LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB

<p>Abstract</p> <p>Background</p> <p>Biochemical networks play an essential role in systems biology. Rapidly growing network data and versatile research activities call for convenient visualization tools to aid intuitively perceiving abstract structures of networks and gaining insights into the functional implications of networks. There are various kinds of network visualization software, but they are usually not adequate for visual analysis of complex biological networks mainly because of the two reasons: 1) most existing drawing methods suitable for biochemical networks have high computation loads and can hardly achieve near real-time visualization; 2) available network visualization tools are designed for working in certain network modeling platforms, so they are not convenient for general analyses due to lack of broader range of readily accessible numerical utilities.</p> <p>Results</p> <p>We present LucidDraw as a visual analysis tool, which features (a) speed: typical biological networks with several hundreds of nodes can be drawn in a few seconds through a new layout algorithm; (b) ease of use: working within MATLAB makes it convenient to manipulate and analyze the network data using a broad spectrum of sophisticated numerical functions; (c) flexibility: layout styles and incorporation of other available information about functional modules can be controlled by users with little effort, and the output drawings are interactively modifiable.</p> <p>Conclusions</p> <p>Equipped with a new grid layout algorithm proposed here, LucidDraw serves as an auxiliary network analysis tool capable of visualizing complex biological networks in near real-time with controllable layout styles and drawing details. The framework of the algorithm enables easy incorporation of extra biological information, if available, to influence the output layouts with predefined node grouping features.</p

Transcranial Magnetic Stimulation Reveals Executive Control Dissociation in the Rostral Prefrontal Cortex

Although previous studies have shown that the rostral prefrontal cortex (rPFC) plays a crucial role in executive tasks, the various functions of the rPFC in the humans are still understudied. Here we used transcranial magnetic stimulation (TMS) with continuous theta burst stimulation (cTBS) to interfere with the executive control functions of the right rostrolateral PFC (RLPFC) or the right rostromedial PFC (RMPFC). Subjects performed a task-switching paradigm, which included spatial detection (SD), prospective memory (PM) and working memory (WM) tasks, after cTBS. The performance of 18 healthy volunteers was evaluated on different days after cTBS over the right RLPFC, the right RMPFC, and the vertex (serving as a control site). The application of cTBS over the RLPFC significantly increased the switching costs (SCs) of the error rates (ERs) when switching to the PM task, while RMPFC-cTBS decreased SCs of ERs when switching to the WM task, compared with the control vertex site. These findings provide evidence for a differential role of the RLPFC and the RMPFC in executive functions, with a specific involvement of the RLPFC and the RMPFC in PM, and WM, respectively

A Survey of Chain of Thought Reasoning: Advances, Frontiers and Future

Chain-of-thought reasoning, a cognitive process fundamental to human intelligence, has garnered significant attention in the realm of artificial intelligence and natural language processing. However, there still remains a lack of a comprehensive survey for this arena. To this end, we take the first step and present a thorough survey of this research field carefully and widely. We use X-of-Thought to refer to Chain-of-Thought in a broad sense. In detail, we systematically organize the current research according to the taxonomies of methods, including XoT construction, XoT structure variants, and enhanced XoT. Additionally, we describe XoT with frontier applications, covering planning, tool use, and distillation. Furthermore, we address challenges and discuss some future directions, including faithfulness, multi-modal, and theory. We hope this survey serves as a valuable resource for researchers seeking to innovate within the domain of chain-of-thought reasoning.Comment: 26 pages. Resources are available at https://github.com/zchuz/CoT-Reasoning-Surve

Synthesis and biological characterization of organoruthenium complexes with 8-hydroxyquinolines

In this study we report the synthesis, characterization and a thorough biological evaluation of twelve organoruthenium–8-hydroxyquinolinato (Ru-hq) complexes. The chosen hqH ligands bear various halogen atoms in different positions which enables to study effect of the substituents on physico-chemical and biological properties. The determined crystal structures of novel complexes expectedly show the cymene ring, a bidentately coordinated deprotonated hq and a halide ligand (chlorido or iodido) coordinated to the ruthenium central ion. In previous studies the anticancer potential of organoruthenium complex with 8-hydroxyquinoline ligand clioquinol was well established and we have decided to perform an extended biological evaluation (antibacterial and antitumor activity) of the whole series of halo-substituted analogs. Beside the cytotoxic potential of studied compounds also the effect of two selected complexes (9 and 10) on apoptosis induction in MG-63 and A549 cells was also studied via externalization of phosphatidylserine at the outer plasma membrane leaflet. Both selected complexes that gave best preliminary cytotoxicity results contain bromo substituted hq ligands. Apoptosis induction results are in agreement with the cell viability assays suggesting the higher and more selective anticancer activity of complex 10 in comparison to complex 9 on MG-63 cells.Centro de Química Inorgánic

Synthesis and biological characterization of organoruthenium complexes with 8-hydroxyquinolines

In this study we report the synthesis, characterization and a thorough biological evaluation of twelve organoruthenium–8-hydroxyquinolinato (Ru-hq) complexes. The chosen hqH ligands bear various halogen atoms in different positions which enables to study effect of the substituents on physico-chemical and biological properties. The determined crystal structures of novel complexes expectedly show the cymene ring, a bidentately coordinated deprotonated hq and a halide ligand (chlorido or iodido) coordinated to the ruthenium central ion. In previous studies the anticancer potential of organoruthenium complex with 8-hydroxyquinoline ligand clioquinol was well established and we have decided to perform an extended biological evaluation (antibacterial and antitumor activity) of the whole series of halo-substituted analogs. Beside the cytotoxic potential of studied compounds also the effect of two selected complexes (9 and 10) on apoptosis induction in MG-63 and A549 cells was also studied via externalization of phosphatidylserine at the outer plasma membrane leaflet. Both selected complexes that gave best preliminary cytotoxicity results contain bromo substituted hq ligands. Apoptosis induction results are in agreement with the cell viability assays suggesting the higher and more selective anticancer activity of complex 10 in comparison to complex 9 on MG-63 cells.Centro de Química Inorgánic

Synthesis and biological characterization of organoruthenium complexes with 8-hydroxyquinolines

In this study we report the synthesis, characterization and a thorough biological evaluation of twelve organoruthenium–8-hydroxyquinolinato (Ru-hq) complexes. The chosen hqH ligands bear various halogen atoms in different positions which enables to study effect of the substituents on physico-chemical and biological properties. The determined crystal structures of novel complexes expectedly show the cymene ring, a bidentately coordinated deprotonated hq and a halide ligand (chlorido or iodido) coordinated to the ruthenium central ion. In previous studies the anticancer potential of organoruthenium complex with 8-hydroxyquinoline ligand clioquinol was well established and we have decided to perform an extended biological evaluation (antibacterial and antitumor activity) of the whole series of halo-substituted analogs. Beside the cytotoxic potential of studied compounds also the effect of two selected complexes (9 and 10) on apoptosis induction in MG-63 and A549 cells was also studied via externalization of phosphatidylserine at the outer plasma membrane leaflet. Both selected complexes that gave best preliminary cytotoxicity results contain bromo substituted hq ligands. Apoptosis induction results are in agreement with the cell viability assays suggesting the higher and more selective anticancer activity of complex 10 in comparison to complex 9 on MG-63 cells.Centro de Química Inorgánic

In vitro fermentation properties of magnesium hydride and related modulation effects on broiler cecal microbiome and metabolome

Magnesium hydride (MGH), a highly promising hydrogen-producing substance/additive for hydrogen production through its hydrolysis reaction, has the potential to enhance broiler production. However, before incorporating MGH as a hydrogen-producing additive in broiler feed, it is crucial to fully understand its impact on microbiota and metabolites. In vitro fermentation models provide a fast, reproducible, and direct assessment tool for microbiota metabolism and composition. This study aims to investigate the effects of MGH and coated-magnesium hydride (CMG) on fermentation characteristics, as well as the microbiota and metabolome in the culture of in vitro fermentation using cecal inocula from broilers. After 48 h of incubation, it was observed that the presence of MGH had a significant impact on various factors. Specifically, the content of N-NH3 decreased, while the total hydrogen gas and total SCFAs increased. Furthermore, the presence of MGH promoted the abundance of SCFA-producing bacteria such as Ruminococcus, Blautia, Coprobacillus, and Dysgonomonas. On the other hand, the presence of CMG led to an increase in the concentration of lactic acid, acetic acid, and valeric acid. Additionally, CMG affected the diversity of microbiota in the culture, resulting in an enrichment of the relative abundance of Firmicutes, as well as genera of Lactobacillus, Coprococcus, and Eubacterium. Conversely, the relative abundance of the phylum Proteobacteria and pathogenic bacteria Shigella decreased. Metabolome analysis revealed that MGH and CMG treatment caused significant changes in 21 co-regulated metabolites, primarily associated with lipid, amino acid, benzenoids, and organooxygen compounds. Importantly, joint correlation analysis revealed that MGH or CMG treatments had a direct impact on the microbiota, which in turn indirectly influenced metabolites in the culture. In summary, the results of this study suggested that both MGH and coated-MGH have similar yet distinct positive effects on the microbiota and metabolites of the broiler cecal in an in vitro fermentation model

Effect of fermented heat-treated rice bran on performance and possible role of intestinal microbiota in laying hens

Rice bran is a high-quality and renewable livestock feed material rich in nutrients and bioactive substances. To investigate the effects of dietary supplementation with fermented heat-treated rice bran on the performance, apparent digestibility of nutrients, cecal microbiota and metabolites in laying hens, a total of 128 18-week-old Hy-Line brown layers were randomly assigned to four treatment groups: 2.5% HRB (basal diet contained 2.5% heat-treated rice bran), 5.0% HRB (5.0% heat-treated rice bran), 2.5% FHRB (2.5% fermented heat-treated rice bran), 5.0% FHRB (5.0% fermented heat-treated rice bran). Results showed that FHRB supplementation significantly increased the average daily feed intake (ADFI) during 25–28 weeks, and improved apparent digestibility of dry matter (DM), crude protein (CP), ether extract (EE) and crude fiber (CF) in laying hens. Moreover, feeding 5.0% of HRB and FHRB resulted higher egg production (EP) and average egg weight (AEW) during the feeding period, and decreased the feed conversion ratio (FCR) during 21 to 28 weeks. The alpha and beta diversity indices indicated that FHRB altered the cecal microbiota. In particular, dietary supplementation with FHRB significantly increased the relative abundances of Lachnospira and Clostridium. Compared with the 2.5% level of supplementation, supplementing 5.0% HRB and 5.0% FHRB increased the relative abundances of Firmicutes, Ruminococcus and Peptococcus, and lowered the relative abundance of Actinobacteria. Furthermore, dietary FHRB supplementation significantly increased the concentration of short-chain fatty acids in cecum and changed the overall metabolome. The results of correlation analysis showed a close interaction between cecal microbiota, metabolites and apparent digestibility of nutrients. Taken together, we revealed that FHRB supplementation can induce characteristic structural and metabolic changes in the cecal microbiome, which could potentially promote nutrient digestion and absorption, and improve the production performance of laying hens

New pyrido[3,4-b]pyrazine-based sensitizers for efficient and stable dye-sensitized solar cells

A series of new pyrido[3,4-b]pyrazine-based organic sensitizers (PP-I and APP-I–IV) containing different donors and p-spacers have been synthesized and employed in dye-sensitized solar cells (DSSCs). The absorption spectra properties of dyes are analysed by density functional theory (DFT). The calculated results in combination with the experiments suggest that the absorption characteristics and excited state features will mainly be dominated by charge transfer transitions from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO) and to higher LUMO orbitals. Furthermore, attaching the octyloxy groups significantly extends the π-conjugation of the donor in APP- IV, which raises the HOMO energy and facilitates its oxidation. As a consequence, APP-IV exhibits the lowest HOMO–LUMO energy gap among all dyes, which, in turn, corresponds well with the red shift of the absorption spectra. Transient photovoltage and photocurrent decay experiments as well as electrochemical impedance spectroscopy indicate that the electron lifetime and charge recombination resistance are increased due to the introduction of octyloxy chains on the donor unit, resulting in the high photovoltage based on APP-IV. It was found that APP-IV based DSSCs with liquid electrolyte display the highest power conversion efficiency (PCE) of 7.12%. Importantly, a PCE of 6.20% has been achieved for APP-IV based DSSCs with ionic-liquid electrolytes and retained 97% of the initial value after continuous light soaking for 1000 h at 60 C. This renders these pyrido[3,4-b]pyrazine-based sensitizers quite promising candidates for highly efficient and stable DSSCs