Incremental eigenpair computation for graph Laplacian matrices: theory and applications

The smallest eigenvalues and the associated eigenvectors (i.e., eigenpairs) of a graph Laplacian matrix have been widely used for spectral clustering and community detection. However, in real-life applications, the number of clusters or communities (say, K) is generally unknown a priori. Consequently, the majority of the existing methods either choose K heuristically or they repeat the clustering method with different choices of K and accept the best clustering result. The first option, more often, yields suboptimal result, while the second option is computationally expensive. In this work, we propose an incremental method for constructing the eigenspectrum of the graph Laplacian matrix. This method leverages the eigenstructure of graph Laplacian matrix to obtain the Kth smallest eigenpair of the Laplacian matrix given a collection of all previously compute

Neural‑Brane: Neural Bayesian Personalized Ranking for Attributed Network Embedding

Network embedding methodologies, which learn a distributed vector representation for each vertex in a network, have attracted considerable interest in recent years. Existing works have demonstrated that vertex representation learned through an embedding method provides superior performance in many real-world applications, such as node classification, link prediction, and community detection. However, most of the existing methods for network embedding only utilize topological information of a vertex, ignoring a rich set of nodal attributes (such as user profiles of an online social network, or textual contents of a citation network), which is abundant in all real-life networks. A joint network embedding that takes into account both attributional and relational information entails a complete network information and could further enrich the learned vector representations. In this work, we present Neural-Brane, a novel Neural Bayesian Personalized Ranking based Attributed Network Embedding. For a given network, Neural-Brane extracts latent feature representation of its vertices using a designed neural network model that unifies network topological information and nodal attributes. Besides, it utilizes Bayesian personalized ranking objective, which exploits the proximity ordering between a similar node pair and a dissimilar node pair. We evaluate the quality of vertex embedding produced by Neural-Brane by solving the node classification and clustering tasks on four real-world datasets. Experimental results demonstrate the superiority of our proposed method over the state-of-the-art existing methods

Adiponectin gene (ADIPOQ) polymorphisms correlate with the progression of nephropathy in Taiwanese male patients with type 2 diabetes

Aims: Polymorphisms of the ADIPOQ gene were associated with diabetic nephropathy (DN) in case-control studies predominantly among European populations. Gender may modify the ADIPOQ associated risk for DN. We investigated the association of 18 ADIPOQ polymorphisms with DN in a prospective Taiwanese cohort of type 2 diabetes (T2D) and explored whether gender plays a role in this genetic association. Methods: Selected single nucleotide polymorphisms (SNPs) of ADIPOQ were genotyped in 566 T2D patients with normoalbuminuria at baseline. DN was defined based on urinary albumin-to-creatinine ratio (ACR). The Cox proportional hazard model was used to explore the association of individual SNP to DN events under different genetic models over a 6-year follow-up period. Analyses were further stratified by gender. Results: In male patients, the adjusted hazard ratios under the recessive models were 1.81 for rs2241766 TT (vs. GT+GG, 95% CI=1.10-2.96, p=0.019) and 1.89 for rs1063537 CC (vs. CT+TT, 95% CI=1.15-3.11, p=0.013). In the Kaplan-Meier survival curve, males carrying rs2241766 TT (vs. GT+GG, p=0.050) and rs1063537 CC (vs. CT+TT, p=0.037) recessive homozygotes also had a reduced nephropathy-free survival rate. SNPs rs2241767 and rs2082940, both in strong correlation with tag SNP rs1063537 (r≥0.96), were also associated with DN progression in males. In females, ADIPOQ polymorphisms were not associated with the progression of DN. Conclusions: ADIPOQ genetic polymorphisms rs2241766 (+45T>G), rs1063537, rs2241767 and rs2082940 were correlated with the progression of DN in Taiwanese male patients with T2D. The role of gender in this ADIPOQ genetic association needs to be further investigated in other populations

Dietary glycaemic index, glycaemic load and head and neck cancer risk: A pooled analysis in an international consortium

High dietary glycaemic index (GI) and glycaemic load (GL) may increase cancer risk. However, limited information was available on GI and/or GL and head and neck cancer (HNC) risk. We conducted a pooled analysis on 8 case-control studies (4081 HNC cases; 7407 controls) from the International Head and Neck Cancer Epidemiology (INHANCE) consortium. We estimated the odds ratios (ORs) and 95% confidence intervals (CIs) of HNC, and its subsites, from fixed- or mixed-effects logistic models including centre-specific quartiles of GI or GL. GI, but not GL, had a weak positive association with HNC (O

Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina

Gene regulatory networks (GRNs), consisting of transcription factors and their target sites, control neurogenesis and cell-fate specification in the developing central nervous system. In this study, we use integrated single-cell RNA and single-cell ATAC sequencing (scATAC-seq) analysis in developing mouse and human retina to identify multiple interconnected, evolutionarily conserved GRNs composed of cell-type-specific transcription factors that both activate genes within their own network and inhibit genes in other networks. These GRNs control temporal patterning in primary progenitors, regulate transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type. We confirm that NFI transcription factors selectively activate expression of genes promoting late-stage temporal identity in primary retinal progenitors and identify other transcription factors that regulate rod photoreceptor specification in postnatal retina. This study inventories cis- and trans-acting factors that control retinal development and can guide cell-based therapies aimed at replacing retinal neurons lost to disease

Pentaplacodinium saltonense gen. et sp. nov. (Dinophyceae) and its relationship to the cyst-defined genus Operculodinium and yessotoxin-producing Protoceratium reticulatum

Strains of a dinoflagellate from the Salton Sea, previously identified as Protoceratium reticulatum and yessotoxin producing, have been reexamined morphologically and genetically and Pentaplacodinium saltonense n. gen. et sp. is erected to accommodate this species. Pentaplacodinium saltonense differs from Protoceratium reticulatum (Claparède et Lachmann 1859) Bütschli 1885 in the number of precingular plates (five vs. six), cingular displacement (two widths vs. one), and distinct cyst morphology. Incubation experiments (excystment and encystment) show that the resting cyst of Pentaplacodinium saltonense is morphologically most similar to the cyst-defined species Operculodinium israelianum (Rossignol, 1962) Wall (1967) and O. psilatum Wall (1967). Collections of comparative material from around the globe (including Protoceratium reticulatum and the genus Ceratocorys) and single cell PCR were used to clarify molecular phylogenies. Variable regions in the LSU (three new sequences), SSU (12 new sequences) and intergenic ITS 1-2 (14 new sequences) were obtained. These show that Pentaplacodinium saltonense and Protoceratium reticulatum form two distinct clades. Pentaplacodinium saltonense forms a monophyletic clade with several unidentified strains from Malaysia. LSU and SSU rDNA sequences of three species of Ceratocorys (C. armata, C. gourreti, C. horrida) from the Mediterranean and several other unidentified strains from Malaysia form a well-supported sister clade. The unique phylogenetic position of an unidentified strain from Hawaii is also documented and requires further examination. In addition, based on the V9 SSU topology (bootstrap values >80%), specimens from Elands Bay (South Africa), originally described as Gonyaulax grindleyi by Reinecke (1967), cluster with Protoceratium reticulatum. The known range of Pentaplacodinium saltonense is tropical to subtropical, and its cyst is recorded as a fossil in upper Cenozoic sediments. Protoceratium reticulatum and Pentaplacodinium saltonense seem to inhabit different niches: motile stages of these dinoflagellates have not been found in the same plankton sample

Effects of a Mineralized Human Cancellous Bone Allograft in Regeneration of Mandibular Class II Furcation Defects

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141918/1/jper0416.pd