Abstract
Phylogenomics data have grown exponentially over the last decades. It is currently common for genome-wide projects to generate hundreds or even thousands of phylogenetic trees and multiple ...sequence alignments, which may also be very large in size. However, the analysis and interpretation of such data still depends on custom bioinformatic and visualisation workflows that are largely unattainable for non-expert users. Here, we present PhyloCloud, an online platform aimed at hosting, indexing and exploring large phylogenetic tree collections, providing also seamless access to common analyses and operations, such as node annotation, searching, topology editing, automatic tree rooting, orthology detection and more. In addition, PhyloCloud provides quick access to tools that allow users to build their own phylogenies using fast predefined workflows, graphically compare tree topologies, or query taxonomic databases such as NBCI or GTDB. Finally, PhyloCloud offers a novel tree visualisation system based on ETE Toolkit v4.0, which can be used to explore very large trees and enhance them with custom annotations and multiple sequence alignments. The platform allows for sharing tree collections and specific tree views via private links, or make them fully public, serving also as a repository of phylogenomic data. PhyloCloud is available at https://phylocloud.cgmlab.org
Graphical Abstract
Graphical abstract
PhyloCloud is an online platform aimed at hosting, organizing, sharing, exploring and analyzing trees and alignments from their phylogenomics projects.
Nonalternant topologies have attracted considerable attention due to their unique physiochemical characteristics in recent years. Here, three novel topological nanographenes molecular models of ...nitrogen (N)-doped Stone-Thrower-Wales (S-T-W) defect were achieved through direct arylation. Their chemical structures were unambiguously elucidated by single crystal analysis. Among them, threefold intramolecular direct arylation compound (C42H21N) is the largest nanographene bearing a N-doped nonalternant topology to date, in which the non-benzenoid rings account for 83% of the total molecular skeleton. The absorption maxima of this compound was located in the near-infrared region with a long tail up to 900 nm, which was much longer than those reported for similarly sized N-doped nanographene with six-membered rings (C40H15N). In addition, the electronic energy gaps of these series compounds obviously decreased with the introduction of nonalternant topologies (from 2.27 eV to 1.50 eV). It is noteworthy that C42H21N possesses such a low energy gap (Egopt = 1.40 eV; Egcv = 1.50 eV), yet is highly stable under ambient conditions. Our work reported herein demonstrates that the nonalternant topology could significantly influence the electronic configurations of nanocarbons, where the introduction of a nonalternanting topology may be an effective way to narrow the energy gap without extending the molecular π-conjugation.
Donor and acceptor (D-A) compounds based on benzophenone (BP) and carbazole (Cz) were recently reported to exhibit an extraordinary long afterglow phosphorescence in the solid state. However, the BP ...derivatives' mechanism of long afterglow phosphorescence is obscure. BP-
o
-Cz, BP-
m
-Cz, and BP-
p
-Cz were designed by coupling Cz at the
ortho
-,
meta
- and
para
-positions of the BP's benzene ring to uncover the excited-state evolution of BP-Cz molecules. Femtosecond and nanosecond transient absorption and excited-state theoretical calculations were carried out to detect and trace the photophysical process of BP-Cz dyads. After the excitation, all dyads experience intramolecular charge transfer (ICT) and intersystem crossing (ISC) processes. The resulting charge-transfer (
1
CT and
3
CT) state of BP-
o
-Cz will decay to the ground state directly and quickly
via
the fast charge recombination (CR) process, which may be caused by through-space D-A interaction due to the enforced proximity between BP and Cz. In contrast, for BP-
m
-Cz and BP-
p
-Cz dyads, the complete separation of HOMOs and LUMOs leads to extended ICT and slow CR processes, producing an obvious Cz cation radical intermediate and an ultralong-lived triplet state species after the
3
CT. Herein, we demonstrated that the excited-state evolution channels could be modified by tuning the substituted positions of D-A dyads. This may pave the way for designing efficient D-A type luminescent materials.
Excited state evolution channels of BP-Cz dyads can be modified by tuning the substituted position of donor and acceptor,
ortho
-substituted BP-
o
-Cz undergoes slow ISC and fast CR processes,
meta
- and
para
-substituted BP-
m
-Cz and BP-
p
-Cz experience fast ISC and slow CR processes.
Regioisomerism is an efficient strategy for finely tuning the structures of molecules in the isolated or the aggregated state. Herein, two regioisomers of perylene diimide (PDI) derivatives have been ...designed and synthesized. The positions of the substituent anthraquinone groups display distinct influences on their molecular conformation and aggregate structures, resulting in different fluorescence properties upon one- and two-photon excitation. In addition, owing to the bright emission, cellular imaging tests based on their nanoparticles were also conducted.
The isomerism effect on the aggregate emission properties of perylene diimide derivatives is studied. Banking on their bright emission, a cellular imaging test based on their nanoparticles is also conducted.
The C═C photoswitching molecules 1,2-di(4-pyridyl)ethylene (DPE), 4-styrylpyridine (SP), and
-1,2-stilbene (TS) show favorable photoisomerization characteristics. Although the solid states of ...photoswitching molecules are usually used in optical devices, their excited state's evolution has been little explored. Here, the excited state's relaxation of DPE, SP, and TS in nanocrystal/microcrystal suspensions as well as in solution phase was studied to uncover the early events of their excited states. The dynamics of nanocrystal/microcrystal suspensions was tremendously accelerated in comparison to the kinetics obtained in the solution for these molecules under excitation. DPE exhibits the slowest decay rate, while SP shows the fastest decay rate in nanocrystal suspensions or solution, suggesting SP may be the best candidate for the photoswitching device. The intermolecular interactions and space restriction of the crystal lead to the acceleration of the excited state's evolution for DPE, SP, and TS. This provides new insight into the design of optical materials.
Semantic segmentation, which aims to accurately identify each pixel, is a meaningful and challenging task. Recently, we witness a strong tendency to improve model efficiency in low-computing ...applications. However, most real-time methods ignore hierarchical features and context information to improve efficiency, leading to a decrease in the accuracy of semantic segmentation. To this end, we propose a novel system named hierarchical semantic-aware network (HSNet) to refine multilevel context information. HSNet mainly has the following two core modules: 1) hierarchical feature refinement module (HFRM) and 2) cross-scale pyramid fusion module (CPFM). By aggregating hierarchical feature maps, the proposed HFRM learns multilevel feature representation to recover spatial details. Afterward, the dual attention mechanism is developed to refine features from both channel and spatial levels, thereby alleviating the multilevel semantic gap. Meanwhile, the CPFM, which fuses local and global context information in a cross-scale manner, is proposed to enrich semantic information to improve accuracy. Furthermore, HSNet is carefully designed to improve the efficiency of the model by reusing shallow features and reducing channel capacity. Extensive experiments show that our method is effective and superior in segmentation accuracy and inference speed compared with state-of-the-art methods.
Charge transfer plays an important role in photophysical and photochemical reactions. However, the factors affecting the excited charge-transfer state are unclear. Here, two donor−π–acceptor dyads ...with an excellent blue fluorescence quantum yield are designed by integrating 1,2-diphenylphenanthroimidazole (PPI) as an electron donor and 1,2,4-triazolopyridine (TP) as an electron acceptor through phenyl (P) bridges. In the solvents dichloromethane (DCM) and dimethyl formamide (DMF), the dynamics of intramolecular charge transfer (ICT) of the two dyads (TP-P-PPI and TP-P-P-PPI) is located at the Marcus normal region, while the dynamics of charge recombination (CR) is situated at the Marcus inverted region. Therefore, TP-P-P-PPI with a long π-chain exhibits a longer lifetime of ICT but a shorter lifetime of CR than TP-P-PPI does with a short π-chain. In contrast, when the two dyads are spin-coated into a film, the dynamics of ICT and CR processes of the two dyads are restored to be positively correlated with the π-chain length because of the inhibition of intramolecular torsion between PPI and TP in the excited state of the film. This work demonstrates a specific approach via the molecular torsion to tune the dynamics of the ICT and CR among donor−π–acceptor systems.
In this paper, novel UiO‐66‐AO‐based adsorption‐filtration hybrid membranes (UAMs) are prepared via an irradiation‐mediated growth strategy to simultaneously improve water flux and accelerate uranium ...extraction from water resources. The UAM shows an equilibrium adsorption that is four times faster than UiO‐66‐AO powder and an adsorption capacity that is over two times higher. UAM also achieves a record synergy of high flux and high uranium removal ratio from simulated seawater (1358.8 L m−2 h−1, 84.5%) by one‐time filtration under ambient temperature and pressure (the adsorption is 1.83 mg g−1 in 90 min). The excellent uranium extraction performance is attributed to the unique UAM structure, in which water flows through the channels of thin metal‐organic framework (MOF) film without blocking by substrate leading to the high flux during filtration, and the full contact of uranium with abundant exposed active sites promotes the adsorption. This work will be conducive to overcoming the bottleneck problems of uranium extraction from water resources.
Novel metal‐organic framework (MOF)‐based adsorption‐filtration hybrid membranes are prepared which could improve water flux and accelerate uranium extraction from water resources. The excellent uranium extraction performance is attributed to the unique membrane structure, that water flows through the channels without blocking by the substrate during filtration and the full contact of uranium with abundant exposed active sites promotes the adsorption.
By utilizing the bipolarity of 1,2‐diphenylphenanthroimidazole (PPI), two types of asymmetrical tripartite triads (PPI‐TPA and PPI‐PCz) were designed with triphenylamine (TPA) and 9‐phenylcarbazole ...(PCz). These triads are deep‐blue luminescent materials with a high fluorescence quantum yield of nearly 100 %. To trace the photophysical behaviors of these triads, their excited‐state evolution channels and interchromophoric interactions were investigated by ultrafast time‐resolved transient absorption and excited‐state theoretical calculations. The results suggest that the electronic nature, asymmetrical tripartite structure, and electron–hole distance of these triads, as well as solvent polarity, determine the lifetime of intramolecular charge transfer (ICT). Interestingly, PPI‐PCz triads show anti‐Kasha ICT, and the charge‐transfer direction among the triads is adjustable. For the PPI‐TPA triad, the electron is transferred from TPA to PPI, whereas for the PPI‐PCz triad the electron is pushed from PPI to PCz. Exploration of the excited‐state ICT in these triads may pave the way to design better luminescent materials in the future.
Deeper blue: Two types of asymmetrical tripartite triads (PPI‐TPA and PPI‐PCz) were designed as deep‐blue luminescent materials with a high fluorescence quantum yield of nearly 100 %. The electronic nature of the moieties, asymmetrical tripartite structure, and electron‐hole distance of these triads, as well as the polarity of the solvent, determine the lifetimes of excited‐state intramolecular charge transfer (ICT). Interestingly, the CT direction among the triads is adjustable.
Many of the Earth's microbes remain uncultured and understudied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain largely overlooked in ...most metagenomic studies
. Here we analysed 149,842 environmental genomes from multiple habitats
and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel (FESNov) gene families exclusive to uncultivated prokaryotic taxa. All FESNov families span multiple species, exhibit strong signals of purifying selection and qualify as new orthologous groups, thus nearly tripling the number of bacterial and archaeal gene families described to date. The FESNov catalogue is enriched in clade-specific traits, including 1,034 novel families that can distinguish entire uncultivated phyla, classes and orders, probably representing synapomorphies that facilitated their evolutionary divergence. Using genomic context analysis and structural alignments we predicted functional associations for 32.4% of FESNov families, including 4,349 high-confidence associations with important biological processes. These predictions provide a valuable hypothesis-driven framework that we used for experimental validatation of a new gene family involved in cell motility and a novel set of antimicrobial peptides. We also demonstrate that the relative abundance profiles of novel families can discriminate between environments and clinical conditions, leading to the discovery of potentially new biomarkers associated with colorectal cancer. We expect this work to enhance future metagenomics studies and expand our knowledge of the genetic repertory of uncultivated organisms.
