Dimension Reduction for Covariates in Network Data

Summary A problem of major interest in network data analysis is to explain the strength of connections using context information. To achieve this, we introduce a novel approach named network-supervised dimension reduction by projecting covariates onto low-dimensional spaces for revealing the linkage pattern, without assuming a model.We propose a new loss function for estimating the parameters in the resulting linear projection, based on the notion that closer proximity in the low-dimension projection renders stronger connections. Interestingly, the convergence rate of our estimator is shown to depend on a network effect factor which is the smallest number that can partition a graph in a way similar to the graph coloring problem. Our methodology has interesting connections to principal component analysis and linear discriminant analysis, which we exploit for clustering and community detection. The methodology developed is further illustrated by numerical experiments and the analysis of a pulsar candidates data in astronomy.

Lignins Isolated via Catalyst-free Organosolv Pulping from Miscanthus x giganteus, M. sinensis, M. robustus and M. nagara: A Comparative Study

As a low-input crop, Miscanthus offers numerous advantages that, in addition to agricultural applications, permits its exploitation for energy, fuel, and material production. Depending on the Miscanthus genotype, season, and harvest time as well as plant component (leaf versus stem), correlations between structure and properties of the corresponding isolated lignins differ. Here, a comparative study is presented between lignins isolated from M. x giganteus, M. sinensis, M. robustus and M. nagara using a catalyst-free organosolv pulping process. The lignins from different plant constituents are also compared regarding their similarities and differences regarding monolignol ratio and important linkages. Results showed that the plant genotype has the weakest influence on monolignol content and interunit linkages. In contrast, structural differences are more significant among lignins of different harvest time and/or season. Analyses were performed using fast and simple methods such as nuclear magnetic resonance (NMR) spectroscopy. Data was assigned to four different linkages (A: b-O-4 linkage, B: phenylcoumaran, C: resinol, D: b-unsaturated ester). In conclusion, A content is particularly high in leaf-derived lignins at just under 70 % and significantly lower in stem and mixture lignins at around 60 % and almost 65 %. The second most common linkage pattern is D in all isolated lignins, the proportion of which is also strongly dependent on the crop portion. Both stem and mixture lignins, have a relatively high share of approximately 20 % or more (maximum is M. sinensis Sin2 with over 30 %). In the leaf-derived lignins, the proportions are significantly lower on averageStem samples should be chosen highest possible lignin content is desired, specifically from the M. x giganteus genotype which revealed lignin contents up to 27 %.

Exploiting the Amazing Diversity of Natural Source-Derived Polysaccharides: Modern Procedures of Isolation, Engineering, and Optimization of Antiviral Activities

Naturally occurring polysaccharide sulfates are highly diverse, owning variations in the backbone structure, linkage pattern and stereochemistry, branching diversity, sulfate content and positions of sulfate group(s). These structural characteristics bring about diverse sulfated polymers with dissimilar negative charge densities and structure–activity relationships. Herein, we start with a short discussion of techniques needed for extraction, purification, chemical sulfation, and structural characterization of polysaccharides. Processes of isolation and sulfation of plant-derived polysaccharides are challenging and usually involve two steps. In this context, we describe an integrated extraction-sulfation procedure that produces polysaccharide sulfates from natural products in one step, thereby generating additional pharmacological activities. Finally, we provide examples of the spectrum of natural source-derived polysaccharides possessing specific features of bioactivity, in particular focusing on current aspects of antiviral drug development and drug–target interaction. Thus, the review presents a detailed view on chemically engineered polysaccharides, especially sulfated derivatives, and underlines their promising biomedical perspectives.

Altered linkage pattern of N-glycan sialic acids in pseudomyxoma peritonei

Pseudomyxoma peritonei (PMP) is a highly mucinous adenocarcinoma growing in the peritoneal cavity and most commonly originating from the appendix. Glycans play an important role in carcinogenesis, and glycosylation is altered in malignant diseases, including PMP. We have previously demonstrated that fucosylation of N-glycans is increased in PMP, but we did not observe modulation of overall sialylation. As sialic acids can be attached to the rest of the glycan via α2,3- or α2,6-linkage, we have now analyzed the linkage patterns of sialic acids in tissue specimens of normal appendices, low-grade appendiceal mucinous neoplasms (LAMN), low-grade (LG) PMP and high-grade (HG) PMP. For the linkage analysis, the enzymatically released acidic N-glycans were first treated with ethyl esterification or α2,3-sialidase digestion followed by MALDI-TOF mass spectrometry. Significant increase in the relative abundance of α2,6-sialylated and decrease in α2,3-sialylated N-glycans was observed in PMP tumors as compared to the normal appendices (P < 0.025). More specifically, increased α2,6-sialylation (P < 0.05) and decreased α2,3-sialylation (P < 0.01) were detected in afucosylated and monofucosylated N-glycans of PMPs, whereas the less abundant multifucosylated glycans, containing terminal fucose, demonstrated increased α2,3-sialylation (P < 0.01). Importantly, the increase in α2,6-sialylation was also detected between PMP and the appendiceal precursor lesion LAMN (P < 0.01). The identified glycosylation alterations produce ligands for sialic acid-binding immunoglobulin-like lectins (Siglecs) and sialofucosylated glycans binding selectins, which play a role in the peritoneal dissemination and progression of the disease.

PENELUSURAN KAWASAN ALUN-ALUN BUNDER KOTA MALANG SEBAGAI OPEN SPACE RANCANGAN IR KARSTEN

Title: Searching of Alun-Alun Bunder District in Malang City as Open Space which was Built by Ir Karsten Alun-Alun Bunder plays an important role for city of Malang development during Dutch collonialism. Alun-Alun Bunder was the policy for expanding the second city (Bouwplan II) which had the total size of 15.547 M2. the reason of Alun–Alun Bunder designing was to establish the new administration pivot, this main reason became the basis for the governance at that time (Gemeente) to design the second city expansion (Bouwplan II). This district was named as Gouverneur-Generaalbuurt. The design was realized in 1922. In subsequent, this area was known as „Alun-Alun Bunder”. The research purpose are to know the development pattern of Alun-Alun Bunder, identification of landscape function as the landmark which use as interaction space. Analysis technique which is used in this research, consist of ; diachronic reading, descriptive- evaluation related by linkage pattern and synchronic reading. The result shown that Alun-Alun Bunder is the best city hall model which was desired by Dutch government. The infrastructure, among them are; settlement, education and transportation are designed to follow the role of Alun- Alun Bunder as the core of Dutch administration. The strategy to strengthen the historical value in Alun-Alun Bunder is gained by strengthening the linkage towards historic object which exist inside.

The third moments of the site frequency spectrum

The analysis of patterns of segregating (i.e. polymorphic) sites in aligned sequences is routine in population genetics. Quantities of interest include the total number of segregating sites and the number of sites with mutations of different frequencies, the so-called site frequency spectrum. For neutrally evolving sequences, some classical results are available, including the expected value and variance of the spectrum in the Kingman coalescent model without recombination as calculated by Fu (1995).In this work, we use similar techniques to compute the third moments of the site frequency spectrum without recombination. We also account for the linkage pattern of mutations, yielding the full haplotype spectrum of three polymorphic sites. Based on these results, we derive analytical results for the bias of Tajima’s D and other neutrality tests.As an application, we obtain the second moments of the spectrum of linked sites, which is related to the neutral spectrum of chromosomal inversions and other structural variants. These moments can be used for the normalisation of new neutrality tests relying on these spectra.