Multilevel Hierarchical Kernel Spectral Clustering for Real-Life Large Scale Complex Networks

Kernel spectral clustering corresponds to a weighted kernel principal component analysis problem in a constrained optimization framework. The primal formulation leads to an eigen-decomposition of a centered Laplacian matrix at the dual level. The dual formulation allows to build a model on a representative subgraph of the large scale network in the training phase and the model parameters are estimated in the validation stage. The KSC model has a powerful out-of-sample extension property which allows cluster affiliation for the unseen nodes of the big data network. In this paper we exploit the structure of the projections in the eigenspace during the validation stage to automatically determine a set of increasing distance thresholds. We use these distance thresholds in the test phase to obtain multiple levels of hierarchy for the large scale network. The hierarchical structure in the network is determined in a bottom-up fashion. We empirically showcase that real-world networks have multilevel hierarchical organization which cannot be detected efficiently by several state-of-the-art large scale hierarchical community detection techniques like the Louvain, OSLOM and Infomap methods. We show a major advantage our proposed approach i.e. the ability to locate good quality clusters at both the coarser and finer levels of hierarchy using internal cluster quality metrics on 7 real-life networks.Comment: PLOS ONE, Vol 9, Issue 6, June 201

Kernel Spectral Clustering and applications

In this chapter we review the main literature related to kernel spectral clustering (KSC), an approach to clustering cast within a kernel-based optimization setting. KSC represents a least-squares support vector machine based formulation of spectral clustering described by a weighted kernel PCA objective. Just as in the classifier case, the binary clustering model is expressed by a hyperplane in a high dimensional space induced by a kernel. In addition, the multi-way clustering can be obtained by combining a set of binary decision functions via an Error Correcting Output Codes (ECOC) encoding scheme. Because of its model-based nature, the KSC method encompasses three main steps: training, validation, testing. In the validation stage model selection is performed to obtain tuning parameters, like the number of clusters present in the data. This is a major advantage compared to classical spectral clustering where the determination of the clustering parameters is unclear and relies on heuristics. Once a KSC model is trained on a small subset of the entire data, it is able to generalize well to unseen test points. Beyond the basic formulation, sparse KSC algorithms based on the Incomplete Cholesky Decomposition (ICD) and $L_0$, $L_1, L_0 + L_1$, Group Lasso regularization are reviewed. In that respect, we show how it is possible to handle large scale data. Also, two possible ways to perform hierarchical clustering and a soft clustering method are presented. Finally, real-world applications such as image segmentation, power load time-series clustering, document clustering and big data learning are considered.Comment: chapter contribution to the book "Unsupervised Learning Algorithms

Water Masses Variability in Inner Kongsfjorden (Svalbard) During 2010–2020

Kongsfjorden is an Arctic fjord located in the Svalbard archipelago. Its hydrography is influenced by the warm and saline Atlantic Water (AW) in the West Spitsbergen Current and the cold and fresh Polar Water circulating on the shelf. We assess the so-called atlantification of Kongsfjorden in the 2010–2020 decade by inspecting modifications in water properties and water masses variability through moored data and summer CTD surveys. Atlantification in this fjord has emerged as an increasing temperature and salinity, resulting from enhanced advection of Atlantic waters from the West Spitsbergen Current. The water column in inner Kongsfjorden warmed by 0.13°C/yr at 35 m and 0.06°C/yr at 85 m depth from 2010 to 2020, while salinity increased by 0.3 PSU. Depth-averaged temperatures have increased by 0.26°C/yr in the warmest months of the year, whereas they appear relatively stable in the coldest months. Both temperature and salinity present a linear regression change point in January 2017, with latter years featuring decreasing values. Highly diluted AW is found at the beginning of the decade, which give way to more and more pure AW in latter years, culminating in extensive intrusions in 2016 and 2017 determining the warmest and saltiest conditions over the decade in inner Kongsfjorden. Observations in the 2010–2020 decade confirm that Kongsfjorden has transitioned to an Atlantic-type fjord, featuring depleted sea ice conditions and rather regular shallow intrusions of AW in summer and frequently also in winter. Although single intrusions of AW are associated with dynamical events on the shelf, we found that the long-term temperature evolution in the inner Kongsfjord is consistent with the meridional temperature transport of the West Spitsbergen Current. The AW current flowing northward from lower latitudes along the western Svalbard archipelago thus has profoundly driven local conditions in the inner fjord in this decade

Immunodepletion in xenotransplantation

Xenograft transplantation is perhaps the most immunologically difficult problem in transplantation today. An overwhelming hyperacute rejection reaction (HAR) occurs within minutes of organ implantation. Preformed antibodies are thought to initiate this process. We used a pig-to-dog renal xenograft transplant model and investigated methods of decreasing the severity of hyperacute rejection. Female pigs weighing 15-20 kg were used as donors. Recipients were mongrel dogs weighing 15-25 kg. Experimental dogs were all given a number of treatments of IgG depletion using an antibody removal system (Dupont-Excorim). This machine immunoadsorbs plasma against a column containing immobilized staphylococcal protein A, which is known to bind the IgG Fc receptor. An 84% reduction in the IgG levels and a 71% reduction in IgM levels was achieved. Postoperative assessment was made of urine output, time to onset of HAR, and histopathological examination of the rejected kidneys. Although cross-matches between donor lymphocytes and recipient sera remained strongly positive in the treated dogs, there was a two- to fourfold reduction in the titers. The time to onset of HAR was prolonged in the experimental group, and the urine output was increased slightly. The histopathologic changes in the experimental group generally showed signs of HAR, but of less intensity than in the nonimmunodepleted control group. © 1990 Informa UK Ltd All rights reserved: reproduction in whole or part not permitted

Late Holocene sedimentation in coastal areas of the northwestern Ross Sea (Antarctica).

Sediment cores and box cores collected in two coastal areas of the northwestern Ross Sea (Antarctica) highlight the possibility of studying the Late Holocene period in detail. In this work we propose a study on two box cores and two gravity cores collected in the Cape Hallett and Wood Bay areas during the 2005 PNRA oceanographic cruise. The two sites are feed by Eastern Antarctic Ice Shelf (EAIS) and previous studies have highlighted a complex postglacial sedimentary sequence, also influenced by local morphology. This study is performed within the framework of the PNRA-ESF PolarCLIMATE HOLOCLIP (Holocene climate variability at high-southern latitudes: an integrated perspective) Project. The data set includes: magnetic susceptibility, X-ray analyses, 210Pb, 14C dating, diatoms and foraminifera assemblages, organic carbon, and grain-size analyses. Furthermore XRF core scanner analyses, colour analysis from digital images, and major, minor and trace element concentration analyses (ICP-AES) are performed. Data show that the box core and upper core sediments represent a very recent sedimentation in which it is possible to observe the parameter variability probably linked to climate variability/changes: these variation will be compared with isotopic record form ice cores collected form the same Antarctic sector

Zircon ages in granulite facies rocks: decoupling from geochemistry above 850 °C?

Granulite facies rocks frequently show a large spread in their zircon ages, the interpretation of which raises questions: Has the isotopic system been disturbed? By what process(es) and conditions did the alteration occur? Can the dates be regarded as real ages, reflecting several growth episodes? Furthermore, under some circumstances of (ultra-)high-temperature metamorphism, decoupling of zircon U–Pb dates from their trace element geochemistry has been reported. Understanding these processes is crucial to help interpret such dates in the context of the P–T history. Our study presents evidence for decoupling in zircon from the highest grade metapelites (> 850 °C) taken along a continuous high-temperature metamorphic field gradient in the Ivrea Zone (NW Italy). These rocks represent a well-characterised segment of Permian lower continental crust with a protracted high-temperature history. Cathodoluminescence images reveal that zircons in the mid-amphibolite facies preserve mainly detrital cores with narrow overgrowths. In the upper amphibolite and granulite facies, preserved detrital cores decrease and metamorphic zircon increases in quantity. Across all samples we document a sequence of four rim generations based on textures. U–Pb dates, Th/U ratios and Ti-in-zircon concentrations show an essentially continuous evolution with increasing metamorphic grade, except in the samples from the granulite facies, which display significant scatter in age and chemistry. We associate the observed decoupling of zircon systematics in high-grade non-metamict zircon with disturbance processes related to differences in behaviour of non-formula elements (i.e. Pb, Th, U, Ti) at high-temperature conditions, notably differences in compatibility within the crystal structure

How a Diverse Research Ecosystem Has Generated New Rehabilitation Technologies: Review of NIDILRR’s Rehabilitation Engineering Research Centers

Over 50 million United States citizens (1 in 6 people in the US) have a developmental, acquired, or degenerative disability. The average US citizen can expect to live 20% of his or her life with a disability. Rehabilitation technologies play a major role in improving the quality of life for people with a disability, yet widespread and highly challenging needs remain. Within the US, a major effort aimed at the creation and evaluation of rehabilitation technology has been the Rehabilitation Engineering Research Centers (RERCs) sponsored by the National Institute on Disability, Independent Living, and Rehabilitation Research. As envisioned at their conception by a panel of the National Academy of Science in 1970, these centers were intended to take a “total approach to rehabilitation”, combining medicine, engineering, and related science, to improve the quality of life of individuals with a disability. Here, we review the scope, achievements, and ongoing projects of an unbiased sample of 19 currently active or recently terminated RERCs. Specifically, for each center, we briefly explain the needs it targets, summarize key historical advances, identify emerging innovations, and consider future directions. Our assessment from this review is that the RERC program indeed involves a multidisciplinary approach, with 36 professional fields involved, although 70% of research and development staff are in engineering fields, 23% in clinical fields, and only 7% in basic science fields; significantly, 11% of the professional staff have a disability related to their research. We observe that the RERC program has substantially diversified the scope of its work since the 1970’s, addressing more types of disabilities using more technologies, and, in particular, often now focusing on information technologies. RERC work also now often views users as integrated into an interdependent society through technologies that both people with and without disabilities co-use (such as the internet, wireless communication, and architecture). In addition, RERC research has evolved to view users as able at improving outcomes through learning, exercise, and plasticity (rather than being static), which can be optimally timed. We provide examples of rehabilitation technology innovation produced by the RERCs that illustrate this increasingly diversifying scope and evolving perspective. We conclude by discussing growth opportunities and possible future directions of the RERC program

Nanostring-based multigene assay to predict recurrence for gastric cancer patients after surgery

10.1371/journal.pone.0090133PLoS ONE93-POLN

Detection of collagen triple helix repeat containing-1 and nuclear factor (erythroid-derived 2)-like 3 in colorectal cancer

<p>Abstract</p> <p>Background</p> <p>Collagen Triple Helix Repeat Containing-1 (CTHRC1) and Nuclear factor (erythroid-derived 2)-like 3 (NFE2L3) may be useful biomarker candidates for the diagnosis of colorectal cancer (CRC) since they have shown an increase messenger RNA transcripts (mRNA) expression level in adenomas and colorectal tumours when compared to normal tissues.</p> <p>Methods</p> <p>To evaluate CTHRC1 and NFE2L3 as cancer biomarkers, it was generated and characterised several novel specific polyclonal antibodies (PAb), monoclonal antibodies (MAbs) and soluble Fab fragments (sFabs) against recombinant CTHRC1 and NFE2L3 proteins, which were obtained from different sources, including a human antibody library and immunised animals. The antibodies and Fab fragments were tested for recognition of native CTHRC1 and NFE2L3 proteins by immunoblotting analysis and enzyme-linked immunosorbent assay (ELISA) in colorectal cell lines derived from tumour and cancer tissues.</p> <p>Results</p> <p>Both, antibodies and a Fab fragment showed high specificity since they recognised only their corresponding recombinant antigens, but not a panel of different unrelated- and related proteins.</p> <p>In Western blot analysis of CTHRC1, a monoclonal antibody designated CH21D7 was able to detect a band of the apparent molecular weight of a full-length CTHRC1 in the human colon adenocarcinoma cell line HT29. This result was confirmed by a double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) with the monoclonal antibodies CH21D7 and CH24G2, detecting CTHRC1 in HT29 and in the colon adenocarcinoma cell line SW620.</p> <p>Similar experiments were performed with PAb, MAbs, and sFab against NFE2L3. The immunoblot analysis showed that the monoclonal antibody 41HF8 recognised NFE2L3 in HT29, and leukocytes. These results were verified by DAS-ELISA assay using the pairs PAb/sFab E5 and MAb 41HF8/sFab E5.</p> <p>Furthermore, an immunoassay for simultaneous detection of the two cancer biomarkers was developed using a Dissociation-Enhanced Lanthanide Fluorescent Immunoassay technology (DELFIA).</p> <p>Conclusions</p> <p>In conclusion, the antibodies obtained in this study are specific for CTHRC1 and NFE2L3 since they do not cross-react with unrelated- and related proteins and are useful for specific measurement of native CTHRC1 and NFE2L3 proteins. The antibodies and immunoassays may be useful for the analysis of CTHRC1 and NFE2L3 in clinical samples and for screening of therapeutic compounds in CRC.</p