The curves of connectivity density against for different ranking measures in the ECT and HST.

<p>The curves of connectivity density against for different ranking measures in the ECT and HST.</p

Clusters, members, rankings and statistical characteristics of the identified top-30 nodes in the ECT.

<p>Clusters, members, rankings and statistical characteristics of the identified top-30 nodes in the ECT.</p

Evaluation of <i>I</i>^score via ROC curves with composite reference standards for the five networks.

<p>(a) <i>T</i>₀ = 10%. A node is defined as important if either its rankings by the in, out, total degree, PageRank, motif centrality or the betweenness are at the top-<i>T</i>₀ level. (b) Similarly to (a), but with <i>T</i>₀ = 20%.</p

Clusters, members, rankings and statistical characteristics of the identified top-30 nodes in the CEN.

<p><i>R</i>_in and <i>R</i>_out represent the rankings by the in and out-degree. <i>R</i>_total and <i>R</i>_p represent the results from the total degree and PageRank <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106132#pone.0106132-Brin1" target="_blank">[21]</a>. <i>R</i>_mc and <i>R</i>_bet denote the results from the motif centrality <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106132#pone.0106132-Koschtzki1" target="_blank">[25]</a> and betweenness. Similarly hereinafter.</p><p>Clusters, members, rankings and statistical characteristics of the identified top-30 nodes in the CEN.</p

Trapping Methylglyoxal by Genistein and Its Metabolites in Mice

Increasing evidence supports dicarbonyl stress such as methylglyoxal (MGO) as one of the major pathogenic links between hyperglycemia and diabetic complications. <i>In vitro</i> studies have shown that dietary flavonoids can inhibit the formation of advanced glycation end products (AGEs) by trapping MGO. However, whether flavonoids can trap MGO <i>in vivo</i> and whether biotransformation limits the trapping capacity of flavonoids remain virtually unknown. In this study, we investigated whether genistein (GEN), the major soy isoflavone, could trap MGO in mice by promoting the formation of MGO adducts of GEN and its metabolites. Two different mouse studies were conducted. In the acute study, a single dose of MGO and GEN were administered to mice via oral gavage. In the chronic study, MGO was given to mice in drinking water for 1 month and then GEN was given to mice for 4 consecutive days via oral gavage. Two mono-MGO adducts of GEN and six mono-MGO adducts of GEN phase I and microbial metabolites were identified in mouse urine samples from these studies using liquid chromatography/electrospray ionization tandem mass spectrometry. The structures of these MGO adducts were confirmed by analyzing their MS^<i>n</i> (<i>n</i> = 1–4) spectra as well as by comparing them with the tandem mass spectra of authentic standards. All of the MGO adducts presented in their phase II conjugated forms in mouse urine samples in the acute and chronic studies. To our knowledge, this is the first <i>in vivo</i> evidence to demonstrate the trapping efficacy of GEN in mice and to show that the metabolites of GEN remain bioactive

Clusters, members, rankings and statistical characteristics of the identified top-30 ranked nodes in the YT.

<p>Clusters, members, rankings and statistical characteristics of the identified top-30 ranked nodes in the YT.</p

Cluster analysis for the identified top-30 nodes in the five networks based on the <i>I</i>^score.

<p>Cluster analysis for the identified top-30 nodes in the five networks based on the <i>I</i>^score.</p

Statistical indexes for the five directed biological networks.

<p>“-” denotes no such item.</p><p>Statistical indexes for the five directed biological networks.</p

How High Valence Transition Metal Spreads Its Activity over Nonmetal Oxoes: A Proof-of-Concept Study

Here we present a comprehensive survey on identification of the active sites for <i>n</i>-butane activation over binary vanadium phosphorus oxides. Density functional theory calculations show that the activity can be spread over all PO sites through −OP– chain(s). With an increase in the −OP– chain(s), the activities are gradually decayed. We demonstrate that such a tendency can be quantitatively described by the center of PO lone-pair band (ε_lp)

Table1_RECCIPE: A new framework assessing localized cell-cell interaction on gene expression in multicellular ST data.XLSX

Cell-cell interaction (CCI) plays a pivotal role in cellular communication within the tissue microenvironment. The recent development of spatial transcriptomics (ST) technology and associated data analysis methods has empowered researchers to systematically investigate CCI. However, existing methods are tailored to single-cell resolution datasets, whereas the majority of ST platforms lack such resolution. Additionally, the detection of CCI through association screening based on ST data, which has complicated dependence structure, necessitates proper control of false discovery rates due to the multiple hypothesis testing issue in high dimensional spaces. To address these challenges, we introduce RECCIPE, a novel method designed for identifying cell signaling interactions across multiple cell types in spatial transcriptomic data. RECCIPE integrates gene expression data, spatial information and cell type composition in a multivariate regression framework, enabling genome-wide screening for changes in gene expression levels attributed to CCIs. We show that RECCIPE not only achieves high accuracy in simulated datasets but also provides new biological insights from real data obtained from a mouse model of Alzheimer’s disease (AD). Overall, our framework provides a useful tool for studying impact of cell-cell interactions on gene expression in multicellular systems.</p