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

The Identity of \u3cem\u3eZachaenus roseus\u3c/em\u3e Cope, 1890 (Anura: \u3cem\u3eSpecies Inquirenda\u3c/em\u3e)

Zachaenus roseus Cope, 1890, has puzzled systematists working in southern South America. A single individual, the holotype, has ever been collected and this specimen is in extremely poor preservation condition. Herein, the precise location of the type locality of Z. roseus is determined based on a historical review of the literature. Furthermore, following a careful comparison with all species that inhabit the southern austral forest, and that could potentially correspond to Zachaenus roseus, we conclude that this taxon is placed in the synonymy of Eupsophus calcaratus (Günther, 1881

The identity of Zachaenus roseus Cope, 1890 (Anura: species inquirenda)

Zachaenus roseus Cope, 1890, has puzzled systematists working in southern South America. A single individual, the holotype, has ever been collected and this specimen is in extremely poor preservation condition. Herein, the precise location of the type locality of Z. roseus is determined based on a historical review of the literature. Furthermore, following a careful comparison with all species that inhabit the southern austral forest, and that could potentially correspond to Zachaenus roseus, we conclude that this taxon is placed in the synonym of Eupsophus calcaratus (Günther, 1881).Fil: Lavilla, Esteban Orlando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina. Fundación Miguel Lillo; ArgentinaFil: Nuñez, J. J.. Universidad Austral de Chile; ChileFil: Rabanal, F. E.. Universidad Austral de Chhile; ChileFil: Langone, José A.. Museo Nacional de Historia Natural; UruguayFil: de Sá, Rafael O.. University of Richmon; Estados Unido

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

Reconstructing Bioinvasion Dynamics Through Micropaleontologic Analysis Highlights the Role of Temperature Change as a Driver of Alien Foraminifera Invasion

Invasive alien species threaten biodiversity and ecosystem structure and functioning, but incomplete assessments of their origins and temporal trends impair our ability to understand the relative importance of different factors driving invasion success. Continuous time-series are needed to assess invasion dynamics, but such data are usually difficult to obtain, especially in the case of small-sized taxa that may remain undetected for several decades. In this study, we show how micropaleontologic analysis of sedimentary cores coupled with radiometric dating can be used to date the first arrival and to reconstruct temporal trends of foraminiferal species, focusing on the alien Amphistegina lobifera and its cryptogenic congener A. lessonii in the Maltese Islands. Our results show that the two species had reached the Central Mediterranean Sea several decades earlier than reported in the literature, with considerable implications for all previous hypotheses of their spreading patterns and rates. By relating the population dynamics of the two foraminifera with trends in sea surface temperature, we document a strong relationship between sea warming and population outbreaks of both species. We conclude that the micropaleontologic approach is a reliable procedure for reconstructing the bioinvasion dynamics of taxa having mineralized remains, and can be added to the toolkit for studying invasions

Identification of Plasmodium falciparum var1CSA and var2CSA domains that bind IgM natural antibodies

Malaria in pregnancy is responsible for maternal anaemia, low-birth-weight babies and infant deaths. Plasmodium falciparum infected erythrocytes are thought to cause placental pathology by adhering to host receptors such as chondroitin sulphate A (CSA). CSA binding infected erythrocytes also bind IgM natural antibodies from normal human serum, a process that may facilitate placental adhesion or promote immune evasion. The parasite ligands that mediate placental adhesion are thought to be members of the variant erythrocyte surface antigen family P. falciparum erythrocyte membrane protein 1 (PfEMP1), encoded by the var genes. Two var gene sub-families, var1CSA and var2CSA, have been identified as parasite CSA binding ligands and are leading candidates for a vaccine to prevent pregnancy-associated malaria. We investigated whether these two var gene subfamilies implicated in CSA binding are also the molecules responsible for IgM natural antibody binding. By heterologous expression of domains in COS-7 cells, we found that both var1CSA and var2CSA PfEMP1 variants bound IgM, and in both cases the binding region was a DBL epsilon domain occurring proximal to the membrane. None of the domains from a control non-IgM-binding parasite (R29) bound IgM when expressed in COS-7 cells. These results show that PfEMP1 is a parasite ligand for non-immune IgM and are the first demonstration of a specific adhesive function for PfEMP1 epsilon type domains