On Low-Rank Directed Acyclic Graphs and Causal Structure Learning.

Despite several advances in recent years, learning causal structures represented by directed acyclic graphs (DAGs) remains a challenging task in high-dimensional settings when the graphs to be learned are not sparse. In this article, we propose to exploit a low-rank assumption regarding the (weighted) adjacency matrix of a DAG causal model to help address this problem. We utilize existing low-rank techniques to adapt causal structure learning methods to take advantage of this assumption and establish several useful results relating interpretable graphical conditions to the low-rank assumption. Specifically, we show that the maximum rank is highly related to hubs, suggesting that scale-free (SF) networks, which are frequently encountered in practice, tend to be low rank. Our experiments demonstrate the utility of the low-rank adaptations for a variety of data models, especially with relatively large and dense graphs. Moreover, with a validation procedure, the adaptations maintain a superior or comparable performance even when graphs are not restricted to be low rank.

Infiltration Profile of Regulatory T Cells in Osteoarthritis-Related Pain and Disability.

Emerging evidence indicates that regulatory T cells (Treg) intervene in the inflammatory processes that drive osteoarthritis (OA). However, whether polarized Tregs affect clinical features of the disease in the short- or long-term, and if so, what their role in OA-related pain and functional disability really is, remains elusive. Thus, the aim of the current study was to characterize the infiltration profile of Tregs in systemic (peripheral blood) and joint-derived (synovial fluid and synovial membrane) samples from patients with knee OA in relation to OA-induced symptoms. To this end, Treg infiltration (CD4+CD25+/high CD127low/-) was analyzed in matched samples of peripheral blood (PB), synovial fluid (SF) and synovial membrane (SM) from a total of 47 patients undergoing elective knee arthroplasty using flow cytometry. At the same time, knee pain and function were assessed and correlated with Treg proportions in different compartments (PB, SF, SM). Interestingly, matched-pair analysis revealed significantly higher Treg proportions in joint-derived samples than in PB, which was mainly attributed to the high Treg frequency in SF. Moreover, we found significant associations between infiltrating Tregs and OA-related symptoms which indicate that lower Treg proportions-especially in the SM-are related to increased pain and functional disability in knee OA. In conclusion, this study highlights the importance of local cellular inflammatory processes in OA pathology. Intra-articular Treg infiltration might play an important role not only in OA pathogenesis but also in the development of OA-related symptoms.

Exploring Diagnostic Biomarkers and Comorbid Pathogenesis for Osteoarthritis and Metabolic Syndrome via Bioinformatics Approach.

BACKGROUND: Metabolic syndrome (MS) has grown in recognition to contribute to the pathogenesis of osteoarthritis (OA), which is the most prevalent arthritis characterized by joint dysfunction. However, the specific mechanism between OA and MS remains unclear. METHODS: The gene expression profiles and clinical information data of OA and MS were retrieved from the Gene Expression Omnibus (GEO) database. The genes in the key module of MS were identified by weighted gene co-expression network analysis (WGCNA), which intersected with the differentially expressed genes (DEGs) between control and MS samples to obtain hub genes for MS. The potential functions and pathways of hub genes were detected through the Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) analyses. The genes involved in the different KEGG pathways between the control and OA samples overlapped with the DEGs between the two groups via the Venn analysis to gain the hub genes for OA affected by MS (MOHGs). Additionally, the least absolute shrinkage and selection operator (LASSO) was performed on the MOHGs to establish a diagnostic model for each disease. RESULTS: A total of 61 hub genes for MS were identified that significantly enriched in platelet activation, complement and coagulation cascades, and hematopoietic cell lineage. Besides, 4 candidate genes (ELOVL7, F2RL3, GP9, and ITGA2B) were screened among the 6 MOHGs to construct a diagnostic model, showing good performance for distinguishing controls from patients with MS and OA. GSEA suggested that these diagnostic genes were closely associated with immune response, adipocytokine signaling, fatty acid metabolism, cell cycle, and platelet activation. CONCLUSION: Taken together, we identified 4 potential gene biomarkers for diagnosing MS and OA patients, providing a theoretical basis and reference for the diagnostics and treatment targets of MS and OA.

Synthesis and X-ray characterization of 15- and 16-vertex closo-carboranes.

Carboranes are a class of carbon-boron molecular clusters with three-dimensional aromaticity, and inherent robustness. These endowments enable carboranes as valuable building blocks for applications ranging from functional materials to pharmaceuticals. Thus, the chemistry of carboranes has received tremendous research interest, and significant progress has been made in the past decades. However, many attempts to the synthesis of carboranes with more than 14 vertices had been unsuccessful since the report of a 14-vertex carborane in 2005. The question arises as to whether these long sought-after molecules exist. We describe in this article the synthesis and structural characterization of 15- and 16-vertex closo-carboranes as well as 16-vertex ruthenacarborane. Such a success relies on the introduction of silyl groups to both cage carbons, stabilizing the corresponding nido-carborane dianions and promoting the capitation reaction with HBBr2·SMe2. This work would shed some light on the preparation of carboranes with 17 vertices or more, and open the door for studying supercarborane chemistry.

T Helper Cell Infiltration in Osteoarthritis-Related Knee Pain and Disability.

Despite the growing body of literature demonstrating a crucial role of T helper cell (Th) responses in the pathogenesis of osteoarthritis (OA), only few clinical studies have assessed interactions between Th cells and OA-related symptoms. Yet, the inclusion of clinical data in the interpretation of cellular analyses of Th cell infiltration is essential to reveal the mechanisms underlying the complex pathophysiology of OA pain and disability. Thus, the aim of the study was to analyze the infiltration pattern of Th cells in systemic (peripheral blood) and joint-derived (synovial membrane and fluid) samples from patients with knee OA in relation to OA-induced pain and disability. Therefore, radiographic OA severity, knee pain and function of 47 OA patients undergoing knee arthroplasty were evaluated prior to surgery. In parallel, samples of peripheral blood (PB), synovial membrane (SM) and synovial fluid (SF) were harvested and analyzed for different Th subsets using flow cytometry. According to surface marker expression Th cells (CD3+ CD4+ CD8-) were assigned to the Th subsets Th1 (CXCR3+, CCR5+), Th2 (CCR3+, CCR4+) and Th17 (CD161+, CCR6+). Interestingly, infiltration of the SM with all Th subtypes (Th1, Th2, Th17) significantly correlated with OA-induced disability. Most importantly, synovial CCR5+ and CCR3+ Th cell infiltration was associated with OA-related knee pain and disability. Furthermore, higher percentage rates of CXCR3+ Th cells in all tissue samples (PB, SM, SF) showed significant associations with OA severity. In contrast, increasing percentage rates of CD161+ Th cells in SM samples corresponded to a better functional outcome. In conclusion, the current study provides an extensive profile of the Th cell infiltration pattern in PB, SF and SM from patients with clinically relevant knee OA. Th cell infiltration of the SM might play a crucial role not only in the pathogenesis of OA but also in the development of OA-related knee pain and disability.

Synovial Cytokines Significantly Correlate with Osteoarthritis-Related Knee Pain and Disability: Inflammatory Mediators of Potential Clinical Relevance.

The aim of this study was to identify inflammatory mediators of potential clinical relevance in synovial fluid (SF) samples of patients with knee osteoarthritis (OA). Therefore, radiographic OA severity, knee pain and function of 34 OA patients undergoing unicompartmental (UC) and bicompartmental (BC) knee arthroplasty were assessed prior to surgery and SF samples were analyzed for a broad variety of inflammatory mediators, including interleukins (ILs), interferons (IFNs), C-X-C motif ligand chemokines (CXCLs), and growth factors (nerve growth factor; NGF, vascular endothelial growth factor; VEGF, and stem cell growth factor ß; SCGF-ß) using multiplex assay. Significant differences were observed between the SF levels of different inflammatory markers. When compared to UC OA, significantly higher concentrations of IL-7, IL-8, IL-10, IL-12, IL-13, IFN-γ, VEGF and CXCL1 were detected in BC OA. Correlation analyses revealed significant associations between OA severity and IL-6, IL-8, IFN-γ, SCGF-ß, VEGF, CXCL1. Interestingly, increases in both anti- (IL-10, IL-13) and pro-inflammatory (IL-7, IL-12, IFN-γ) cytokines, as well as growth factors (SCGF-ß, VEGF), correlated significantly with the level of knee pain. Poorer knee function was associated with higher IL-6, IL-10, IL-12, IL-13, IL-18, ßNGF, SCGF-ß, VEGF and CXCL9 levels. In conclusion, this study provides an extensive profile of synovial inflammatory mediators in knee OA and identifies cytokines of potential clinical relevance. In fact, five of the mediators examined (IL-10, IL-12, IL-13, SCGF-ß, VEGF) significantly correlate with both knee pain and function.

Regioselective Nucleophilic Alkylation/Arylation of B-H Bonds in o-Carboranes: An Alternative Method for Selective Cage Boron Functionalization.

A new protocol for regioselective nucleophilic cage B-H substitution in o-carboranes has been proposed that is complementary to the strategies of transition metal catalysis and electrophilic substitution. Magnesium-mediated site-selective nucleophilic cage B(3,6)-H and B(9)-H substitution reactions of o-carboranes give a series of B(3,6)-dialkylated and B(9)-alkylated/arylated o-carboranes in high yields. Both steric and electronic factors of cage C substituents play crucial roles in controlling the site selectivity.

Borylene Insertion into Cage B-H Bond: A Route to Electron-Precise B-B Single Bond.

A new strategy to construct electron-precise B-B single bond via direct borylene insertion into B-H bond is described. Reduction of bromoborylene stabilized by carborane-fused silylenes with 2 equiv of sodium gives a new compound with a B-B single bond. Both experimental and density functional theory results suggest that such an electron-precise B-B single bond is formed via in situ generated borylene insertion into B-H bond.

Causal Discovery from Nonstationary/Heterogeneous Data: Skeleton Estimation and Orientation Determination.

It is commonplace to encounter nonstationary or heterogeneous data, of which the underlying generating process changes over time or across data sets (the data sets may have different experimental conditions or data collection conditions). Such a distribution shift feature presents both challenges and opportunities for causal discovery. In this paper we develop a principled framework for causal discovery from such data, called Constraint-based causal Discovery from Nonstationary/heterogeneous Data (CD-NOD), which addresses two important questions. First, we propose an enhanced constraint-based procedure to detect variables whose local mechanisms change and recover the skeleton of the causal structure over observed variables. Second, we present a way to determine causal orientations by making use of independence changes in the data distribution implied by the underlying causal model, benefiting from information carried by changing distributions. Experimental results on various synthetic and real-world data sets are presented to demonstrate the efficacy of our methods.

Reversible Photothermal Isomerization of Carborane-Fused Azaborole to Borirane: Synthesis and Reactivity of Carbene-Stabilized Carborane-Fused Borirane.

A fully reversible photothermal isomerization between carborane-fused trigonal-planar azaborole (dark-purple) and tetrahedral borirane (pale-yellow) has been observed, leading to the isolation and structural characterization of the first example of carborane-fused borirane. DFT calculations indicate that the azaborole is thermodynamically more stable than the borirane by 11.2 kcal mol-1 , and the energy barrier for the thermal conversion from azaborole to borirane is 35.5 kcal mol-1 . The reactivity studies show that the B-C(cage) bond in borirane can be broken in the reaction with CuCl, HCl, or elemental sulfur.

Direct Nucleophilic Substitution Reaction of Cage B-H Bonds by Grignard Reagents: A Route to Regioselective B4-Alkylation of o-Carboranes.

Direct nucleophilic substitution reaction of cage B-H bonds of o-carboranes by Grignard reagents in the absence of any transition metals has been achieved for the first time, and leads to the regioselective synthesis of a series of 4-alkyl-1,2-diaryl-o-carboranes in very high yields. The presence of two electron-withdrawing aryl groups on the cage carbon atoms is crucial to realizing the reaction. The regioselectivity is controlled by both electronic and steric factors. This work represents a new strategy for the development of methods for carborane functionalization.

Engineering a Small HOMO-LUMO Gap and Intramolecular C-H Borylation by Diborene/Anthracene Orbital Intercalation.

The diborene 1 was synthesized by reduction of a mixture of 1,2-di-9-anthryl-1,2-dibromodiborane(4) (6) and trimethylphosphine with potassium graphite. The X-ray structure of 1 shows the two anthryl rings to be parallel and their π(C14 ) systems perpendicular to the diborene π(B=B) system. This twisted conformation allows for intercalation of the relatively high-lying π(B=B) orbital and the low-lying π* orbital of the anthryl moiety with no significant conjugation, resulting in a small HOMO-LUMO gap (HLG) and ultimately a C-H borylation of the anthryl unit. The HLG of 1 was estimated to be 1.57 eV from the onset of the long wavelength band in its UV/Vis absorption spectrum (THF, λonset =788 nm). The oxidation of 1 with elemental selenium afforded diboraselenirane 8 in quantitative yield. By oxidative abstraction of one phosphine ligand by another equivalent of elemental selenium, the B-B and C1 -H bonds of 8 were cleaved to give the cyclic 1,9-diborylanthracene 9.

Mechanistic Elucidation of Zirconium-Catalyzed Direct Amidation.

The mechanism of the zirconium-catalyzed condensation of carboxylic acids and amines for direct formation of amides was studied using kinetics, NMR spectroscopy, and DFT calculations. The reaction is found to be first order with respect to the catalyst and has a positive rate dependence on amine concentration. A negative rate dependence on carboxylic acid concentration is observed along with S-shaped kinetic profiles under certain conditions, which is consistent with the formation of reversible off-cycle species. Kinetic experiments using reaction progress kinetic analysis protocols demonstrate that inhibition of the catalyst by the amide product can be avoided using a high amine concentration. These insights led to the design of a reaction protocol with improved yields and a decrease in catalyst loading. NMR spectroscopy provides important details of the nature of the zirconium catalyst and serves as the starting point for a theoretical study of the catalytic cycle using DFT calculations. These studies indicate that a dinuclear zirconium species can catalyze the reaction with feasible energy barriers. The amine is proposed to perform a nucleophilic attack at a terminal η2-carboxylate ligand of the zirconium catalyst, followed by a C-O bond cleavage step, with an intermediate proton transfer from nitrogen to oxygen facilitated by an additional equivalent of amine. In addition, the DFT calculations reproduce experimentally observed effects on reaction rate, induced by electronically different substituents on the carboxylic acid.

Behind Distribution Shift: Mining Driving Forces of Changes and Causal Arrows.

We address two important issues in causal discovery from nonstationary or heterogeneous data, where parameters associated with a causal structure may change over time or across data sets. First, we investigate how to efficiently estimate the "driving force" of the nonstationarity of a causal mechanism. That is, given a causal mechanism that varies over time or across data sets and whose qualitative structure is known, we aim to extract from data a low-dimensional and interpretable representation of the main components of the changes. For this purpose we develop a novel kernel embedding of nonstationary conditional distributions that does not rely on sliding windows. Second, the embedding also leads to a measure of dependence between the changes of causal modules that can be used to determine the directions of many causal arrows. We demonstrate the power of our methods with experiments on both synthetic and real data.

Unique properties of C,C'-linked nido-biscarborane tetraanions. Synthesis, structure and bonding of ruthenium monocarbollide via unprecedented cage carbon extrusion.

Four reaction pathways have been found in the reaction of a C,C'-linked nido-biscarborane tetraanionic salt with [Ru(p-cymene)Cl2]2, leading to the isolation and structural characterization of redox, triple cage B-H oxidative addition, cage expansion and cage carbon extrusion products. Among these, the unprecedented cage carbon extrusion results in the formation of a new 6π-electron carboranyl ligand [C2B10H10](2-). The bonding interactions between this ligand and the Ru(ii) center have also been discussed on the basis of DFT calculations.

Facile Synthesis of N-Carboranyl Amines through an ortho-Carboryne Intermediate.

The efficient o-carboryne precursor 1-Li-2-OTf-o-C2 B10 H10 reacts with lithium amides at room temperature to give a series of N-carboranyl amines in moderate to high isolated yields. This reaction is compatible with a broad substrate scope from primary to secondary, alkyl to aryl amines. The reaction mechanism is also proposed on the basis of experimental results and DFT calculations. This represents the first general and efficient method for the synthesis of 1-NR(1) R(2) -o-carboranes.

An Unprecedented Formal [5 + 2] Cycloaddition of Nitrones with o-Carboryne via Tandem [3 + 2] Cycloaddition/Oxygen Migration/Aromatization Sequence.

Heterocyclic skeletons are widespread among natural products as well as bioactive molecules. Cycloaddition reaction has created new opportunities to access heterocycles of great complexity due to its advantage of multiple bond formation in a single step. Here, we describe an unprecedented formal [5 + 2] cycloaddition of nitrone with o-carboryne to afford carborane-fused seven-membered heterocycles. Experimental and theoretical data suggest that a sequence of [3 + 2] cycloaddition, N-O bond cleavage, oxygen migration and rearomatization is involved in this unprecedented reaction. In this process, the nitrone moieties serve as five-atom coupling partners with both heteroatoms being incorporated into the framework of the final products. This new methodology also offers new insight into the chemistry of nitrones.

The synthesis and structure of a carbene-stabilized iminocarboranyl-boron(I) compound.

A carbene-stabilized iminocarboranylboron(I) compound has been synthesized and structurally characterized. Single-crystal X-ray analyses and DFT calculations show that the π back donation of the lone pair of electrons on the boron(I) center onto the π* orbital of the imine unit is crucial for removing the electron density of the boron center thereby stabilizing such species, in which the carbene serves solely as a σ donor. This work also demonstrates that imines play a similar role to that of carbenes in the stabilization of low valent boron compounds.

Dearomative [2 + 2] Cycloaddition and Formal C-H Insertion Reaction of o-Carboryne with Indoles: Synthesis of Carborane-Functionalized Heterocycles.

o-Carboryne (1,2-dehydro-o-carborane) is a very useful synthon for the synthesis of a variety of carborane-functionalized heterocycles. Reaction of o-carboryne with N-protected indoles gave carborane-fused indolines if the protecting group was TMS via dearomative [2 + 2] cycloaddition or carboranyl indoles for N-alkyl ones through formal C-H insertion reaction. For N-aryl indoles, both reactions were observed, giving two products, in which the product ratio was dependent upon the nature of the substituents on the aryl rings. In general, electron-withdrawing substituents favor [2 + 2] cycloaddition, whereas electron-donating substituents promote a formal C-H insertion pathway. This reaction is also compatible with other heteroaromatics. Thus, a stepwise reaction mechanism was proposed to account for the experimental observations. These protocols offer general and efficient methods for the preparation of carborane-functionalized indoles and indolines as well as other heterocycles. The observed dearomative [2 + 2] cycloaddition represents the first example of indoles to undergo such reaction in the absence of transition metals or without UV irradiation. All new compounds were fully characterized by (1)H, (13)C, and (11)B NMR spectroscopy as well as HRMS spectrometry. Some were further confirmed by single-crystal X-ray analyses.

o-Carborane functionalized pentacenes: synthesis, molecular packing and ambipolar organic thin-film transistors.

New 6,13-bis[1'-(C≡C)-2'-R-1',2'-C2B10H10]pentacenes (R = H, Me, Et, n-Bu) are synthesized and fully characterized. The results show that the alkyl substituents on the second cage carbon have a significant impact on the molecular packing, and the incorporation of the o-carboranyl moiety into a π conjugated system can lower both LUMO and HOMO energy levels, converting a typical p-type semiconductor into an ambipolar one.