Search Results (138)

Background/Objectives: Histologic remission has emerged as a key treatment target in inflammatory bowel disease (IBD), but routine assessment requires repeated endoscopy and biopsies. Blood-based indices reflecting inflammation, nutritional status and atherogenic risk are inexpensive and widely available, yet their integrated contribution to histologic activity remains unclear. This study addresses this gap by simultaneously analyzing a broad panel of 44 variables—including nutritional status indicators, CBC-derived inflammation indices, and atherogenic lipid indices—in IBD patients. Methods: In this retrospective study, 100 patients with IBD (50 Crohn’s disease [CD], 50 ulcerative colitis [UC]) without additional comorbidities and with concomitant histologic assessment were analyzed. Histologic activity was coded as active vs. remission. At the time of biopsy, the complete blood count, biochemistry and lipid profile were used to calculate immuno-nutritional indices (CONUT score, prognostic nutritional index), inflammatory indices (neutrophil-to-platelet ratio, platelet-to-lymphocyte ratio, lymphocyte-to-monocyte ratio [LMR], systemic immune-inflammation index, systemic immune-inflammation index, systemic inflammation response index [SIRI], aggregate index of systemic inflammation, C-reactive protein to albumin ratio) and atherogenic indices (atherogenic index of plasma [AIP], triglyceride-to-HDL cholesterol ratio). Variable selection was performed separately for CD and UC using least absolute shrinkage and selection operator (LASSO) regression and sparse partial least squares discriminant analysis (sPLS-DA). Independently associated predictors were then entered into multivariable logistic regression models, and their discriminative performance was evaluated using ROC analysis with bootstrap-derived 95% confidence intervals. Results: LASSO analysis identified a broadly similar systemic profile associated with histologic activity in CD and UC, dominated by the CONUT score, SIRI, AIP, LMR and red blood cell parameters, whereas demographic features and most routine biochemical markers were shrunk towards zero. Cross-validated AUCs for the LASSO models were 0.93 in CD and 0.87 in UC. sPLS-DA confirmed this pattern: CONUT, SIRI and AIP consistently showed the highest variable importance in projection scores and loadings on the first latent component. In multivariable regression, the CONUT score, SIRI and AIP remained independent predictors of histologic activity in CD, while hematocrit, CONUT score, SIRI and AIP were independently associated with histologic activity in UC. In ROC analysis, AUCs for CONUT, SIRI and AIP were 0.81, 0.89 and 0.87 in UC, and 0.72, 0.82 and 0.83 in CD, respectively. Conclusions: Histologic activity in IBD is characterized by a coupled systemic profile in which immuno-nutritional compromise (captured by CONUT) forms the core signal, supplemented by systemic inflammation (SIRI) and atherogenic dyslipidemia (AIP). These readily available blood-based indices may help to approximate histologic disease activity in clinical practice. However, considering that comorbid diseases may affect these indices, the strict exclusion criteria applied in this study may limit the generalizability of the findings among patients with IBD. Consequently, further validation in larger prospective cohorts is warranted. Full article

Background/Objectives: Dapagliflozin is an SGLT2 inhibitor prescribed for the management of type 2 diabetes mellitus. The drug lowers blood glucose levels by increasing urinary glucose excretion (UGE). Despite established efficacy, dapagliflozin demonstrates significant inter-individual variability in pharmacokinetics (PK) and pharmacodynamics (PD), with potential impact on treatment outcomes. Methods: To evaluate the sources of variability and to support patient stratification and model-informed individualized therapy, we developed a physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of dapagliflozin using curated data from 28 clinical studies. This framework integrates absorption, distribution, metabolism, excretion, and pharmacodynamics, and accounts for key determinants of variability including renal and hepatic function, and food effects. Results: The simulations reproduced dose-dependent pharmacokinetics with predicted C_max and AUC values typically within 10–15% of observed data. Renal impairment reduced UGE by 40–60% despite modest changes in plasma exposure, while hepatic impairment produced only small shifts in PK and PD. The model also reproduced the fed-state reduction of peak concentrations, consistent with the 30–50% decrease reported clinically. Conclusions: All model files, code, and curated datasets are openly available in line with FAIR standards and Open Science practices, enabling transparent and reproducible analyses and providing a mechanistic basis for individualized therapy in type 2 diabetes. Full article

Dielectronic recombination (DR) is widely recognized as a fundamental atomic process in many astrophysical and laboratory plasmas, where it plays a crucial role in determining ionization balance and level populations over a broad temperature range. Reliable DR resonance strengths and plasma rate coefficients for such plasma modeling can be computed using the Jena Atomic Calculator (JAC)—a relativistic code based on the multiconfiguration Dirac–Hartree–Fock (MCDHF) method. In this work, we investigate the DR of Li-like Ar¹⁵⁺ ions in their ground state (2s), focusing on resonances associated with the fine-structure core excitations $2s_{1/2}\to 2p_{1/2,3/2}$. The resulting fine-structure-resolved DR resonance strengths and plasma rate coefficients are in good agreement with recent high-resolution DR measurements of Ar¹⁵⁺ ions performed at the Main Cooler Storage Ring (CSRm) in Lanzhou, China. These results provide a stringent benchmark for JAC calculations and support their applicability in plasma modeling. Full article

Partially ionized plasma physics has attracted increased attention recently due to numerous technological applications made possible by the increased sophistication of computer modelling, the depth of the theoretical analysis, and the technological applications to a vast field of manufacturing for computer components. Partially ionized plasma is characterized by a significant presence of neutral particles in contrast to the fully ionized plasma. The theoretical analysis is based upon solutions of the kinetic Boltzmann equation, yielding the non-Maxwellian electron energy distribution function (EEDF), thereby emphasizing the difference with a fully ionized plasma. The impact of the effect on discharges in inert and molecular gases is described in detail, yielding the complex nonlinear phenomena resulting in plasma selforganization. A few examples of such phenomena are given, including the non-monotonic EEDFs in the discharge afterglow in a mixture of argon with the molecular gas NF₃; the explosive generation of cold electron populations in capacitive discharges, hysteresis of EEDF in inductively coupled plasmas. Recently, highly advanced computer codes were developed in order to address the outstanding challenges in plasma technology. These developments are briefly described in general terms. Full article

Monte Carlo simulations of the transport of atoms in gases related to the deposition process and the contamination of amorphous carbon thin films during deposition in magnetron discharges have been performed. These films are of interest in accelerator technology due to their low secondary electron yield when their structures are dominated by sp² carbon. Two codes, which practically share the same algorithm, are introduced: TAGs 1 simulates the transport of sputtered atoms from the target to the substrate, and TAGs 2 simulates the transport of atoms from the plasma towards the target and the substrate. The similar results of TAGs 1 and the well-established SIMTRA for the same input parameters imply the algorithm’s accuracy. The codes were used to model the transport of different atoms (C, H, O, D) in a magnetron Ar discharge. The simulations reveal that the operating pressure should be higher than 1 Pa for a sample-target distance of 90 mm to secure sp² carbon formation. The contamination mechanisms of amorphous carbon coatings were then studied by merging the results obtained with both programs. Preliminary comparisons with experiments suggest that the combined results of TAGs 1 and 2 agree very well with the experiments. Full article

Background: The ACE Y215C mutation is a common, functionally damaging missense variant (~1.5% allele frequency) associated with reduced plasma ACE levels and increased Alzheimer’s disease (AD) risk. In CHO and HEK cell models, this mutation caused a ~3–6-fold decrease in ACE surface expression, soluble ACE levels, and ACE enzymatic activity compared to those of wild-type ACE. Methods: Circulating ACE levels and activity were measured in EDTA plasma obtained from 84 carriers of the ACE Y215C mutation using a set of mAbs to the ACE. The mAbs 5B3/1G12 binding ratio was revealed as a sensitive marker for the circulating Y215C ACE mutant. Whole-exome and whole-genome sequencing (WES/WGS) were performed to identify genetic variants potentially modifying circulating ACE levels. In parallel, published sequencing and proteomic data from 35,559 Icelanders participants were analyzed to identify genes influencing ACE shedding. Sequence comparison was performed between carriers with elevated and reduced ACE concentrations to identify the potential protective variants that may compensate for decreased ACE levels due to the Y215C mutation itself. Results: Most carriers of the Y215C ACE mutation demonstrated significantly decreased ACE levels (median is 62% of control ACE levels). However, substantial inter-individual variability was observed in plasma ACE activity among carriers. Comparative sequencing analysis revealed 9648 variants unique to individuals with elevated ACE, mapping to 5779 protein-coding genes and enriched for pathways related to intracellular and transmembrane transport. Conclusions: The presence of the damaging ACE mutation Y215C does not invariably result in low plasma ACE or, likely, elevated AD risk. Therefore, combined blood ACE phenotyping and whole-exome sequencing are recommended to more accurately assess ACE-related AD susceptibility in mutation carriers. Full article

Intervertebral disc (IVD) herniation is a complex and multifactorial condition with a challenging diagnosis and limited therapeutic options, highlighting the need for reliable biomarkers to improve clinical decision-making. The aim of this study was to identify circulating prognostic biomarkers of IVD herniation regression. The plasma proteomic profile and the expression of circulating non-coding RNAs were analysed in a rat model of IVD herniation and were correlated with herniation size. Four candidate proteins (TNC, COPS3, JUP, and GNAI2) were significantly correlated with herniation size, with TNC further validated by ELISA. Additionally, miR-143-3p, miR-10b-5p, miR-27a-3p, miR-140-5p, miR-155-5p, miR-146a-5p, and miR-21-5p were positively correlated with herniation size. Moreover, TNC, COPS3, JUP, and GNAI2 were found to be potential targets of miR-155-5p. This study provides the first combined proteomic and miRNA account of preclinical plasma biomarkers of IVD herniation size, where TNC-miR-155-5p emerge as promising elements of a regulatory module with IVD herniation prognostic potential. Full article

Recent advances in non-local thermodynamic equilibrium (non-LTE) plasma simulations, for example in modeling kilonova ejecta, have emphasized the need for consistent and reliable atomic data. Unlike LTE modeling, non-LTE calculations must include a consistent treatment of various photon-induced and collisional processes in order to describe realistic electron and photon distributions in the plasma. However, the available atomic data are often incomplete, inconsistently formatted, or even fail to indicate the main dependencies on the level structure and plasma parameters, thus limiting their practical use. To address these issues, we have extended Jac, the Jena Atomic Calculator (version v0.3.0), to provide direct access to relevant cross sections, plasma rates, and rate coefficients. Emphasis is placed on photoexcitation and ionization processes as well as their time-reversed counterparts—photo-de-excitation and photorecombination. Whereas most of these data are still based on empirical expressions, their dependence on the ionic level structure and plasma temperature is made explicit here. Moreover, the electron and photon distributions can be readily controlled and adjusted by the user. This transparent representation of atomic data for photon-mediated processes, together with a straightforward use, facilitates their integration into existing plasma codes and improves the interpretation of high-energy astrophysical phenomena. It may support also more accurate and flexible non-LTE plasma simulations. Full article

The modelling of plasma–wall interactions (PWIs) depends on distributions describing the angle and energy distribution of particles scattered at the first wall of fusion devices. Most PWI codes rely on extensive tables based on data from reflection simulations, employing a Monte Carlo method. At first glance, the uncertainty distribution of the data should be assumed Gaussian. However, in order to obtain the resulting particle distribution, the reflected ions are counted within angle sections of the upper hemisphere, which hints to a Poisson uncertainty distribution. In this paper, we let Bayesian model comparison decide which uncertainty model should be taken. Full article

Background: Non-small cell lung cancer (NSCLC) progression is driven by dysregulated competing endogenous RNA (ceRNA) networks, where non-coding RNAs sequester miRNAs to modulate oncogene expression. The tumor-suppressor miR-145 is frequently downregulated in NSCLC, but its lncRNA-mediated regulation remains incompletely characterized. Methods: Integrated transcriptomic analysis of NSCLC datasets (GSE135304: blood RNA from 712 patients; GSE203510: plasma miRNAs) was used to identify dysregulated genes (|log2FC| > 0.1, p < 0.05) and miRNAs (|log2FC| > 1, p < 0.05). Experimentally validated targets from miRTarBase/TarBase were intersected with dysregulated genes, followed by WikiPathways/GO enrichment. ceRNA networks were constructed via co-expression analysis. RT-qPCR validated miR-145-3p expression in A549/MRC-5 cells and NSCLC tissues. GEPIA assessed FN1/CCND1 clinical relevance. Results: We identified 8271 dysregulated genes and 52 miRNAs. miR-145-3p, critical in immune regulation, was significantly downregulated (log2FC = −1.24, p = 0.036). Intersection analysis revealed 27 miR-145-3p targets (e.g., FN1, CCND1, SMAD3) enriched in immune pathways (FDR < 0.05) and TGF-β-mediated EMT within the dysregulated geneset. Six immune-linked hub genes emerged. LncRNAs LOC729919 and LOC100134412 showed strong co-expression with hub genes and competitively bind miR-145-3p, derepressing the expression of the metastasis drivers FN1 (ECM regulator) and CCND1 (cell cycle controller). This ceRNA axis operates within a broader dysregulation of ATM-dependent DNA damage, Hippo signaling, and cell cycle pathways. RT-qPCR confirmed significant miR-145-3p suppression in NSCLC models (p < 0.05). GEPIA revealed a significant FN1-CCND1 co-expression (p = 0.0017). Conclusions: We characterize a novel LOC729919/LOC100134412–miR-145–FN1/CCND1 ceRNA axis in NSCLC pathogenesis. FN1’s prognostic value and functional linkage to CCND1 underscores its potential clinical relevance for therapeutic disruption. Full article

CREATE-FXB is a Finite Element Method solver specifically developed to address the fixed boundary problem, namely the determination of the Magnetohydrodynamic equilibrium of an axisymmetric plasma confined within a toroidal nuclear fusion device. Although several solvers are already available and widely used, CREATE-FXB represents a valuable alternative with further improvements, as it introduces a set of distinctive capabilities that extend its applicability and accuracy in modelling this class of problems. Its key features include the design of plasma scenarios in tokamaks, the derivation of linearized plasma response with high accuracy, the treatment of a wide class of current density profiles including non-smooth distributions, and an improved capability of interfacing with other existing codes. Full article

MicroRNAs (miRNAs), small non-coding RNAs, have emerged as promising diagnostic and prognostic biomarkers for various diseases. However, their role in the pathogenesis of type 2 diabetes mellitus (T2DM) remains insufficiently defined. This case–control study investigated associations between genetic variants in miRNA genes and susceptibility to T2DM in a Greek population. A total of 716 individuals with T2DM and 569 controls (HbA1c < 6.5% and fasting plasma glucose < 126 mg/dL) were included. Genomic DNA was extracted from whole blood and genotyped using the Illumina Infinium PsychArray platform. Polymorphisms in MIR124a, MIR27a, MIR146a, MIR34a, MIRLET7A2, MIR128a, MIR196a2, MIR499a, MIR4513, and MIR149 were analyzed, with all SNPs within 20 kb upstream and downstream of each gene assessed. Allele frequencies were compared between cases and controls using PLINK. Significant associations with increased T2DM risk were observed for rs1531212 (OR = 1.375, p = 0.018) in MIR23aHG (containing MIR27a) and rs6120777 (OR = 1.27, p = 0.018) in MYH7B, upstream of MIR499a. Conversely, rs2425012 (OR = 0.794, p = 0.018) upstream of MIR27a, as well as rs883517 (OR = 0.728, p = 0.024) and rs2961920 (OR = 0.80, p = 0.041) upstream of MIR146a, appeared protective. Under the dominant model, two additional associations emerged: rs3746435 (OR = 1.239, p = 0.025) in MYH7B (upstream of MIR499a) and rs3746444 (OR = 1.235, p = 0.046) in MIR499a. In conclusion, this study identifies three novel genetic variants near MIR27a and MIR499a that may influence susceptibility to T2DM. These findings warrant validation in larger cohorts and functional studies to clarify their role in T2DM pathogenesis. Full article

Schizophrenia is a highly polygenic and clinically heterogeneous disorder. In this paper, we first review layer-specific evidence across genetics, epigenetics, transcriptomics, proteomics, and patient-derived induced pluripotent stem cell (iPSC) models, then integrate cross-layer findings. Genetics research identifies widespread risk architecture. Hundreds of loci from common, rare, and CNV analyses. Epigenetics reveals disease-associated DNA methylation and histone-mark changes. These occur at neuronally active enhancers and promoters, together with chromatin contacts that link non-coding risk to target genes. Transcriptomics show broad differential expression, isoform-level dysregulation, and disrupted co-expression modules. These alterations span synaptic signaling, mitochondrial bioenergetics, and immune programs. Proteomics demonstrates coordinated decreases in postsynaptic scaffold and mitochondrial respiratory-chain proteins in cortex, with complementary inflammatory signatures in serum/plasma. iPSC models recapitulate disease-relevant phenotypes: including fewer synaptic puncta and excitatory postsynaptic currents, electrophysiological immaturity, oxidative stress, and progenitor vulnerability. These same models show partial rescue under targeted perturbations. Integration across layers highlights convergent pathways repeatedly supported by ≥3 independent data types: synaptic signaling, immune/complement regulation, mitochondrial/energetic function, neurodevelopmental programs and cell-adhesion complexes. Within these axes, several cross-layer convergence genes/proteins (e.g., DLG4/PSD-95, C4A, RELN, NRXN1/NLGN1, OXPHOS subunits, POU3F2/BRN2, PTN) recur across cohorts and modalities. Framing results through cross-layer and shared-pathway convergence organizes heterogeneous evidence and prioritizes targets for mechanistic dissection, biomarker development, and translational follow-up. Full article

We present three dimensional particle-in-cell simulations of current-voltage characteristics of the hemispherical Langmuir probe (LAP), onboard the China Seismo-Electromagnetic Satellite (CSES). Using realistic plasma parameters and background magnetic fields obtained from the International Reference Ionosphere (IRI) and International Geomagnetic Reference Field (IGRF) models, we simulate probe–plasma interactions at three locations: the equatorial region and two magnetically conjugate mid-latitude sites: Millstone Hill (Northern Hemisphere) and Rothera (Southern Hemisphere). The simulations, performed using the PTetra PIC code, incorporate realistic LAP geometry and spacecraft motion in the ionospheric plasma. Simulated current voltage characteristics or I–V curves are compared against in-situ LAP measurements from CSES Orbit-026610, with Pearson’s correlation coefficients used to assess agreement. Our findings indicate how plasma temperature, density, and magnetization affect sheath structure and probe floating potential. The study highlights the significance of kinetic modeling in enhancing diagnostic accuracy, particularly in variable sheath regimes where classic analytical models such as the Orbital-Motion-Limited (OML) theory may be inadequate. Full article

A three-dimensional (3-D) Multi-Layers Method (MLM) of an extension of the axisymmetric version has been developed to compute non-axisymmetric tokamak plasma equilibria with a separatrix. Conventional axisymmetric tokamak control codes cannot simulate non-axisymmetric effects, while stellarator equilibrium solvers such as VMEC do not include the effects of conducting structures. Moreover, VMEC cannot obtain equilibria with separatrices since it uses magnetic coordinates. The 3-D MLM removes these limitations by using a deformable circuit model of a magnetic confinement system. Plasma is modeled by multiple current layers coinciding with magnetic surfaces, and equilibria are obtained as solutions of a variational problem of a free energy functional with current sources. Validations of equilibrium solutions against a stellarator vacuum field and a VMEC solution for a small non-axisymmetric tokamak show good agreement in magnetic configurations, pressure profile, and plasma current. By incorporating conducting structures and extension to dynamic simulations, the 3-D MLM establishes a method for simulating tokamak plasma control under non-axisymmetric magnetic fields. Full article