Applying an edit distance to the matching of tree ring sequences in dendrochronology

AbstractIn dendrochronology wood samples are dated according to the tree rings they contain. The dating process consists of comparing the sequence of tree ring widths in the sample to a dated master sequence. Assuming that a tree forms exactly one ring per year a simple sliding algorithm solves this matching task.But sometimes a tree produces no ring or even two rings in a year. If a sample sequence contains this kind of inconsistencies it cannot be dated correctly by the simple sliding algorithm. We therefore introduce a O(α2mn+α4(m+n)) algorithm for dating such a sample sequence against an error-free master sequence, where n and m are the lengths of the sequences. Our algorithm takes into account that the sample might contain up to α missing or double rings and suggests possible positions for these kind of inconsistencies. This is done by employing an edit distance as the distance measure

Emerging Trends in Dendrochronology

Tato prce se zabv popisem souÄasnch a experimentln­ch metod odbÄru vzork pomoc­ presslerova nebozezu, vez z kmene, fotografie, rentgenu, poÄ­taÄov© tomografie a magnetick© rezonance na poli dendrochronologick©ho vzkumu. V prci jsou rozeb­rny destruktivn­ a nedesktruktivn­ metody odbÄru vzork. Je tak© kladen draz na pvod vzork: zdali je mono vyu­t destruktivn­ metody nebo zdali je to nemon© jako v p­padÄ vzcnch archeologickch objekt. Dle popisuje standardn­ optometrickou metody a dal­ experimentln­ metody fungujic­ na principu kontranstn­ho zpracovn­ obrazu za Äelem rozeznn­ letokruh. V prci jsou tak© popsny rzn© druhy metod softwarov©ho zpracovnn­ kde jako vstup slou­ buÄ s©rie dat nebo obraz letokruh. Dal­ rozd­ly tvo­ vymezen© spektrum uvedench prac­, nÄkter© prce se zamÄuj­ na zpracovn­ obrazu od p­ky tedy od po­zen© fotografie a po hotov© datovan­, nÄkter© vak zaj­m pouze zk sektor dendrochronologie jako jsou nap­klad vady Äi patnÄ rozeznateln© letokruhy.This thesis deals with a description of current and experimental methods of sample extraction with the increment borer, cuts from sawn logs, photos, X-rays, computed tomography and magnetic resonance in the field of dendrochronology. This work deals with destructive and non-destructive sample acquisition methods. Difference between the possibilities of usage of these methods is also emphasized: whether or not is it possible to use destructive methods - especially the case of the rare archaeological objects. Along with the description of current optometric method other methods of image processing based on contrast recognition for the purpose of the tree ring recognition are given. Description of different software methods are given with the respect to the data input (image or data series). Other differences are in the spectre of interest of presented programs, some of them are programed to analyse the rings from input image whereas some deal only with narrow spectre of dendrochronology such as faults in tree ring formation or poorly recognizable rings.

Summarizing Diverging String Sequences, with Applications to Chain-Letter Petitions

Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider chain letters, which contain a growing sequence of signatories added as the letter propagates. The unusual constellation of features exhibited by chain letters (one-ended growth, divergence, and mutation) make their propagation, and thus the corresponding reconstruction problem, both distinctive and rich. Here, inspired by these chain letters, we formally define the problem of computing an optimal summary of a set of diverging string sequences. From a collection of these sequences of names, with each sequence noisily corresponding to a branch of the unknown tree $T$ representing the letter's true dissemination, can we efficiently and accurately reconstruct a tree $T' \approx T$? In this paper, we give efficient exact algorithms for this summarization problem when the number of sequences is small; for larger sets of sequences, we prove hardness and provide an efficient heuristic algorithm. We evaluate this heuristic on synthetic data sets chosen to emulate real chain letters, showing that our algorithm is competitive with or better than previous approaches, and that it also comes close to finding the true trees in these synthetic datasets.Comment: 18 pages, 6 figures. Accepted to Combinatorial Pattern Matching (CPM) 202

Silver fir (Abies alba Mill.) is able to thrive and prosper under meso-Mediterranean conditions

The potential ecological envelope of silver fir (Abies alba Mill.) based on its present distribution suggests a high suitability for moist rather than warm and dry environments. This contrasts with paleoecological evidence reporting its former presence at low elevations under meso-Mediterranean conditions. In this study, we evaluated the growth performance of silver fir at low elevation (20–60 m a.s.l.) under meso-Mediterranean climatic conditions in Tuscany (central Italy). We conducted a dendroecological analysis on Abies alba trees along a geomorphological gradient (from depression to upper slope conditions). Climate-growth relationships were assessed by means of correlations, response functions, pointer years, and superposed epoch analysis. Silver fir was found to grow and regenerate well in these stands mixed with evergreen (e.g., Quercus ilex L.) and thermophilous deciduous Mediterranean tree species (e.g., Q. cerris L.). Summer drought was the most growth-influencing factor, with immediate (i.e., current season) negative impacts on tree-ring widths (TRW). No significant impacts were observed in the four years following extreme summer droughts, but the TRW series (which started between the 1930s and 1950s) showed a growth decline since the mid-1990s that is likely drought-related. Our results show that, provided there is a sufficiently large soil water holding capacity, silver fir provenances exist which are able to withstand Mediterranean summer droughts, can naturally and regularly regenerate in these systems, and may even dominate over typical meso-Mediterranean species. As long as annual precipitation is not too low (i.e., >850 mm) and summer drought conditions not too extreme (i.e., less than three months), silver fir has thus the potential to thrive under warm Mediterranean conditions.ISSN:0378-1127ISSN:1872-704

SAMPI: Protein Identification with Mass Spectra Alignments

BACKGROUND: Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database. However, existing tools for analyzing PMFs often suffer from missing or heuristic analysis of the significance of search results and insufficient handling of missing and additional peaks. RESULTS: We present an unified framework for analyzing Peptide Mass Fingerprints that offers a number of advantages over existing methods: First, comparison of mass spectra is based on a scoring function that can be custom-designed for certain applications and explicitly takes missing and additional peaks into account. The method is able to simulate almost every additive scoring scheme. Second, we present an efficient deterministic method for assessing the significance of a protein hit, independent of the underlying scoring function and sequence database. We prove the applicability of our approach using biological mass spectrometry data and compare our results to the standard software Mascot. CONCLUSION: The proposed framework for analyzing Peptide Mass Fingerprints shows performance comparable to Mascot on small peak lists. Introducing more noise peaks, we are able to keep identification rates at a similar level by using the flexibility introduced by scoring schemes

Studies in the Roman and Medieval Archaeology of Exeter

This second volume presenting the research carried out through the Exeter: A Place in Time project presents a series of specialist contributions that underpin the general overview published in the first volume. Chapter 2 provides summaries of the excavations carried out within the city of Exeter between 1812 and 2019, while Chapter 3 draws together the evidence for the plan of the legionary fortress and the streets and buildings of the Roman town. Chapter 4 presents the medieval documentary evidence relating to the excavations at three sites in central Exeter (High Street, Trichay Street and Goldsmith Street), with the excavation reports being in Chapter 5-7. Chapter 8 reports on the excavations and documentary research at Rack Street in the south-east quarter of the city. There follows a series of papers covering recent research into the archaeometallurgical debris, dendrochronology, Roman pottery, Roman ceramic building material, Roman querns and millstones, Claudian coins, an overview of the Roman coins from Exeter and Devon, medieval pottery, and the human remains found in a series of medieval cemeteries

Studies in the Roman and Medieval Archaeology of Exeter

This second volume presenting the research carried out through the Exeter: A Place in Time project presents a series of specialist contributions that underpin the general overview published in the first volume. Chapter 2 provides summaries of the excavations carried out within the city of Exeter between 1812 and 2019, while Chapter 3 draws together the evidence for the plan of the legionary fortress and the streets and buildings of the Roman town. Chapter 4 presents the medieval documentary evidence relating to the excavations at three sites in central Exeter (High Street, Trichay Street and Goldsmith Street), with the excavation reports being in Chapter 5-7. Chapter 8 reports on the excavations and documentary research at Rack Street in the south-east quarter of the city. There follows a series of papers covering recent research into the archaeometallurgical debris, dendrochronology, Roman pottery, Roman ceramic building material, Roman querns and millstones, Claudian coins, an overview of the Roman coins from Exeter and Devon, medieval pottery, and the human remains found in a series of medieval cemeteries

IKUWA6. Shared Heritage

Celebrating the theme ‘Shared heritage’, IKUWA6 (the 6th International Congress for Underwater Archaeology), was the first such major conference to be held in the Asia-Pacific region, and the first IKUWA meeting hosted outside Europe since the organisation’s inception in Germany in the 1990s. A primary objective of holding IKUWA6 in Australia was to give greater voice to practitioners and emerging researchers across the Asia and Pacific regions who are often not well represented in northern hemisphere scientific gatherings of this scale; and, to focus on the areas of overlap in our mutual heritage, techniques and technology. Drawing together peer-reviewed presentations by delegates from across the world who converged in Fremantle in 2016 to participate, this volume covers a stimulating diversity of themes and niche topics of value to maritime archaeology practitioners, researchers, students, historians and museum professionals across the world