k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations.

One of the key challenges of k-means clustering is the seed selection or the initial centroid estimation since the clustering result depends heavily on this choice. Alternatives such as k-means++ have mitigated this limitation by estimating the centroids using an empirical probability distribution. However, with high-dimensional and complex datasets such as those obtained from molecular simulation, k-means++ fails to partition the data in an optimal manner. Furthermore, stochastic elements in all flavors of k-means++ will lead to a lack of reproducibility. K-means N-Ary Natural Initiation (NANI) is presented as an alternative to tackle this challenge by using efficient n-ary comparisons to both identify high-density regions in the data and select a diverse set of initial conformations. Centroids generated from NANI are not only representative of the data and different from one another, helping k-means to partition the data accurately, but also deterministic, providing consistent cluster populations across replicates. From peptide and protein folding molecular simulations, NANI was able to create compact and well-separated clusters as well as accurately find the metastable states that agree with the literature. NANI can cluster diverse datasets and be used as a standalone tool or as part of our MDANCE clustering package.

Cross-sectional studies of the causal link between asthma and osteoporosis: insights from Mendelian randomization and bioinformatics analysis.

The study, using data from Chongqing, China, and employing Mendelian randomization along with bioinformatics, establishes a causal link between asthma and osteoporosis, beyond glucocorticoid effects. Asthma may contribute to osteoporosis by accelerating bone turnover through inflammatory factors, disrupting the coupling between osteoblasts and osteoclasts, ultimately leading to osteoporosis. INTRODUCTION: Asthma and osteoporosis are prevalent health conditions with substantial public health implications. However, their potential interplay and the underlying mechanisms have not been fully elucidated. Previous research has primarily focused on the impact of glucocorticoids on osteoporosis, often overlooking the role of asthma itself. METHODS: We conducted a multi-stage stratified random sampling in Chongqing, China and excluded individuals with a history of glucocorticoid use. Participants underwent comprehensive health examinations, and their clinical data, including asthma status, were recorded. Logistic regression and Mendelian randomization were employed to investigate the causal link between asthma and osteoporosis. Furthermore, bioinformatics analyses and serum biomarker assessments were conducted to explore potential mechanistic pathways. RESULTS: We found a significant association between asthma and osteoporosis, suggesting a potential causal link. Mendelian Randomization analysis provided further support for this causal link. Bioinformatics analyses revealed that several molecular pathways might mediate the impact of asthma on bone health. Serum alkaline phosphatase levels were significantly elevated in the asthma group, suggesting potential involvement in bone turnover. CONCLUSION: Our study confirms a causal link between asthma and osteoporosis and highlights the importance of considering asthma in osteoporosis prediction models. It also suggests that asthma may accelerate osteoporosis by increasing bone turnover through inflammatory factors, disrupting the coupling between osteoblasts and osteoclasts, ultimately leading to bone loss.

Insights into Hildebrand Solubility Parameters - Contributions from Cohesive Energies or Electrophilicity Densities?

We introduce certain concepts and expressions from conceptual density functional theory (DFT) to study the properties of the Hildebrand solubility parameter. The original form of the Hildebrand solubility parameter is used to qualitatively estimate solubilities for various apolar and aprotic substances and solvents and is based on the square root of the cohesive energy density. Our results show that a revised expression allows the replacement of cohesive energy densities by electrophilicity densities, which are numerically accessible by simple DFT calculations. As an extension, the reformulated expression provides a deeper interpretation of the main contributions and, in particular, emphasizes the importance of charge transfer mechanisms. All calculated values of the Hildebrand parameters for a large number of common solvents are compared with experimental values and show good agreement for non- or moderately polar aprotic solvents in agreement with the original formulation of the Hildebrand solubility parameters. The observed deviations for more polar and protic solvents define robust limits from the original formulation which remain valid. Likewise, we show that the use of machine learning methods leads to only slightly better predictability.

Quantitative Solvation Energies from Gas-Phase Calculations: First-Principles Charge Transfer and Perturbation Approaches.

We present a first-principles approach for the calculation of solvation energies and enthalpies with respect to different ion pair combinations in various solvents. The method relies on the conceptual density functional theory (DFT) of solvation, from which detailed expressions for the solvation energies can be derived. In addition to fast and straightforward gas phase calculations, we also study the influence of modified chemical reactivity descriptors in terms of electronic perturbations. The corresponding phenomenological changes in molecular energy levels can be interpreted as the influence of continuum solvents. Our approach shows that the introduction of these modified expressions is essential for a quantitative agreement between the calculated and the experimental results.

Achieving robust mainstream nitritation by implementing light irradiation: long-term performance and microbial dynamics.

The effective inhibition of nitrite-oxidizing bacteria (NOB) is widely acknowledged to be a critical issue for mainstream short-cut biological nitrogen removal. This study demonstrated a stable mainstream nitritation by implementing light irradiation. A sequencing batch reactor with ultraviolet-A (UVA) irradiation was operated for 250 days, and a high nitrite accumulation ratio was achieved and stabilized at about 90 %. UVA irradiation also positively impacts denitrification activity, with total nitrogen removal up to 63 %. Microbial community analysis confirmed that the UVA effectively and stably decreased the abundance of Nitrospira (the only detected NOB) from 6.0 % to 0.1 %, while it showed no effect on Nitrosomonas. The enriched genus Rhodocyclaceae was the major contributor to the increase in denitrification activity in the light-induced nitritation system. The proposed UVA irradiation strategy has the potential to be integrated with an anoxic/aerobic (A/O) or integrated fixed-film activated sludge (IFAS) process for achieving mainstream short-cut biological nitrogen removal.

Ionic Liquid-Mediated Interfacial Polymerization for Fabrication of Reverse Osmosis Membranes.

This study revealed the effects of incorporating ionic liquid (IL) molecules: 1-ethyl, 1-butyl, and 1-octyl-3-methyl-imidazolium chlorides with different alkyl chain lengths, in interfacial polymerization (IP) on the structure and property (i.e., permeate-flux and salt rejection ratio) relationships of resulting RO membranes. The IL additive was added in the aqueous meta-phenylene diamine (MPD; 0.1% w/v) phase, which was subsequently reacted with trimesoyl chloride (TMC; 0.004% w/v) in the hexane phase to produce polyamide (PA) barrier layer. The structure of resulting free-standing PA thin films was characterized by grazing incidence wide-angle X-rays scattering (GIWAXS), which results were correlated with the performance of thin-film composite RO membranes having PA barrier layers prepared under the same IP conditions. Additionally, the membrane surface properties were characterized by zeta potential and water contact angle measurements. It was found that the membrane prepared by the longer chain IL molecule generally showed lower salt rejection ratio and higher permeation flux, possibly due to the inclusion of IL molecules in the PA scaffold. This hypothesis was supported by the GIWAXS results, where a self-assembled surfactant-like structure formed by IL with the longest aliphatic chain length was detected.