Browse Articles

Loss of structural specificity in 3D genome organization upon viral infection is predicted by polymer physics

In the last years, it has been proved that some viruses are able to re-structure chromatin organization and alter the epigenomic landscape of the host genome. In addition, they are able to affect the physical mechanisms shaping chromatin 3D structure, with a consequent impact on gene activity. Here, we investigate with polymer physics genome re-organization of the host genome upon SARS-CoV-2 viral infection and how it can impact structural variability within the population of single-cell chromatin configurations. Using published Hi-C data and molecular dynamics simulations, we build ensembles of 3D configurations representing single-cell chromatin conformations in control and SARS-CoV-2 infected conditions. We focus on genomic length scales of TADs and consider, as a case study, models of real loci containing DDX58 and IL6 genes, belonging, respectively, to the antiviral interferon response and pro-inflammatory genes. Clustering analysis applied to the ensemble of polymer configurations reveals a generally increased variability and a more heterogeneous population of 3D structures in infected conditions. This points toward a scenario in which viral infection leads to a loss of chromatin structural specificity with, likely, a consequent impact on the correct regulation of host cell genes.

Sodium selenite enhanced the selenium content in black soldier fly

Molecular orientation of dielectric layers at indigo/dielectric interfaces impacts the ordering of indigo films in organic field-effect transistors

Organic multilayer systems, which are stacked layers of different organic materials, are used in various organic electronic devices such as organic light-emitting diodes (OLEDs) and organic field-effect transistors (OFETs). In particular, OFETs are promising as key components in flexible electronic devices. In this study, we investigated how the inclusion of an insulating tetratetracontane (TTC) interlayer in ambipolar indigo-based OFETs can be used to alter the crystallinity and electrical properties of the indigo charge transport layer. We find that the inclusion of a 20-nm-thick TTC film thermally annealed at a low temperature of 70 °C acts to significantly increase the ambipolar electrical transport of the indigo layer. X-ray diffraction, atomic force microscopy, and vibrational sum frequency generation measurements showed that annealing the TTC film significantly improved its ordering. The electronic sum-frequency generation spectra of TTC/indigo bilayers show that this improved ordering of TTC films promotes the growth of crystalline indigo films that exhibit charge mobilities in OFET that are nearly an order of magnitude larger than those measured for devices grown on unannealed TTC layers. Furthermore, using vibrational sum-frequency generation spectroscopy, we found that pre-annealing the TTC layer prior to indigo deposition can suppress the formation of defects within the TTC layer during indigo film growth, which also contributes to enhanced charge transport. Our results highlight the importance of controlling the molecular ordering within the interlayer contacts in OFET structures to achieve an enhanced performance.

Rapid quantitative analysis of double-stranded plasmid DNA with capillary gel electrophoresis for applications in quality control and radiation research

AbstractThe quantification of different structures, isoforms and types of damage in plasmid DNA is of importance for applications in radiation research, DNA based bio-dosimetry, and pharmaceutical applications such as vaccine development. The standard method for quantitative analysis of plasmid DNA damage such as single-strand breaks (SSB), double-strand breaks (DSB) or various types of base-damage is Agarose gel electrophoresis (AGE). Despite being well established, AGE has various drawbacks in terms of time consuming handling and analysis procedures. A more modern, faster, cheaper and more reliable method is capillary gel electrophoresis (CGE). However, to establish this method in biotechnology, radiation-research and related fields, certain criteria in terms of accuracy, repeatability and linearity have to be tested and protocols have to be established. This study performs the relevant tests with a common model plasmid (pUC19, double-stranded DNA with 2686 basepairs) to establish a CGE based methodology for quantitative analysis with readily available commercial CGE systems. The advantages and limitations of the methods are evaluated and discussed, and the range of applicability is presented. As a further example, the kinetics of enzyme digestion of plasmid DNA by capillary gel electrophoresis was studied. The results of the study show for a model system consisting out of pUC19, the suitability of CGE for the quantification of different types of DNA damage and the related isoforms, such as supercoiled, open-circular and linear plasmid DNA.

Mean lifetime of diffusing particle in cylindrical cavity with absorbing spots of arbitrary radii on its bases

This paper deals with the trapping of a particle diffusing in a cylindrical cavity by two circular absorbing spots of arbitrary radii located in the centers of the cavity bases. The focus is on the mean particle lifetime, which is its mean first-passage time to one of the spots. When the spots are small and their radii are well below the cavity radius, this time can be analyzed using the narrow escape (NE) theory, which describes it as a function of the spot radii and the only parameter of the cavity, its volume, independent of the cavity shape and the particle initial position. We derive an approximate analytical solution for the mean particle lifetime that goes beyond the scope of the NE theory. In particular, our solution shows how this mean lifetime depends on the cavity shape, i.e., its length and radius, the particle initial position in the cavity, and the spot radii, which can be arbitrary. It reduces to the NE solution, as the spot radii tend to zero. To check the accuracy of our approximate result, we determine the mean lifetimes from three-dimensional Brownian dynamics simulations. The comparison shows excellent agreement between the theoretical predictions and simulation results when the initial distance from the particle to both cavity bases exceeds the cavity radius.

A cutting-edge neural network approach for predicting the thermoelectric efficiency of defective gamma-graphyne nanoribbons

Bee-yond the plateau: Training QNNs with swarm algorithms

In the quest to harness the power of quantum computing, training quantum neural networks (QNNs) presents a formidable challenge. This study introduces an innovative approach, integrating the Bees Optimization Algorithm (BOA) to overcome one of the most significant hurdles—barren plateaus. Our experiments across varying qubit counts and circuit depths demonstrate the BOA’s superior performance compared to the Adam algorithm. Notably, BOA achieves faster convergence, higher accuracy, and greater computational efficiency. This study confirms BOA’s potential to enhance the applicability of QNNs in complex quantum computations.

A novel approach to assess acid diversion efficiency in horizontal wells

AbstractUsing an acid to stimulate a heterogeneous carbonate reservoir during matrix acidizing may lead to over-treating the high permeability zones, leaving low permeability zones untreated. This is particularly exacerbated in long horizontal sections, necessitating the use of acid diverters for effective acid distribution across the formation. In previous studies, conventional core flooding systems were utilized where single inlet and outlet lines were used or, at best, two outlet lines for dual-core flooding. This paper proposes a new method for simulating matrix acidizing in horizontal wells by introducing five injection points and two outlet lines. The injection points are perpendicular to the core samples to simulate multiple perforations in a horizontal well while the outlet lines are parallel. Four experiments were conducted in this study using Indiana limestone cores that were 1.5 inches in diameter. For the first three tests, the length of the core was 12 inches, and the cores’ average permeabilities were 16 mD. For the fourth one, two 6-inch length cores with different average permeability (10 and 50 mD) were employed. Hydrochloric acid was used in the first experiment, while hydrochloric acid with viscoelastic surfactant (VES) was used in subsequent experiments. To the best of our knowledge, this is the first study to introduce a multi-point injection system with enhanced coverage and distribution, resulting in a more precise representation of acidizing a horizontal well.

Endohedral vs exohedral boron in C60: Bonding nature and impact on hot-electron relaxation dynamics

Endohedral and exohedral fullerenes have both been employed as electron acceptors in polymer solar cells (PSCs). However, their differences in hot-electron relaxation dynamics remain unclear. Previous studies have shown that the location of a single atom, whether inside or outside the fullerene cage, results in significant differences in charge distribution. In this work, the hot-electron relaxations of endohedral B@C60+ and exohedral C60B+ are investigated using nonadiabatic molecular dynamics simulations. Our results reveal that the location of the boron atom—inside or outside the fullerene—significantly impacts the bonding interactions between boron and C60. Compared to C60B+, the weaker interactions in B@C60+ reduce the orbital overlap between LUMO+3 and LUMO+2 and increase the energy gap between them. This, in turn, slows hot-electron relaxation by weak nonadiabatic coupling, making B@C60+ more suitable for PSC applications. This study provides valuable insights into how atomic positioning affects the electronic properties in fullerene-based materials, contributing to the design of more efficient electron acceptors for photovoltaic devices.

Randomized controlled trial on effect of different routes of dexmedetomidine on Haemodynamics in patients undergoing saphenectomy under epidural anaesthesia

Tunable phase behaviors of diblock copolyelectrolytes under alternating electric fields: A coarse-grained molecular dynamics study

Diblock copolyelectrolytes have significant potential in applications such as solid-state single-ion conductors, but precisely controlling their nanostructures for efficient ion transport remains a challenge. In this study, we explore the phase behavior and microphase transitions of AX BY-type diblock copolyelectrolytes under alternating electric fields using coarse-grained molecular dynamics simulations. We systematically investigate the effects of various electric field features, including unipolar and bipolar square-waves, as well as offset and non-offset sine-waves, focusing on how field strength and period influence the self-assembling morphology of the copolyelectrolytes. Under unipolar square-waves, both the lamellar and cylindrical phase regions expand, while the disordered phase regions shrink as the field strength increases. In contrast, bipolar square-waves maintain lamellar structures more robustly, with reversed stretching behavior observed in the polymer chains. As the electric field period exceeds a critical value, both waveforms converge with the results seen under constant electric fields. In addition, sine-waves induce smoother phase transitions, expanding the ordered phase regions, particularly the cylindrical phase, due to continuous field variation. We further examine the detailed structural and dynamic properties, such as mean-square displacement, polymer conformation, and chain orientation during these transitions. This work provides fundamental insights into the structural regulation of diblock copolyelectrolytes under oscillating electric fields, guiding the design of advanced polymeric electrolytes with tailored nanostructures.

The associations between dietary advanced glycation-end products intake and self-reported infertility in U.S. women: data from the NHANES 2013–2018

Direct Givens rotation method based on error back-propagation algorithm for self-consistent field solution

The self-consistent field (SCF) procedure is the standard technique for solving the Hartree–Fock and Kohn–Sham density functional theory calculations, while convergence is not theoretically guaranteed. Direct minimization methods, such as the augmented Lagrangian method (ALM) and second-order SCF (SOSCF), obtain the SCF solution by minimizing the Lagrangian with the gradient. In SOSCF, molecular orbitals are optimized by truncating the Taylor expansion of a unitary matrix represented in exponential form to ensure the orthonormality condition. This study proposes an alternative algorithm for direct-energy minimization to obtain an SCF solution using ALM Lagrangian by adopting sequential Givens rotations between occupied and virtual orbitals. The Givens rotation corresponds to unitary transformations that guarantee orthogonality and avoid variational collapse. Complex gradients for sequential Givens rotation were obtained by the error back-propagation method, which is based on the chain rule. Illustrative applications clarified the features of the present DGR methods by comparing with other SCF algorithms such as direct inversion in iterative subspace, SOSCF, and ALM.

Publisher Correction: Novel metal–organic framework biosensing platform for detection of COVID-19 RNA

Surface structure characterization of rubrene(001) single crystal with sum frequency generation spectroscopy and reflection high-energy electron diffraction

Rubrene is one of the leading organic semiconductors in scientific and industrial research, showing good conductivities and utilities in devices such as organic field-effect transistors. In these applications, the rubrene crystals often contact ionic liquids and other materials. Consequently, their surface properties and interfacial interactions influence the device’s performance. Although rubrene has been extensively studied with multiple structure characterization techniques, a complete description of the structure of rubrene single-crystal surfaces at the molecular level remains elusive. This study elucidates the molecular orientation and arrangement on the surface of rubrene single crystals with sum frequency generation (SFG) spectroscopy and reflection high-energy electron diffraction, respectively. The results confirm the near-surface unit cells with in-plane lattice parameters of a = 7.24 Å and b = 14.3 Å and an out-of-plane constant of c = 26.9 Å. Furthermore, the SFG analysis yields the tilt and rotation angles of θ = 15° and φ = 43° with respect to the crystalline c and a axes, respectively, and an in-plane twist of ψ = 3° for the surface phenyl rings.

Multi-dimensional scaling for space-time transformation to achieve sustainable planning and management of water resource under changing land use pattern

Path integral Monte Carlo in a discrete variable representation with Gibbs sampling: Dipolar planar rotor chain

In this work, we propose a path integral Monte Carlo approach based on discretized continuous degrees of freedom and rejection-free Gibbs sampling. The ground state properties of a chain of planar rotors with dipole–dipole interactions are used to illustrate the approach. Energetic and structural properties are computed and compared to exact diagonalization and numerical matrix multiplication for N ≤ 3 to assess the systematic Trotter factorization error convergence. For larger chains with up to N = 100 rotors, Density Matrix Renormalization Group calculations are used as a benchmark. We show that using Gibbs sampling is advantageous compared to traditional Metropolis–Hastings rejection importance sampling. Indeed, Gibbs sampling leads to lower variance and correlation in the computed observables.

Mitochondrial DNA lineages determine tumor progression through T cell reactive oxygen signaling

Mitochondrial DNA (mtDNA) is highly polymorphic, and host mtDNA variation has been associated with altered cancer severity. To determine the basis of this mtDNA–cancer association, we analyzed conplastic mice with the C57BL/6J (B6) nucleus but two naturally occurring mtDNA lineages, mtDNA B6 and mtDNA NZB , where mtDNA NZB mitochondria generate more oxidative phosphorylation (OXPHOS)-derived reactive oxygen species (mROS). In a cardiac transplant model, mtDNA B6 Foxp3+ T regulatory (Treg) cells supported long-term allograft survival, whereas mtDNA NZB Treg cells failed to suppress host T effector (Teff) cells, leading to acute rejection. When challenged with melanoma or colon cancer cells, the mtDNA NZB mice exhibited strikingly impaired tumor growth while mtDNA B6 mice showed Treg-dependent inhibition of Teff cells and allowed rapid tumor growth. Transcriptional analysis showed that activation of mtDNA NZB Teff cells increased mitochondrial gene expression while activation of mtDNA NZB Treg cells impaired mitochondrial gene expression and resulted in mtDNA NZB Treg cell exhaustion. Induction of the mitochondrially targeted catalytic antioxidant, mCAT, in hematopoietic cells normalized mtDNA NZB Treg function in both transplant and tumor models, indicating a key role for mROS in promoting Treg dysfunction. Anti-PD-L1 therapy did not modulate these effects, indicating that modulation of host mitochondrial function provides an independent approach for enhancing tumor cell destruction.

Changing patterns of general practice services during a period of public sector investment in Britain

Introduction Given the importance of GP care to the public’s health, it is important that we understand how patterns of service use change as levels of investment change. This study investigated GP use in Britain in conjunction with use of outpatient services during a period of investment and during a period of austerity. Method The study used data from the British Household Panel Survey (BHPS) that included service use, morbidity (as an indicator of need) and socio-demographic characteristics (e.g., employment, age, education, and sex). Data for 2000, 2004, and 2008, were specifically chosen for comparison with data from 2015, 2016 and 2017. Service use and respondent characteristics were described using measures of central tendency and dispersion. Multivariable analyses were undertaken using recursive bivariate probit (RBVP) and probit analyses separately for each study year. All analyses were adjusted for cross-sectional weighting. Results BHPS respondents who used outpatient services or GP services had higher morbidity compared to survey participants who did not. Older people, people with lower educational attainment and employed people had higher mean morbidity indices in each study year as did females. Morbidity among service users tended to decline slightly over time. RBVP analyses revealed a significant positive correlation in residuals between outpatient and GP functions in 2000 and 2004 but not 2008. GP consultations and outpatient use remained largely unrelated to socio-economic factors in each year. Survey participants who reported hearing or vision impairment conditions were consistently less likely to use GP or outpatient services in 2000 and 2004, in 2008. Conclusion The results are broadly indicative of stable relationships in service use during a period of healthcare investment but change during austerity. Those who reported, vision, hearing, and skin conditions were consistently less likely to report use of GP or outpatient services, controlling for other aspects of health.

The assessment of chemical composition and biological activity of faba bean pods as a potential feed additive utilized in piglets nutrition

AbstractThe study addresses the utilization of food waste by-products from faba bean (Vicia faba L.) pods (FBP) as an alternative feed supplement to promote sustainable piglet growth by reducing antimicrobial use. Objectives include evaluation of FBP in terms of nutritional components (proximate composition, fibres, minerals), phytochemical composition (total phenols, HPLC-MS profiling), and in vitro biological activities. Air-dried FBP from the cultivar ‘Bizon’ contained high levels of crude protein (144 g/kg), dietary fibre (413 g/kg), potassium (27.8 g/kg), and iron (126 mg/kg). Phytochemical analysis of methanolic extract from FBP revealed significant levels of polyphenols, including vestitol, piscidic acid, hydroxyeucomic acid, quercetin, and kaempferol glycosides with no detectable tannins. The extract showed negligible activity against porcine digestive enzymes (α-amylase, lipase, and trypsin) (IC50 > 4 mg/mL) and demonstrated a dose-dependent antibacterial activity against Escherichia coli and Salmonella enterica in concentrations of 1–8 mg/mL. The extract had low cytotoxicity (IC50 = 432.6 µg/mL) against IPEC-J2 – cells derived from porcine jejunal epithelium. The results indicate that FBP ‘Bizon’ is a valuable source of bioactive compounds with antibacterial properties, without adverse effects on porcine enzymes or IPEC-J2 cells, supporting its potential as a sustainable feed in piglet nutrition, in line with circular economy concepts.