Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations.

Despite advancements in understanding the structure and functions of the Calcium Sensing Receptor (CaSR), gaps persist in our knowledge of the specific functions of its residues. In this study, we used phylogeny-based techniques to identify functionally equivalent orthologs of CaSR, predict residue significance, and compute specificity-determining position (SDP) scores to understand its evolutionary basis. The analysis revealed exceptional conservation of the CaSR subfamily, emphasizing the critical role of residues with high SDP scores in receptor activation and pathogenicity.

Dynamics of transcription-coupled repair of cyclobutane pyrimidine dimers and (6-4) photoproducts in .

DNA repair processes modulate genotoxicity, mutagenesis, and adaption. Nucleotide excision repair removes bulky DNA damage, and in , basal excision repair, carried out by UvrA, B, C, and D, with DNA PolI and DNA ligase, occurs genome-wide. In transcription-coupled repair (TCR), the Mfd protein targets template strand (TS) lesions that block RNA polymerase for accelerated repair by the basal repair enzymes.

Axial, planar-diagonal, body-diagonal fields on the cubic-spin spin glass in d=3: A plethora of ordered phases under finite fields.

A nematic phase, previously seen in the d=3 classical Heisenberg spin-glass system, occurs in the n-component cubic-spin spin-glass system, between the low-temperature spin-glass phase and the high-temperature disordered phase, for number of spin components n≥3, in spatial dimension d=3, thus constituting a liquid-crystal phase in a dirty (quenched-disordered) magnet. Furthermore, under application of a variety of uniform magnetic fields, a veritable plethora of phases is found. Under uniform magnetic fields, 17 different phases and two spin-glass phase diagram topologies (meaning the occurrences and relative positions of the many phases), qualitatively different from the conventional spin-glass phase diagram topology, are seen.

Phase Prediction via Crystal Structure Similarity in the Periodic Number Representation.

The periodic number (PN) representation of the chemical systems, introduced by Dmitri Mendeleev, uncovers the fundamental principle of chemical similarity in a straightforward way. In this framework, the rows correspond to the principal quantum numbers of the elements' electronic configurations when considered isolated atoms. This systematic arrangement allows for a deeper understanding of the relationships and patterns among the elements.

Exploring the potential of Sn-Ge based hybrid organic-inorganic perovskites: A density functional theory based computational screening study.

Hybrid organic-inorganic perovskite solar cells have attracted significant attention in the field of optoelectronics due to their exceptional photovoltaic and optoelectronic properties. Although lead (Pb)-based perovskites exhibit the highest power conversion efficiencies, concerns about their toxicity and environmental impact have prompted significant research activities to explore alternative compositions. In this regard, a special emphasis has been devoted to tin (Sn) and germanium (Ge) based perovskites.

Optimization of CHARMM force field parameters for ryanodine receptor inhibitory drug dantrolene using FFTK and FFParam.

Context: Ryanodine receptors (RyRs) are large intracellular ligand-gated calcium release ion channels. Mutations in human RyR1 in combination with a volatile anesthetic or muscle relaxant are known to cause leaky RyRs resulting in malignant hyperthermia (MH). This has long been primarily treated with the RyR inhibitory drug dantrolene.

NICE-FF: A non-empirical, intermolecular, consistent, and extensible force field for nucleic acids and beyond.

A new non-empirical ab initio intermolecular force field (NICE-FF in buffered 14-7 potential form) has been developed for nucleic acids and beyond based on the dimer interaction energies (IEs) calculated at the spin component scaled-MI-second order Møller-Plesset perturbation theory. A fully automatic framework has been implemented for this purpose, capable of generating well-polished computational grids, performing the necessary ab initio calculations, conducting machine learning (ML) assisted force field (FF) parametrization, and extending existing FF parameters by incorporating new atom types. For the ML-assisted parametrization of NICE-FF, interaction energies of ∼18 000 dimer geometries (with IE < 0) were used, and the best fit gave a mean square deviation of about 0.

Powering quantum Otto engines only with q-deformation of the working substance.

We consider a quantum Otto cycle with a q-deformed quantum oscillator working substance and classical thermal baths. We investigate the influence of the quantum statistical deformation parameter q on the work and efficiency of the cycle. In usual quantum Otto cycle, a Hamiltonian parameter is varied during the quantum adiabatic stages while the quantum statistical character of the working substance remains fixed.

Downregulated NPAS4 in multiple brain regions is associated with major depressive disorder.

Major Depressive Disorder (MDD) is a commonly observed psychiatric disorder that affects more than 2% of the world population with a rising trend. However, disease-associated pathways and biomarkers are yet to be fully comprehended. In this study, we analyzed previously generated RNA-seq data across seven different brain regions from three distinct studies to identify differentially and co-expressed genes for patients with MDD.

Cross-species investigation into the requirement of XPA for nucleotide excision repair.

After reconstitution of nucleotide excision repair (excision repair) with XPA, RPA, XPC, TFIIH, XPF-ERCC1 and XPG, it was concluded that these six factors are the minimal essential components of the excision repair machinery. All six factors are highly conserved across diverse organisms spanning yeast to humans, yet no identifiable homolog of the XPA gene exists in many eukaryotes including green plants. Nevertheless, excision repair is reported to be robust in the XPA-lacking organism, Arabidopsis thaliana, which raises a fundamental question of whether excision repair could occur without XPA in other organisms.

Stable and metastable crystal structures and ammonia dynamics in strontium chloride ammines.

Metal halide ammines are promising ammonia storage materials due to their high ammonia densities and suitable decomposition properties. Here, we studied the polymorphism of ammines with a general formula of Sr(NH)Cl ( = 1, 2, 4, 6, and 8) by combining the Fast and Flexible CrystAl Structure Predictor (FFCASP) with density functional theory (DFT) calculations. Furthermore, the lattice stability and the minimum energy paths for bulk and surface diffusion of NH were investigated by performing phonon and nudged elastic band (NEB) calculations.

Merged Potts-clock model: Algebraic and conventional multistructured multicritical orderings in two and three dimensions.

A spin system is studied with simultaneous permutation-symmetric Potts and spin-rotation-symmetric clock interactions in spatial dimensions d=2 and 3. The global phase diagram is calculated from the renormalization-group solution with the recently improved (spontaneous first-order detecting) Migdal-Kadanoff approximation or, equivalently, with hierarchical lattices with the inclusion of effective vacancies. Five different ordered phases are found: Conventionally ordered ferromagnetic, quadrupolar, antiferromagnetic phases and algebraically ordered antiferromagnetic, antiquadrupolar phases.

Correction: and antiproliferative activity of organo-nickel SCS-pincer complexes on estrogen responsive MCF7 and MC4L2 breast cancer cells. Effects of amine fragment substitutions on BSA binding and cytotoxicity.

Correction for ' and antiproliferative activity of organo-nickel SCS-pincer complexes on estrogen responsive MCF7 and MC4L2 breast cancer cells. Effects of amine fragment substitutions on BSA binding and cytotoxicity' by Mahboubeh Hosseini-Kharat , , 2018, , 16944-16957, https://doi.org/10.

Designing Potent Anticancer Peptides by Aurein 1.2 Key Residues Mutation and Catenate Cell-Penetrating Peptide.

Purpose: Aurein 1.2 (Aur) peptide is known for possessing anticancer characteristics devoid of conventional therapeutics side effects. For improving Aur peptide anticancer functionality, different anticancer peptides were constructed based on Aur peptide through targeting two separate strategies, including (1) sequence-based mutations and (2) adding a cell-penetrating peptide linker.

Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis.

Sequence content is heterogeneous throughout genomes. Therefore, genome-wide next-generation sequencing (NGS) reads biased towards specific nucleotide profiles are affected by the genome-wide heterogeneous nucleotide distribution. Boquila generates sequences that mimic the nucleotide profile of true reads, which can be used to correct the nucleotide-based bias of genome-wide distribution of NGS reads.

Enantiomer detection via quantum Otto cycle.

Enantiomers are chiral molecules that exist in right-handed and left-handed conformations. Optical techniques of enantiomers' detection are widely employed to discriminate between left- and right-handed molecules. However, identical spectra of enantiomers make enantiomer detection a very challenging task.

The interplay of 3D genome organization with UV-induced DNA damage and repair.

The 3D organization of the eukaryotic genome is crucial for various cellular processes such as gene expression and epigenetic regulation, as well as for maintaining genome integrity. However, the interplay between UV-induced DNA damage and repair with the 3D structure of the genome is not well understood. Here, we used state-of-the-art Hi-C, Damage-seq, and XR-seq datasets and in silico simulations to investigate the synergistic effects of UV damage and 3D genome organization.

COVID-19 modeling based on real geographic and population data.

Background: : Intercity travel is one of the most important parameters for combating a pandemic. The ongoing COVID-19 pandemic has resulted in different computational studies involving intercity connections. In this study, the effects of intercity connections during an epidemic such as COVID-19 are evaluated using a new network model.

Nematic ordering in the Heisenberg spin-glass system in three dimensions.

Nematic ordering, where the spins globally align along a spontaneously chosen axis irrespective of direction, occurs in spin-glass systems of classical Heisenberg spins in d=3. In this system where the nearest-neighbor interactions are quenched randomly ferromagnetic or antiferromagnetic, instead of the locally randomly ordered spin-glass phase, the system orders globally as a nematic phase. This nematic ordering of the Heisenberg spin-glass system is dramatically different from the spin-glass ordering of the Ising spin-glass system.

The Mfd protein is the transcription-repair coupling factor (TRCF) in Mycobacterium smegmatis.

In vitro and in vivo experiments with Escherichia coli have shown that the Mfd translocase is responsible for transcription-coupled repair, a subpathway of nucleotide excision repair involving the faster rate of repair of the transcribed strand than the nontranscribed strand. Even though the mfd gene is conserved in all bacterial lineages, there is only limited information on whether it performs the same function in other bacterial species. Here, by genome scale analysis of repair of UV-induced cyclobutane pyrimidine dimers, we find that the Mfd protein is the transcription-repair coupling factor in Mycobacterium smegmatis.

Common and selective signal transduction mechanisms of GPCRs.

G protein-coupled receptors (GPCRs) are coupled by four major subfamilies of G proteins. GPCR coupling is processed through a combination of common and selective activation mechanisms together. Common mechanisms are shared for a group of receptors.

Heat transport and rectification via quantum statistical and coherence asymmetries.

Recent experiments at the nanoscales confirm that thermal rectifiers, the thermal equivalent of electrical diodes, can operate in the quantum regime. We present a thorough investigation of the effect of different particle exchange statistics, coherence, and collective interactions on the quantum heat transport of rectifiers with two-terminal junctions. Using a collision model approach to describe the open system dynamics, we obtain a general expression of the nonlinear heat flow that fundamentally deviates from the Landauer formula whenever quantum statistical or coherence asymmetries are present in the bath particles.

Equiatomic binary phases of Copper-Rare Earth Elements. An overview of monocuprides from first-principles calculations.

Equiatomic binary phases of copper with rare earth (RE) elements exhibit either primitive cubic ( ) or orthorhombic (Pnma) structures and in some cases both. By using density functional theory (DFT), we calculated the enthalpies of formation along the series of RE elements combined equimolarly with copper. For RE from Sc to Lu, the calculated enthalpies of formation fall in the range -49.