Computing coset leaders and leader codewords of binary codes

In this paper we use the Gr\"obner representation of a binary linear code $\mathcal C$ to give efficient algorithms for computing the whole set of coset leaders, denoted by $\mathrm{CL}(\mathcal C)$ and the set of leader codewords, denoted by $\mathrm L(\mathcal C)$. The first algorithm could be adapted to provide not only the Newton and the covering radius of $\mathcal C$ but also to determine the coset leader weight distribution. Moreover, providing the set of leader codewords we have a test-set for decoding by a gradient-like decoding algorithm. Another contribution of this article is the relation stablished between zero neighbours and leader codewords

Reactivity of dolomitizing fluids and Mg source evaluation of fault-controlled dolomitization at the Benicàssim outcrop analogue (Maestrat Basin, E Spain)

Peer reviewedPostprin

Origen de la alunita y la natroalunita del depósito de caolín de Mina Equivocada (Prov. de Río Negro, Argentina)

The origin of alunite and natroalunite from a kaolin deposit (Equivocada Mine, Rio Negro Province) has been studied. Chemical analysis showed that alunite is K<sub>0.89</sub> and natroalunite Na<sub>0.97</sub>, in agreement with X ray diffraction data. The high contents of minor elements in alunite, especially Ba and Sr are compatible with a hydrothermal origin in contrast to natroalunite whose very low values suggest a secondary origin. Alunite has a δ<sup>34<sup/>S = +15.9‰ and a δ<sup>18</sup>O = +12.9‰, while in natroalunite these values are -5.8‰ and +19.0‰ respectively. δ<sup>34<sup/>S values suggest that alunite formed from a hypogenic process of hydrothermal origin whereas natroalunite is probably related to a supergen origin. The occurrence of alunite in veins crosscutting the other minerals, indicates that it was the last mineral to crystallize

Automatic Zig-Zag sampling in practice

Novel Monte Carlo methods to generate samples from a target distribution, such as a posterior from a Bayesian analysis, have rapidly expanded in the past decade. Algorithms based on Piecewise Deterministic Markov Processes (PDMPs), non-reversible continuous-time processes, are developing into their own research branch, thanks their important properties (e.g., correct invariant distribution, ergodicity, and super-efficiency). Nevertheless, practice has not caught up with the theory in this field, and the use of PDMPs to solve applied problems is not widespread. This might be due, firstly, to several implementational challenges that PDMP-based samplers present with and, secondly, to the lack of papers that showcase the methods and implementations in applied settings. Here, we address both these issues using one of the most promising PDMPs, the Zig-Zag sampler, as an archetypal example. After an explanation of the key elements of the Zig-Zag sampler, its implementation challenges are exposed and addressed. Specifically, the formulation of an algorithm that draws samples from a target distribution of interest is provided. Notably, the only requirement of the algorithm is a closed-form function to evaluate the target density of interest, and, unlike previous implementations, no further information on the target is needed. The performance of the algorithm is evaluated against another gradient-based sampler, and it is proven to be competitive, in simulation and real-data settings. Lastly, we demonstrate that the super-efficiency property, i.e. the ability to draw one independent sample at a lesser cost than evaluating the likelihood of all the data, can be obtained in practice.Comment: Small edits from previous version following some minor revisions requeste

Single Amino Acid Mutation Controls Hole Transfer Dynamics in DNA-Methyltransferase HhaI Complexes

Different mutagenic effects are generated by DNA oxidation that implies the formation of radical cation states (so-called holes) on purine nucleobases. The interaction of DNA with proteins may protect DNA from oxidative damage owing to hole transfer (HT) from the stack to aromatic amino acids. However, how protein binding affects HT dynamics in DNA is still poorly understood. Here, we report a computational study of HT in DNA complexes with methyltransferase HhaI with the aim of elucidating the molecular factors that explain why long-range DNA HT is inhibited when the glutamine residue inserted in the double helix is mutated into a tryptophan. We combine molecular dynamics, quantum chemistry, and kinetic Monte Carlo simulations and find that protein binding stabilizes the energies of the guanine radical cation states and significantly impacts the corresponding electronic couplings, thus determining the observed behavior, whereas the formation of a tryptophan radical leads to less efficient HT

Systematic review and meta-analysis on the adjunctive use of host immune modulators in non-surgical periodontal treatment in healthy and systemically compromised patients.

Considering the central role of inflammation in the pathogenesis of periodontitis, the combination of NSPT with different agents that can modulate the host immune-inflammatory response has been proposed to enhance the outcomes of NSPT. The aim of this paper is to systematically review the literature on the efficacy of systemic host modulators (HMs) as adjuncts to non-surgical periodontal therapy (NSPT) in improving pocket depth (PD) reduction and clinical attachment level (CAL) gain in healthy and systemically compromised patients. RCTs with ≥ 3 months follow-up were independently searched by two reviewers. Meta-analysis was performed when ≥ 3 studies on the same HM were identified. The quality of the evidence was rated according to the GRADE approach to rate the certainty of evidence. 38 articles were included in the qualitative assessment and 27 of them were included in the meta-analysis. There is low/very low evidence that the adjunctive use of sub-antimicrobial dose of doxycicline, melatonin and the combination of omega-3 and low dose aspirin (in type 2 diabetic patients) to NSPT would improve PD and/or CAL. Conflicting evidence is available on the efficacy of probiotics. Future studies controlling for confounding factors, using composite outcomes to define the endpoint of therapy and considering not only the patient- but also as the site-specific effect of systemic HMs are warranted. The dosage, posology and long-term effect of HMs still need to be clarified, also in association to the presence of systemic conditions potentially affecting the response to HMs administration

How abasic sites impact hole transfer dynamics in GC-rich DNA sequences

Changes in DNA charge transfer properties upon the creation of apurinic and apyrimidinic sites have been used to monitor DNA repair processes, given that such lesions generally reduce charge transfer yields. However, because these lesions translate into distinct intra and extrahelical conformations depending on the nature of the unpaired base and its DNA context, it is unclear the actual impact of such diverse conformations on charge transfer. Here we combine classical molecular dynamics, quantum/molecular mechanics (QM/MM) calculations, and kinetic Monte Carlo simulations to investigate the impact of abasic sites on the structure and hole transfer (HT) properties of DNA. We consider both apurinic and apyrimidinic sites in polyG and polyGC sequences and find that most situations lead to intrahelical conformations where HT rates are significantly slowed down due to the energetic disorder induced by the abasic void. In contrast, the presence of an unpaired C flanked by C bases leads to an extrahelical conformation where stacking among G sites is reduced, leading to an attenuation of electronic couplings and a destabilization of hole states. Interestingly, this leads to an asymmetric HT behavior, given that the 5′ to 3′ transfer along the G strand is slowed down by one order of magnitude while the opposite 3′ to 5′ transfer remains similar to that estimated for the reference polyG sequence. Our simulations thus suggest that electrochemical monitoring of the DNA repair process following changes in charge transfer properties can miss repair events linked to abasic sites adopting extrahelical conformations

Electronic energy transfer in biomacromolecules

Electronic energy transfer is widely used as a molecular ruler to interrogate the structure of biomacromolecules, and performs a key task in photosynthesis by transferring collected energy through specialized pigment-protein complexes. Förster theory, introduced over 70 years ago, allows linking transfer rates to simple structural and spectroscopic properties of the energy‐transferring molecules. In biosystems, however, significant deviations from Förster behavior often arise due to breakdown of the ideal dipole approximation, dielectric screening effects due to the biological environment, or departure from the weak‐coupling regime. In this review, we provide a concise overview of advances in simulations of energy transfer in biomacromolecules that allow overcoming the main limitations of Förster theory. We first discuss advances in quantum chemical methods to compute electronic couplings, their extension to multiscale formulations to include screening effects, and strategies to treat the interplay between coupling fluctuations and energy transfer dynamics. We then examine the spectral overlap term, and how this quantity can be estimated from simulations of the spectral density of exciton-phonon coupling. Finally, we discuss rate theories that can describe energy transfers in situations where strong coupling leads to delocalized excitions, a common situation found in closely packed multichromophoric systems such as photosynthetic complexes and nucleic acids