Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.

The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. Since the first release of the OPTIMADE specification (v1.0), the API has undergone significant development, leading to the v1.

A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort.

Molecular dynamics (MD) simulations are keeping computers busy around the world, generating a huge amount of data that is typically not open to the scientific community. Pioneering efforts to ensure the safety and reusability of MD data have been based on the use of simple databases providing a limited set of standard analyses on single-short trajectories. Despite their value, these databases do not offer a true solution for the current community of MD users, who want a flexible analysis pipeline and the possibility to address huge non-Markovian ensembles of large systems.

Predictors of severity in severe respiratory infection in children with COVID-19 respiratory infection in a developing country.

On March 11, 2020, the WHO declared the COVID-19 pandemic. This name was given to the disease caused by the SARS-CoV 2 virus at its outbreak in December 2019 in Wuhan, Hubei, China. In Colombia, a significant number of cases have been confirmed.

High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations.

Mutations in the kinase domain of the epidermal growth factor receptor (EGFR) can be drivers of cancer and also trigger drug resistance in patients receiving chemotherapy treatment based on kinase inhibitors. knowledge of the impact of EGFR variants on drug sensitivity would help to optimize chemotherapy and design new drugs that are effective against resistant variants before they emerge in clinical trials. To this end, we explored a variety of methods, from sequence-based to "state-of-the-art" atomistic simulations.

Molecular Diagnoses of X-Linked and Other Genetic Hypophosphatemias: Results From a Sponsored Genetic Testing Program.

X-linked hypophosphatemia (XLH), a dominant disorder caused by pathogenic variants in the PHEX gene, affects both sexes of all ages and results in elevated serum fibroblast growth factor 23 (FGF23) and below-normal serum phosphate. In XLH, rickets, osteomalacia, short stature, and lower limb deformity may be present with muscle pain and/or weakness/fatigue, bone pain, joint pain/stiffness, hearing difficulty, enthesopathy, osteoarthritis, and dental abscesses. Invitae and Ultragenyx collaborated to provide a no-charge sponsored testing program using a 13-gene next-generation sequencing panel to confirm clinical XLH or aid diagnosis of suspected XLH/other genetic hypophosphatemia.

Exogenous expression of the glycosyltransferase LARGE1 restores α-dystroglycan matriglycan and laminin binding in rhabdomyosarcoma.

Background: α-Dystroglycan is the highly glycosylated component of the dystrophin-glycoprotein complex (DGC) that binds with high-affinity to extracellular matrix (ECM) proteins containing laminin-G-like (LG) domains via a unique heteropolysaccharide [-GlcA-beta1,3-Xyl-alpha1,3-] called matriglycan. Changes in expression of components of the DGC or in the O-glycosylation of α-dystroglycan result in muscular dystrophy but are also observed in certain cancers. In mice, the loss of either of two DGC proteins, dystrophin or α-sarcoglycan, is associated with a high incidence of rhabdomyosarcoma (RMS).

Layered-Expanded Mesostructured Silicas: Generalized Synthesis and Functionalization.

Mesostructured layered silicas have been prepared through a surfactant-assisted procedure using neutral alkylamines as templates and starting from atrane complexes as hydrolytic inorganic precursors. By adjusting the synthetic parameters, this kinetically controlled reproducible one-pot method allows for obtaining both pure and functionalized (inorganic or organically) lamellar silica frameworks. These are easily deconstructed and built up again, which provides a simple way for expanding the interlamellar space.

Role of dystroglycan in limiting contraction-induced injury to the sarcomeric cytoskeleton of mature skeletal muscle.

Dystroglycan (DG) is a highly expressed extracellular matrix receptor that is linked to the cytoskeleton in skeletal muscle. DG is critical for the function of skeletal muscle, and muscle with primary defects in the expression and/or function of DG throughout development has many pathological features and a severe muscular dystrophy phenotype. In addition, reduction in DG at the sarcolemma is a common feature in muscle biopsies from patients with various types of muscular dystrophy.

Clinical Genetic Testing for the Cardiomyopathies and Arrhythmias: A Systematic Framework for Establishing Clinical Validity and Addressing Genotypic and Phenotypic Heterogeneity.

Advances in DNA sequencing have made large, diagnostic gene panels affordable and efficient. Broad adoption of such panels has begun to deliver on the promises of personalized medicine, but has also brought new challenges such as the presence of unexpected results, or results of uncertain clinical significance. Genetic analysis of inherited cardiac conditions is particularly challenging due to the extensive genetic heterogeneity underlying cardiac phenotypes, and the overlapping, variable, and incompletely penetrant nature of their clinical presentations.

Low-Cost Synthesis of Bimodal Mesoporous Silica-Based Materials by Pseudomorphic Transformation.

Nanoparticulate bimodal porous silica-based materials have been prepared through a surfactant-assisted procedure by using a simple template and starting from inexpensive sodium silicate as silicon source. Different procedural variables, such as pH or the nature and concentration of the surfactant, have been explored to optimize the preparative protocol, which allows, in turn, improved understanding of the formation process. The final bulk materials (called UVM-10 or M-UVM-10) are formed by pseudomorphic transformation of fresh silica-based xerogels under mild basic conditions.

Biomimetic chitosan-mediated synthesis in heterogeneous phase of bulk and mesoporous silica nanoparticles.

Both bulk and mesoporous silica nanoparticles can be obtained in the form of granular aggregates using chitosan flakes as additive under very soft biomimetic reaction conditions.

Nanoparticulated silicas with bimodal porosity: chemical control of the pore sizes.

Nanoparticulated bimodal porous silicas (NBSs) with pore systems structured at two length scales (meso- and large-meso-/macropores) have been prepared through a one-pot surfactant-assisted procedure by using a simple template agent and starting from silicon atrane complexes as hydrolytic inorganic precursors. The final bulk materials are constructed by an aggregation of pseudospherical mesoporous primary nanoparticles process, over the course of which the interparticle (textural) large pore system is generated. A fine-tuning of the procedural variables allows not only an adjustment of the processes of nucleation and growth of the primary nanoparticles but also a modulation of their subsequent aggregation.

Mesosynthesis of ZnO-SiO(2) porous nanocomposites with low-defect ZnO nanometric domains.

Silica-based ZnO-MCM-41 mesoporous nanocomposites with high Zn content (5≤Si/Zn≤50) have been synthesized by a one-pot surfactant-assisted procedure from aqueous solution using a cationic surfactant (CTMABr = cetyltrimethylammonium bromide) as structure-directing agent, and starting from molecular atrane complexes as inorganic hydrolytic precursors. This preparative technique allows optimization of the dispersion of the ZnO nanodomains in the silica walls. The mesoporous nature of the final materials is confirmed by x-ray diffraction (XRD), transmission electron microscopy (TEM) and N(2) adsorption-desorption isotherms.

Heterogeneous oxidation of pyrimidine and alkyl thioethers in ionic liquids over mesoporous Ti or Ti/Ge catalysts.

Heterogeneous catalytic oxidation of a series of thioethers (2-thiomethylpyrimidine, 2-thiomethyl-4,6-dimethyl-pyrimidine, 2-thiobenzylpyrimidine, 2-thiobenzyl-4,6-dimethylpyrimidine, thioanisole, and n-heptyl methyl sulfide) was performed in ionic liquids by using MCM-41 and UVM-type mesoporous catalysts containing Ti, or Ti and Ge. A range of triflate, tetrafluoroborate, trifluoroacetate, lactate and bis(trifluoromethanesulfonyl)imide-based ionic liquids were used. The oxidations were carried out by using anhydrous hydrogen peroxide or the urea-hydrogen peroxide adduct and showed that ionic liquids are very effective solvents, achieving greater reactivity and selectivity than reactions performed in dioxane.

Toward the development of ionically controlled nanoscopic molecular gates.

An ionically controlled nanoscopic molecular gate has been developed by using functionalized mesoporous materials. The system shows that control of mass transport at nanometric scale can be achieved by using suitable rigid solids and pH-active molecules. The design principle suggests new perspectives in the search of ionically tuned tailored materials and devices with a fine control of mass transport for new applications in fields such as drug delivery, selective removal of toxic species, sensing, or catalysis.

Large monolithic silica-based macrocellular foams with trimodal pore system.

Silica-based materials with hierarchical pore systems at three different length scales (small mesopores-large mesopores-macropores) have been prepared through a nanotectonic approach by using mesoporous nanoparticles as building blocks; the resulting materials present a highly accessible foam-like architecture and can be prepared as large monoliths.

A new method for fluoride determination by using fluorophores and dyes anchored onto MCM-41.

A new colourimetric and fluorimetric method for fluoride determination in aqueous samples based on the specific reaction between fluoride and silica has been developed and applied on real samples.

Silica-based powders and monoliths with bimodal pore systems.

Porous pure and doped silicas with pore sizes at two length scales (meso/macroporous) have been prepared and shaped both as powders and monoliths through a one-pot surfactant assisted procedure by using a simple template agent and starting from atrane complexes as inorganic precursors.