On the Theory of Computation and Evolutionary Distances

Reprinted with permission. Society for Industrial and Applied Mathematics SIAM J. Appl. Math, 1974: 26 (4), 787-793 http://epubs.siam.org/doi/10.1137/0126070https://digitalcommons.rockefeller.edu/peter-sellers-memoriam/1003/thumbnail.jp

Computational Techniques in Multispectral Image Processing : Application to the Syriac Galen Palimpsest

Multispectral and hyperspectral image analysis has experienced much development in the last decade. The application of these methods to palimpsests has produced significant results, enabling researchers to recover texts that would be otherwise lost under the visible overtext, by improving the contrast between the undertext and the overtext. In this paper we explore an extended number of multispectral and hyperspectral image analysis methods, consisting of supervised and unsupervised dimensionality reduction techniques, on a part of the Syriac Galen Palimpsest dataset (www.digitalgalen.net). Of this extended set of methods, eight methods gave good results: three were supervised methods Generalized Discriminant Analysis (GDA), Linear Discriminant Analysis (LDA), and Neighborhood Component Analysis (NCA); and the other five methods were unsupervised methods (but still used in a supervised way) Gaussian Process Latent Variable Model (GPLVM), Isomap, Landmark Isomap, Principal Component Analysis (PCA), and Probabilistic Principal Component Analysis (PPCA). The relative success of these methods was determined visually, using color pictures, on the basis of whether the undertext was distinguishable from the overtext, resulting in the following ranking of the methods: LDA, NCA, GDA, Isomap, Landmark Isomap, PPCA, PCA, and GPLVM. These results were compared with those obtained using the Canonical Variates Analysis (CVA) method on the same dataset, which showed remarkably accuracy (LDA is a particular case of CVA where the objects are classified to two classes).Comment: 29 February - 2 March 2016, Second International Conference on Natural Sciences and Technology in Manuscript Analysis, Centre for the study of Manuscript Cultures, Hamburg, German

The Syriac Galen Palimpsest::Research Methods and Latest Discoveries

In this article, we provide an update on the progress of the AHRC-funded Syriac Galen Palimpsest Project, which is directed by Peter E. Pormann at the University of Manchester. We also present a newly identified folio from Book 3 of Galen’s On Simple Drugs—a book hitherto not known to be represented in the manuscript. We offer some preliminary conclusions about the original medical manuscript’s codicological structure, particularly the composition of its quires and the sequence of hair and flesh sides of parchment. Finally, we outline our approach to analysing the undertext’s palaeography, with reference to the methodology devised by Ayda Kaplan

Analyzing Images, Editing Texts: The Manchester Project

This article discusses the methodologies and tools employed in the study of the Syriac Galen Palimpsest. While it focusses on the efforts of the ongoing Manchester Project, attention is also paid to earlier and contemporary work, particularly the most recent phase of research (which can be said to have started in 2009). In this way, the Manchester Project is properly contextualised. We describe the image analysis techniques employed by the Manchester team. The challenge is to reduce the information contained in the set of multi-spectral images and enhance it where it can usefully distinguish between undertext and overtext. One can either use unsupervised or supervised dimensional reduction techniques. An unsupervised method such as principle component analysis (PCA) provides an automatic result, whereas a supervised method such as Canonical Variates Analysis (CVA) requires one to teach the system by identifying blank areas, areas with only overtext, areas with only undertext, and areas with both. Using the resulting improvements to the visibility of the undertext, the Manchester team has been able to make significant advances in identifying where its folios fit into Galen’s Book of Simple Drugs. The use of a program called SketchEngine is outlined, which permits an engagement with parallel Greek and Syriac texts and powerful searches - this is particularly useful for those folios that come from Books 6–8, for which a parallel Syriac manuscript exists. Having completed this initial stage, it became clear that around 100 folios that did not come from Books 6-8 remained to be identified. SketchEngine again has proved to be very useful in facilitating identifications of these folios. To illustrate the different challenges posed by these two distinct scenarios, examples are provided from Books 5 and 8

The Syriac Galen Palimpsest: A Tale of Two Texts

This article presents the Syriac Galen Palimpsest’s double history, of both the original manuscript and its subsequent reuse. The original medical manuscript contained Galen’s Book of Simple Drugs in Syriac translation, was probably produced in northern Mesopotamia or western Syria, and dates to the first half of the ninth century. After only two centuries, it was erased and reused to produce a liturgical text called Octṓēchos, probably at the monastery of Saint Elias on the Black Mountain. This palimpsest was later transferred to Saint Catherine’s monastery in the Sinai, where it remained for several centuries before being offered for sale in Leipzig in 1922 (perhaps due to the activities of Friedrich Grote). We pay close attention to the context, contents, codicology and palaeography of both the original manuscript and the palimpsest. We also contextualise both texts within the wider story of their transmission. Through the skeleton table we present the latest results of our almost complete identification of the undertext. We reconstruct the structure of the original codex through a collation diagram. We draw palaeographical parallels with a dated colophon of the well-known Sahdona-manuscript. This permits us to narrow done the time and place of production of the original manuscript

DNA metabarcoding reveals the dietary profiles of a benthic marine crustacean,Nephrops norvegicus

Norwegian lobster, Nephrops norvegicus, are a generalist scavenger and predator capable of short foraging excursions but can also suspension feed. Existing knowledge about their diet relies on a combination of methods including morphology-based stomach content analysis and stable isotopes, which often lack the resolution to distinguish prey items to species level particularly in species that thoroughly masticate their prey. DNA metabarcoding overcomes many of the challenges associated with traditional methods and it is an attractive approach to study the dietary profiles of animals. Here, we present the diet of the commercially valuable Nephrops norvegicus using DNA metabarcoding of gut contents. Despite difficulties associated with host amplification, our cytochrome oxidase I (COI) molecular assay successfully achieves higher resolution information than traditional approaches. We detected taxa that were likely consumed during different feeding strategies. Dinoflagellata, Chlorophyta and Bacillariophyta accounted for almost 50% of the prey items consumed, and are associated with suspension feeding, while fish with high fisheries discard rates were detected which are linked to active foraging. In addition, we were able to characterise biodiversity patterns by considering Nephrops as natural samplers, as well as detecting parasitic dinoflagellates (e.g., Hematodinium sp.), which are known to influence burrow related behaviour in infected individuals in over 50% of the samples. The metabarcoding data presented here greatly enhances a better understanding of a species’ ecological role and could be applied as a routine procedure in future studies for proper consideration in the management and decision-making of fisheries

Brazil Basin Tracer Release Experiment

The purpose of the Brazil Basin Tracer Release Experiment is to measure diapycnal (across isopycnal) mixing and epipycnal (along-isopycnal) mixing and stirring in the deep ocean. This cruise is the fourth in the overall experiment. In the first cruise in early 1996, 110 kg of sulfur hexafluoride (SF6) were released on an isopycnal surface near 4000 meters depth in the eastern part of the basin on the flanks of the Mid-Atlantic Ridge (MAR). The location of the release was near 21.7 S, 18.4 W. The release site was over a zonal valley that leads to the MAR and is about 5000 m deep. The isopycnal surface of the release was defined as the surface on which the potential density anomaly, referenced to 4000 dbar pressure, was 45.9408 kg/m3. The release streaks and results of initial sampling in 1996 are described in Polzin et al. [1997]

Myo4p is a monomeric myosin with motility uniquely adapted to transport mRNA

The yeast Saccharomyces cerevisiae uses two class V myosins to transport cellular material into the bud: Myo2p moves secretory vesicles and organelles, whereas Myo4p transports mRNA. To understand how Myo2p and Myo4p are adapted to transport physically distinct cargos, we characterize Myo2p and Myo4p in yeast extracts, purify active Myo2p and Myo4p from yeast lysates, and analyze their motility. We find several striking differences between Myo2p and Myo4p. First, Myo2p forms a dimer, whereas Myo4p is a monomer. Second, Myo4p generates higher actin filament velocity at lower motor density. Third, single molecules of Myo2p are weakly processive, whereas individual Myo4p motors are nonprocessive. Finally, Myo4p self-assembles into multi-motor complexes capable of processive motility. We show that the unique motility of Myo4p is not due to its motor domain and that the motor domain of Myo2p can transport ASH1 mRNA in vivo. Our results suggest that the oligomeric state of Myo4p is important for its motility and ability to transport mRNA

The prepower stroke conformation of myosin V

eW have used electron microscopy and single-particle image processing to study head conformation in myosin V molecules. We find that in the presence of ATP, many heads have a sharply angled conformation that is rare in its absence. The sharply angled conformation is similar to a myosin II atomic structure proposed to mimic the prepower stroke state. The leading head in molecules attached to actin by both heads has a similar conformation, but is also sharply angled in a second plane by tethering through the trail head. The lead head lever joins the motor domain ∼5 nm axially from where it joins the trail motor. These positions locate the converter subdomain and show the lead motor is in the prepower stroke conformation. Tethering by the trail head places the lead head motor domain at the correct axial position along the actin for binding, but at the wrong orientation. Attachment is achieved either by bending the lead head lever throughout its length or at the pliant point. The microscopy shows that most of the walking stride is produced by changes in lever angle brought about by converter movement, but is augmented by distortion produced by thermal energy