Stream-based active learning for sliding windows under the influence of verification latency

Stream-based active learning (AL) strategies minimize the labeling effort by querying labels that improve the classifier’s performance the most. So far, these strategies neglect the fact that an oracle or expert requires time to provide a queried label. We show that existing AL methods deteriorate or even fail under the influence of such verification latency. The problem with these methods is that they estimate a label’s utility on the currently available labeled data. However, when this label would arrive, some of the current data may have gotten outdated and new labels have arrived. In this article, we propose to simulate the available data at the time when the label would arrive. Therefore, our method Forgetting and Simulating (FS) forgets outdated information and simulates the delayed labels to get more realistic utility estimates. We assume to know the label’s arrival date a priori and the classifier’s training data to be bounded by a sliding window. Our extensive experiments show that FS improves stream-based AL strategies in settings with both, constant and variable verification latency

ACARORUM CATALOGUS IX. Acariformes, Acaridida, Schizoglyphoidea (Schizoglyphidae), Histiostomatoidea (Histiostomatidae, Guanolichidae), Canestrinioidea (Canestriniidae, Chetochelacaridae, Lophonotacaridae, Heterocoptidae), Hemisarcoptoidea (Chaetodactylidae, Hyadesiidae, Algophagidae, Hemisarcoptidae, Carpoglyphidae, Winterschmidtiidae)

The 9th volume of the series Acarorum Catalogus contains lists of mites of 13 families, 225 genera and 1268 species of the superfamilies Schizoglyphoidea, Histiostomatoidea, Canestrinioidea and Hemisarcoptoidea. Most of these mites live on insects or other animals (as parasites, phoretic or commensals), some inhabit rotten plant material, dung or fungi. Mites of the families Chetochelacaridae and Lophonotacaridae are specialised to live with Myriapods (Diplopoda). The peculiar aquatic or intertidal mites of the families Hyadesidae and Algophagidae are also included.Publishe

An investigation of computer based nominal data record linkage

The Internet now provides access to vast volumes of nominal data (data associated with names e. g. birth/death records, parish records, text articles, multimedia) collected for a range of different purposes. This research focuses on parish registers containing baptism, marriage, and burial records. Mining these data resources involves linkage investigating as to how two records are related with regards to attributes like surname, spatio-temporal location, legal association and inter-relationships. Furthermore, as well as handling the implicit constraints of nominal data, such a system must also be able to handle automatically a range of temporal and spatial rules and constraints. The research examines the linkage rules that apply and how such rules interact. In this investigation a report is given of the current practices in several disciplines (e. g. history, demography, genealogy, and epidemiology) and how these are implemented in current computer and database systems. The practical aspects of this study, and the workbench approach proposed are centred on the extensive Lancashire & Cheshire Parish Register archive held on the MIMAS database computer located at Manchester University. The research also proposes how these findings can have wider applications. This thesis describes some initial research into this problem. It describes three prototypes of nominal data workbench that allow the specification and examination of several linkage types and discusses the merits of alternative name matching methods, name grouping techniques and method comparisons. The conclusion is that in the cases examined so far, effective nominal data linkage is essentially a query optimisation process. The process is made more efficient if linkage specific indexes exist, and suggests that query re-organization based on these indexes, though a complex process, is entirely feasible. To facilitate the use of indexes and to guide the optimization process, the work suggests the use of formal ontologies

Reproductive Isolation, in Individuals and During Evolution, as Result of Gross Genomic Rearrangement in Pigs, Birds and Dinosaurs

Chromosomal (karyotypic) analysis in animals is performed for three primary reasons: to diagnose genetic disease; to map genes to their place in the genome and to retrace evolutionary events by cross species comparison. Technology for analysis has progressed from chromosome banding (cytogenetics), to fluorescence in-situ hybridisation (FISH - molecular cytogenetics) through to microarrays and ultimately whole genome sequence analysis (cytogenomics or chromonomics). Indeed, the past 10-15 years has seen a revolution in whole genome sequencing, first with the human genome project, followed by those of key model and agricultural species and, more recently, ~60 de novo avian genome assemblies. Whole genome analysis provides detailed insight into the biology of chromosome rearrangements that occur both in individuals (for diagnostic purposes) and at an evolutionary level. It permits the study of gene mapping, trait linkage, phylogenomics, and gross genomic organisation and change. An essential pre-requisite however is an unbroken length of contiguous DNA sequence along the length of each chromosome. Most recent de novo genome assemblies fall short of this level of resolution producing lengths of contiguous sequence that are sub-chromosomal in size (scaffolds). Chromosome rearrangements can affect reproductive capability at an individual level (causing reduced fertility) and at a population level leading to reproductive isolation and subsequent speciation. The purpose of this thesis was to implement a step change in the combination of FISH technology with genome sequence data to provide greater insight into the nature of chromosomal rearrangement at an individual and evolutionary level. It therefore had four specific aims: The first was to isolate sub-telomeric sequences from the pig, cattle and chicken genome assemblies to develop a tool for the rapid screening of chromosome rearrangements. Now routinely used for porcine translocation screening (and in the future bovine screening), development work revealed serious integrity errors in the pig genome. The second aim was to isolate evolutionary conserved sequences from avian chromosomes to create a means of screening for macro-and microchromosomal rearrangements in birds. Results confirmed the hypothesis that microchromosomal rearrangements were rare in birds, except for previously known whole chromosomal fusions. The third was to use the above tools to complete scaffold based genome assemblies in two key avian species - the peregrine falcon and the pigeon. Finally, bioinformatic tools were used to infer the overall genome structure of hypothetical saurian and avian ancestors. Retracing of the evolutionary changes that occurred up until the emergence of birds allowed an assessment of chromosome evolution along the saurischia-maniraptora- avialae lineage. Analysis of evolutionary breakpoint regions (EBRs) allowed testing of the hypothesis that the ontology of genes within EBRs corresponded to measurable phenotypic change in the lineage under investigation. An enrichment of genes associated with body height corresponded to rapid size change in the dinosaur linage that led to modern birds. Taken together, these results paint a picture of a genome that, from about 260 million years ago formed a 'signature' highly successful avian-dinosaur karyotype that remained largely unchanged interchromosomally to the present day. These results represent significant insight into amniote genomic organization with the added benefit of developing tools that are widely applicable and transferrable for commercial animal breeding, for constructing de novo genome assemblies and for reconstructing, by inference, the overall genomic structure and evolution of extinct animals

Yersinia pestis genomes of the first and second plague pandemic recovered from ancient DNA

Epidemic infectious diseases have shaped human history, but studies on the history of diseases were in the past limited to indirect evidence due to the elusiveness of the causative agents. This has fundamentally changed through the emergence of ancient pathogen genomics which allows us to reconstruct genomes of microorganisms from ancient DNA. This dissertation focuses on Yersinia pestis, responsible for at least two historical pandemics. The first paper presents eight Y. pestis genomes of the First Pandemic (541–750) covering at least the first century of this pandemic. The results suggest that the Justinianic Plague (541–544) already reached the British Isles, show that the causative lineage diversified early during the pandemic in multiple strains, and give indications for its persistence in Europe or close-by. A deletion discovered in the youngest strains might hold clues for ecological adaptations. The second paper presents 34 genomes of the Second Pandemic (1346–18th c.), recovered from ten sites dating to the 14th-17th c. A genome from Russia testifies the initial entry through East Europe, the low diversity during the Black Death (1346–1353) shows a rapid spread. The close relationship of all Second Pandemic strains suggests a local persistence and diversification. A deletion in one clade similar to the one detected in the first paper, coinciding with an accelerated substitution rate, could be interpreted as convergent evolution. The third paper challenges previous claims in a recently published paper about the origin of the Justinianic Plague through a reanalysis of the two presented genomes. The phylogenetic analysis of one sample suggests rather an identification as a strain potentially basal to the Black Death. The essay gives a short introduction on the history of plague research and a comprehensive overview of the recent discoveries of archaeogenetic studies, including insights into the evolution of the bacterium enabled by prehistoric plague genomes.Durch die Geschichte hindurch hatten Infektionskrankheiten und Epidemien einen prägenden Einfluss auf Populationen, Gesellschaften, Mentalitäten und unsere Umwelt. Die Seuchengeschichte war in der Vergangenheit jedoch weitgehend auf indirekte Zeugnisse beschränkt, da die Erreger schwer greifbar sind. Dies hat sich jüngst durch die Entwicklung der ‚Paläopathogenomik‘ aus der Paläogenetik fundamental verändert. Diese Methodik erlaubt die Rekonstruktion von bakteriellen, viralen und Protozoen-Genomen aus alter DNA, gewonnen aus menschlichen Überresten. Diese Dissertation widmet sich Yersinia pestis, dem Erreger der Beulenpest, verantwortlich für mindestens zwei historische Pandemien: Die Erste Pandemie (541–750), die mit der Justinianischen Pest im Mittelmeerraum begann, und der Zweiten Pandemie, die nach dem berüchtigten Schwarzen Tod (1346–1353) für mehr als 400 Jahre in Europa wütete. Frühere Studien konnten bereits Y. pestisals Erreger beider Pandemien identifizieren, ließen jedoch viele Fragen offen, die hier in drei Studien, einem Essay und der abschließenden Diskussion angesprochen werden sollen. Die erste Studie stellt acht Y.-pestis-Genome der Ersten Pandemie von Fundorten in Deutschland, England, Frankreich und Spanien vor, die zumindest das erste Jahrhundert dieser Pandemie abdecken. Die Ergebnisse legen nahe, dass bereits die Justinianische Pest (541-544) die Britischen Inseln erreicht hat, dass der verantwortliche Stamm bereits im frühen Stadium der Pandemie diversifizierte, und dass die Pest möglicherweise in Europa oder benachbarten Regionen überdauerte. Eine Deletion in den jüngsten Stämmen könnte auf eine ökologische Anpassung hindeuten. Die zweite Studie bietet neue Einblicke in den Beginn und Verlauf der zweiten Pandemie durch 34 alte Genome aus Deutschland, England, Frankreich, Russland und der Schweiz, datiert auf das 14.–17. Jh. Ein Genom aus Russland bezeugt den Eintrag der Pest über Osteuropa, die geringe Diversität während des Schwarzen Todes eine rasante Ausbreitung. Die enge Verwandtschaft aller Stämme der Zweiten Pandemie deutet an, dass der Erreger lokal überdauerte und diversifizierte. In einer Klade wurde neben einer erhöhten Substitutionsrate eine Deletion ähnlich jener der ersten Studie beobachtet, was möglicherweise als konvergente Evolution interpretiert werden kann. Die dritte Studie ficht die Behauptungen einer kürzlich publizierten Studie zum Ursprung der Justinianischen Pest durch eine Neuanalyse der vorgestellten Genome an. Die phylogenetische Analyse eines der Genome zeigt vielmehr, dass es basal zum Schwarzen Tod fallen könnte. Der Essay bietet einen kurzen Abriss zur Geschichte der Pestforschung und eine umfassende Übersicht über die neuesten Entdeckungen der Archäogenetik, darunter auch die Einblicke in die Evolution des Erregers, die durch prähistorische Pestgenome gewonnen wurden. Im letzten Teil werden die Ergebnisse der Studien vergleichend und in einem weiteren Rahmen unter drei Schwerpunkten – methodische Herausforderungen, Ursprünge der beiden Pandemien sowie Verlauf und Persistenz – diskutiert, mit einem kritischen Blick auf die Grenzen des archäogenetischen Ansatzes und einem Ausblick auf zukünftige Forschungsfelder