Notes

Spatial variation throughout cortex-muscle coherence looked at with magnetoencephalography along with high-density surface area electromyography.
We benchmark pathway2vec performance based on node-clustering, embedding visualization and pathway prediction using MetaCyc as a trusted source. In the pathway prediction task, results indicate that it is possible to leverage embeddings to improve prediction outcomes.

The software package and installation instructions are published on http//github.com/pathway2vec.

[email protected].

Supplementary data are available at Bioinformatics online.
Supplementary data are available at Bioinformatics online.We evaluated the growth and the susceptibility to oxidative stress of Sporothrix spp., exposed to different iron concentrations in culture medium, and the susceptibility of Sporothrix spp. to itraconazole, alone and in combination with to the iron chelator deferasirox. The results showed that the growth of S. brasiliensis isolates was more affected by iron availability in comparison to S. schenckii, but both fungal species conidia became more prone to oxidative stress when iron was added to culture medium. Conversely, the combination of itraconazole and deferasirox only resulted in synergism against a minority of S. schenckii isolates.
Gene expression and regulation, a key molecular mechanism driving human disease development, remains elusive, especially at early stages. Integrating the increasing amount of population-level genomic data and understanding gene regulatory mechanisms in disease development are still challenging. Machine learning has emerged to solve this, but many machine learning methods were typically limited to building an accurate prediction model as a 'black box', barely providing biological and clinical interpretability from the box.

To address these challenges, we developed an interpretable and scalable machine learning model, ECMarker, to predict gene expression biomarkers for disease phenotypes and simultaneously reveal underlying regulatory mechanisms. Particularly, ECMarker is built on the integration of semi- and discriminative-restricted Boltzmann machines, a neural network model for classification allowing lateral connections at the input gene layer. This interpretable model is scalable without needing any prformatics online.
Supplementary data are available at Bioinformatics online.Nuclear import is considered as one of the major limitations for non-viral gene delivery systems and the incorporation of nuclear localization signals (NLS) that mediate nuclear intake can be used as a strategy to enhance internalization of exogenous DNA. In this work, human-derived endogenous NLS peptides based on insulin growth factor binding proteins (IGFBP), namely IGFBP-3 and IGFBP-5, were tested for their ability to improve nuclear translocation of genetic material by non-viral vectors. Several strategies were tested to determine their effect on chitosan mediated transfection efficiency co-administration with polyplexes, co-complexation at the time of polyplex formation, and covalent ligation to chitosan. Our results show that co-complexation and covalent ligation of the NLS peptide derived from IGFBP-3 to chitosan polyplexes yields a 2-fold increase in transfection efficiency, which was not observed for NLS peptide derived from IGFBP-5. These results indicate that the integration of IGFBP-NLS-3 peptides into polyplexes has potential as a strategy to enhance the efficiency of non-viral vectors.ORF7a is an accessory protein common to SARS-CoV1 and the recently discovered SARS-CoV2, which is causing the COVID-19 pandemic. The ORF7a protein has a structural homology with ICAM-1 which binds to the T lymphocyte integrin receptor LFA-1. As COVID-19 has a strong immune component as part of the disease, we sought to determine whether SARS-CoV2 would have a similar structural interaction with LFA-1. Using molecular docking simulations, we found that SARS-CoV2 ORF7a has the key structural determinants required to bind LFA-1 but also the related leukocyte integrin Mac-1, which is also known to be expressed by macrophages. Our study shows that SARS-CoV2 ORF7a protein has a conserved Ig immunoglobulin-like fold containing an integrin binding site that provides a mechanistic hypothesis for SARS-CoV2's interaction with the human immune system. This suggests that experimental investigation of ORF7a-mediated effects on immune cells such as T lymphocytes and macrophages (leukocytes) could help understand the disease further and develop effective treatments.Mixing ionic liquids (ILs) with molecular solvents can extend the practical applications of ILs and overcome the drawbacks of neat ILs. Knowledge on the structure and hydrogen-bond interaction properties of IL-molecular solvent mixtures is essential for chemical applications. In this work, the structure and hydrogen-bond features of N-alkyl-N-methyl-pyrrolidinium bis(trifluoromethylsulfonyl)imide ([CnMPyr][Tf2N], n = 3, 4, 6 and 8) and DMSO mixtures were studied using Fourier transform infrared spectroscopy (FTIR) and density functional theory (DFT) calculations. Excess infrared absorption spectroscopy and two-dimensional correlation spectroscopy (2D-COS) were employed to extract structural information on the mixtures from the C-D systematic stretching vibrational (νs(C-D)) region of the methyl groups in DMSO-d6. It was found that the mixing process of [CnMPyr][Tf2N] and DMSO is non-ideal and interaction complexes form between [CnMPyr][Tf2N] and DMSO-d6. They are ion cluster-DMSO-d6 complexes and ion pair-DMSO-d6 complexes. In the mixing processes, the species present in pure DMSO gradually decrease from DMSO dimer to DMSO monomer with an increase in ILs. Besides, the ion cluster-DMSO complexes gradually increase, while the ion pair-DMSO complexes decrease due to the strong electrostatic interaction between the cation and anion. In the ion cluster-DMSO complexes and ion pair-DMSO complexes, the ring hydrogen atoms of the methylene group directly attached to the nitrogen atom are the preferred interaction sites of the [CnMPyr]+ cations. All the hydrogen bonds in the identified complexes are closed-shell, electrostatically dominant and weak.The sudden arrival of novel coronavirus disease 2019 (COVID-19) has stunned the world with its rapidly spreading virus. Caspase-3 Inhibitor Remdesivir, a broad spectrum anti-viral drug, is now under in vitro and in vivo investigation as a potential agent against SARS-CoV-2. However, the results of this therapy were recently equivocal due to no significant benefit in the clinical trial. Herein, combination molecular docking with dissipative particle dynamics (DPD) simulations is used to theoretically design angiotensin-converting enzyme inhibitor (ACEI)-containing remdesivir-loaded PLGA nanoparticles (NPs) for anti-SARS-CoV-2 therapy. Based on the therapeutic and lung protective effect of ACEI, the classical lisinopril molecule covalently grafted onto PLGA (L-PLGA) has been used to encapsulate remdesivir. A binding model is used to confirm the interactions between lisinopril and ACE on the surface of cells, as well as remdesivir and its intracellular targeting protein (RNA-dependent RNA polymerase (RdRp)). Furthermore, DPD simulations are applied to study the nano-aggregation of drug-free L-PLGA, and remdesivir loaded in L-PLGA. The lisinopril molecules were directly demonstrated to be on the surface of L-PLGA NPs. Molecular docking proved that hydrogen bonding was decisive for the encapsulation of remdesivir. With an increase in concentration, remdesivir loaded L-PLGA formed spherical NPs, and then underwent precipitation. Similar to the above conditions, high remdesivir loading was also observed to cause precipitation formation. Thus, the optimized remdesivir NPs in our study give insights into a rational platform for formulation design against this global pandemic.Tellurene, a two-dimensional (2D) semiconductor, meets the requirements for optoelectronic applications with desirable properties, such as a suitable band gap, high carrier mobility, strong visible light absorption and high air stability. Here, we demonstrate that the band engineering of zigzag tellurene nanoribbons (ZTNRs) via edge-modification can be used to construct highly efficient heterojunction solar cells by using first-principles density functional theory (DFT) calculations. We find that edge-modification enhances the stability of ZTNRs and halogen-modified ZTNRs showing suitable band gaps (1.35-1.53 eV) for sunlight absorption. Furthermore, the band gaps of ZTNRs with tetragonal edges do not strongly depend on the edge-modification and ribbon width, which is conducive to experimental realization. The heterojunctions constructed by halogen-modified ZTNRs show desirable type 2 band alignments and small band offsets with reduced band gaps and enhanced sunlight absorption, resulting in high power conversion efficiency (PCE) in heterojunction solar cells. In particular, the calculated maximum PCE of designed heterojunction solar cells based on halogen-modified ZTNRs can reach as high as 22.6%.The use of boron (B) atoms as transition metal mimics opens the door to new research in catalytic chemistry. An emerging class of compounds, bis(Lewis base)borylenes with an electron-rich B(i) center, are potential metal-free catalysts for dinitrogen bonding and reduction. Here, the molecular geometry, electronic structure, and possible reaction mechanism of a series of bis(Lewis base)borylene-dinitrogen compounds corresponding to the nitrogen reduction reaction have been investigated by using density functional theory (DFT) calculations. Our DFT calculations show that these free borylene compounds possess radical features and have the capability to activate N2 molecules via an effective combination of π(B → N2), π(N2 → B), and σ(N2 → B) electron transfer processes. The possible reaction mechanisms for direct conversion of N2 into NH3 for these bis(Lewis base)borylene-dinitrogen compounds have been systematically investigated along distal and alternating paths. The calculated free energy profiles indicate that the limiting potential of a bis(phosphine)borylene-dinitrogen compound is comparable to that of metal-based catalysts, which is the most promising candidate for the reduction of N2 to NH3via the alternating mechanism among all compounds studied here. The electronic structure analysis shows that the B center plays the role of an electron donor and acceptor alternatively in the consecutive six protonation and reduction processes, and thus acts as the electron transfer medium.Multifunctional nanoprobes with tumor microenvironment response are playing important roles in highly efficient theranostics of cancers. Herein, a kind of theranostic nanoprobe was synthesized by coating manganese dioxide (MnO2) on the surface of black commercial P25 titanium dioxide (b-P25). The resultant nanoprobe (b-P25@MnO2) possessed glutathione (GSH)-responsive magnetic resonance (MR) imaging and enhanced photothermal therapy (PTT). In tumor microenvironments, the excessive GSH was consumed by reacting with MnO2 to generate Mn2+ for GSH-responsive MR imaging, in which the longitudinal relaxation rate of b-P25@MnO2 was up to 30.44 mM-1 s-1, showing excellent cellular and intratumoral MR imaging. Moreover, the prepared b-P25@MnO2 exhibited stable and strong photothermal conversion capability with a high photothermal conversion efficiency of 30.67%, by which the 4T1 tumors disappeared completely, indicating safe and highly efficient PTT performance. The current work developed GSH-responsive b-P25@MnO2 nanoprobes, demonstrated for MR imaging and enhanced PTT in cancers.
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