Tree Damage in Mechanized Uneven-aged Selection Cuttings

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Integrated modelling driven fusion research - Coupling of plasma and neutron transport codes

Funding Information: This work has been carried out within the framework of the EUROfusionConsortium and has received funding from the Euratom research and training programme 2014-2018 and 2019-2020 under grant agreement No 633053. The viewsand opinions expressed herein do not necessarily reflect those of the European Commission. The authors acknowledgethe funding received from the Slovenian Research Agency in the scope of the projects: Trainingof young researchers – 1000-14-0106, Reactor Physics – P2-0073-0106-019, Development of methodology for calibration of neutron detectors with a 14.1 MeV neutron generator - JET fusion reactor case – J2-6752. References [1] O. N. Jarvis, Plasma Phys. Control. Fusion 36, 2 (1994) [2] O. Meneghini et al, Nucl. Fusion, 55, 8 (2015) [3] Ž. Štancar et al, Nucl. Fusion 59, 9 (2019) [4] P. Sirén et al, Nucl. Fusion 58, 1 (2018)Non peer reviewe

A Faster Implementation of Online Run-Length Burrows-Wheeler Transform

Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which runs in $O(n\lg r)$ time and $O(r\lg n)$ bits of space, where $n$ is the length of input string $S$ received so far and $r$ is the number of runs in the BWT of the reversed $S$. We improve the state-of-the-art algorithm for online RLBWT in terms of empirical construction time. Adopting the dynamic list for maintaining a total order, we can replace rank queries in a dynamic wavelet tree on a run-length compressed string by the direct comparison of labels in a dynamic list. The empirical result for various benchmarks show the efficiency of our algorithm, especially for highly repetitive strings.Comment: In Proc. IWOCA201

Virulenssin evoluutio viruksilla

Tiivistelmä. Virulenssin evoluutioon viruksilla vaikuttaa viruksen genomin rakenne, ympäristö sekä isäntäorganismin immuunipuolustus. Yksi eniten vaikuttavista tekijöistä on populaatiotason valintapaine optimoida virulenssin ja leviämiskyvyn suhde. Etenkin isännänvaihdoksen jälkeinen virulenssin evoluutio on tärkeä tutkimuskohde, jonka avulla voidaan ymmärtää uusia infektioita paremmin. Tässä tutkielmassa perehdytään kahden viruksen, myksoomaviruksen ja HIV-1:n virulenssin evoluutioon

At the crossroads of logics: Automating newswork with artificial intelligence : (Re)defining journalistic logics from the perspective of technologists

As artificial intelligence (AI) technologies become more ubiquitous for streamlining and optimizing work, they are entering fields representing organizational logics at odds with the efficiency logic of automation. One such field is journalism, an industry defined by a logic enacted through professional norms, practices, and values. This paper examines the experience of technologists developing and employing natural language generation (NLG) in news organizations, looking at how they situate themselves and their technology in relation to newswork. Drawing on institutional logics, a theoretical framework from organizational theory, we show how technologists shape their logic for building these emerging technologies based on a theory of rationalizing news organizations, a frame of optimizing newswork, and a narrative of news organizations misinterpreting the technology. Our interviews reveal technologists mitigating tensions with journalistic logic and newswork by labeling stories generated by their systems as nonjournalistic content, seeing their technology as a solution for improving journalism, enabling newswork to move away from routine tasks. We also find that as technologists interact with news organizations, they assimilate elements from journalistic logic beneficial for benchmarking their technology for more lucrative industries.Peer reviewe

Identification and Density Estimation of American Martens (Martes americana) Using a Novel Camera-Trap Method

Camera-traps are increasingly used to estimate wildlife abundance, yet few studies exist for small-sized carnivores or comparing efficacy against traditional methods. We developed a camera-trap to identify the unique ventral patches of American martens (Martes americana). Our method was designed to: (1) determine the optimal trap configuration to photograph ventral patches; (2) evaluate the use of temporally clustered photographs to determine independence and improve identification; and (3) determine factors that influence identification probability. We tested our method by comparing camera- and live-trap density estimates using spatial capture–recapture (SCR) models. The ventral patches of radio-collared martens were most visible when traps were placed 15–20 cm above a feeding platform. Radio-collared martens (n = 14) visited camera-traps for long periods (median = 7 min) with long intervals between visits (median = 419 min), and visits by different martens at the same trap \u3c15 min apart was infrequent (n = 3) during both years. Similarly, there was complete agreement among observers that clustered photos of un-collared martens were always of the same individual. Pairwise agreement was high between observers; eight un-collared martens were identifiable by consensus on 90% (54 of 60) of recorded visits. Factors influencing identification probability were directly related to the time martens spent feeding at traps (β = 0.143, P = 0.01) and inversely proportional to the time that elapsed since traps were baited (β = −0.344, P = 0.006). Density estimates were higher and more precise for camera-trapping (0.60, 0.35–1.01 martens/km2) than live-trapping (0.45, 0.16–1.22 martens/km2), providing evidence that SCR density estimates may be biased when capture heterogeneity is present, yet cannot be accounted for due to small sample size. Our camera-trap method provides a minimally invasive and accurate tool for monitoring marten populations

Relative Suffix Trees

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees.Peer reviewe

Low Space External Memory Construction of the Succinct Permuted Longest Common Prefix Array

The longest common prefix (LCP) array is a versatile auxiliary data structure in indexed string matching. It can be used to speed up searching using the suffix array (SA) and provides an implicit representation of the topology of an underlying suffix tree. The LCP array of a string of length $n$ can be represented as an array of length $n$ words, or, in the presence of the SA, as a bit vector of $2n$ bits plus asymptotically negligible support data structures. External memory construction algorithms for the LCP array have been proposed, but those proposed so far have a space requirement of $O(n)$ words (i.e. $O(n \log n)$ bits) in external memory. This space requirement is in some practical cases prohibitively expensive. We present an external memory algorithm for constructing the $2n$ bit version of the LCP array which uses $O(n \log \sigma)$ bits of additional space in external memory when given a (compressed) BWT with alphabet size $\sigma$ and a sampled inverse suffix array at sampling rate $O(\log n)$. This is often a significant space gain in practice where $\sigma$ is usually much smaller than $n$ or even constant. We also consider the case of computing succinct LCP arrays for circular strings

Composite repetition-aware data structures

In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these measures. We describe two data structures whose size depends on multiple measures of repetition at once, and that provide competitive tradeoffs between the time for counting and reporting all the exact occurrences of a pattern, and the space taken by the structure. The key component of our constructions is the run-length encoded BWT (RLBWT), which takes space proportional to the number of BWT runs: rather than augmenting RLBWT with suffix array samples, we combine it with data structures from LZ77 indexes, which take space proportional to the number of LZ77 factors, and with the compact directed acyclic word graph (CDAWG), which takes space proportional to the number of extensions of maximal repeats. The combination of CDAWG and RLBWT enables also a new representation of the suffix tree, whose size depends again on the number of extensions of maximal repeats, and that is powerful enough to support matching statistics and constant-space traversal.Comment: (the name of the third co-author was inadvertently omitted from previous version