both substrates. However, a 40% decrease in phosphate (v1) was detected in WSL. The peak at 1071 cm -1 was higher for sound enamel, indicating the presence of a phosphate band instead of the B-type carbonate. The spectra showed higher intensity of the organic composition at 1295 cm -1 and 1450 cm -1 for WSL. Conclusion: Non-invasive QLF, OCT and Raman spectroscopy were able to distinguish differences in fluorescence, optical properties, and organic/inorganic components, respectively, between sound enamel and WSL, validated by the destructive microhardness analysis.
External Influences on Hurricane Intensity. Part III: Potential Vorticity Structure

Abstract The interaction of Hurricane Elena (1985) with a baroclinic wave was reexamined using both potential vorticity (PV) and a formulation for Eliassen-Palm fluxes in cylindrical coordinates. The hurricane began to deepen rapidly as a narrow upper-level positive PV anomaly became nearly superposed over the low-level center. The intensification appeared to represent an evaporation-wind feedback activated by constructive interference of the PV anomalies. Enhanced convection associated with this process eroded the upper PV anomaly and prevented it from crossing the hurricane and reversing the intensification. The Eliassen–Palm flux divergence showed that maximum eddy activity remained in the upper troposphere prior to the reintensification. This activity was produced in part because the action of the outflow anticyclone of the hurricane contributed to synoptic-scale wave breaking. The upper-level PV anomaly that approached the center was much narrower in extent than the original synoptic-scale trough. Th.