RLZAP: Relative Lempel-Ziv with Adaptive Pointers

Relative Lempel-Ziv (RLZ) is a popular algorithm for compressing databases of genomes from individuals of the same species when fast random access is desired. With Kuruppu et al.'s (SPIRE 2010) original implementation, a reference genome is selected and then the other genomes are greedily parsed into phrases exactly matching substrings of the reference. Deorowicz and Grabowski (Bioinformatics, 2011) pointed out that letting each phrase end with a mismatch character usually gives better compression because many of the differences between individuals' genomes are single-nucleotide substitutions. Ferrada et al. (SPIRE 2014) then pointed out that also using relative pointers and run-length compressing them usually gives even better compression. In this paper we generalize Ferrada et al.'s idea to handle well also short insertions, deletions and multi-character substitutions. We show experimentally that our generalization achieves better compression than Ferrada et al.'s implementation with comparable random-access times

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

Dynamic Fluctuation Phenomena in Double Membrane Films

Dynamics of double membrane films is investigated in the long-wavelength limit including the overdamped squeezing mode. We demonstrate that thermal fluctuations essentially modify the character of the mode due to its nonlinear coupling to the transversal shear hydrodynamic mode. The corresponding Green function acquires as a function of the frequency a cut along the imaginary semi-axis. Fluctuations lead to increasing the attenuation of the squeezing mode it becomes larger than the `bare' value.Comment: 7 pages, Revte

Time-lapsing biodiversity: an open source method for measuring diversity changes by remote sensing

Understanding biodiversity changes in time is crucial to promptly provide management practices against diversity loss. This is overall true when considering global scales, since human-induced global change is expected to make significant changes on the Earth's biota. Biodiversity management and planning is mainly based on field observations related to community diversity, considering different taxa. However, such methods are time and cost demanding and do not allow in most cases to get temporal replicates. In this view, remote sensing can provide a wide data coverage in a short period of time. Recently, the use of Rao's Q diversity as a measure of spectral diversity has been proposed in order to explicitly take into account differences in a neighbourhood considering abundance and relative distance among pixels. The aim of this paper was to extend such a measure over the temporal dimension and to present an innovative approach to calculate remotely sensed temporal diversity. We demonstrated that temporal beta-diversity (spectral turnover) can be calculated pixel-wise in terms of both slope and coefficient of variation and further plotted over the whole matrix / image. From an ecological and operational point of view, for prioritisation practices in biodiversity protection, temporal variability could be beneficial in order to plan more efficient conservation practices starting from spectral diversity hotspots in space and time. In this paper, we delivered a highly reproducible approach to calculate spatio-temporal diversity in a robust and straightforward manner. Since it is based on open source code, we expect that our method will be further used by several researchers and landscape managers

Classification of Dust Days by Satellite Remotely Sensed Aerosol Products

Considerable progress in satellite remote sensing (SRS) of dust particles has been seen in the last decade. From an environmental health perspective, such an event detection, after linking it to ground particulate matter (PM) concentrations, can proxy acute exposure to respirable particles of certain properties (i.e. size, composition, and toxicity). Being affected considerably by atmospheric dust, previous studies in the Eastern Mediterranean, and in Israel in particular, have focused on mechanistic and synoptic prediction, classification, and characterization of dust events. In particular, a scheme for identifying dust days (DD) in Israel based on ground PM10 (particulate matter of size smaller than 10 nm) measurements has been suggested, which has been validated by compositional analysis. This scheme requires information regarding ground PM10 levels, which is naturally limited in places with sparse ground-monitoring coverage. In such cases, SRS may be an efficient and cost-effective alternative to ground measurements. This work demonstrates a new model for identifying DD and non-DD (NDD) over Israel based on an integration of aerosol products from different satellite platforms (Moderate Resolution Imaging Spectroradiometer (MODIS) and Ozone Monitoring Instrument (OMI)). Analysis of ground-monitoring data from 2007 to 2008 in southern Israel revealed 67 DD, with more than 88 percent occurring during winter and spring. A Classification and Regression Tree (CART) model that was applied to a database containing ground monitoring (the dependent variable) and SRS aerosol product (the independent variables) records revealed an optimal set of binary variables for the identification of DD. These variables are combinations of the following primary variables: the calendar month, ground-level relative humidity (RH), the aerosol optical depth (AOD) from MODIS, and the aerosol absorbing index (AAI) from OMI. A logistic regression that uses these variables, coded as binary variables, demonstrated 93.2 percent correct classifications of DD and NDD. Evaluation of the combined CART-logistic regression scheme in an adjacent geographical region (Gush Dan) demonstrated good results. Using SRS aerosol products for DD and NDD, identification may enable us to distinguish between health, ecological, and environmental effects that result from exposure to these distinct particle populations

Cutaneous manifestations of COVID-19: Report of three cases and a review of literature

Background: Various cutaneous manifestations have been observed in patients with COVID-19 infection. However, overall similarities in the clinical presentation of these dermatological manifestations have not yet been summarized. Objective: This review aims to provide an overview of various cutaneous manifestations in patients with COVID-19 through three case reports and a literature review. Methods: A literature search was conducted using PubMed, OVID, and Google search engines for original and review articles. Studies written in the English language that mentioned cutaneous symptoms and COVID-19 were included. Results: Eighteen articles and three additional cases reported in this paper were included in this review. Of these studies, 6 are case series and 12 are case report studies. The most common cutaneous manifestation of COVID-19 was found to be maculopapular exanthem (morbilliform), presenting in 36.1% (26/72) patients. The other cutaneous manifestations included: a papulovesicular rash (34.7%, 25/72), urticaria (9.7%, 7/72), painful acral red purple papules (15.3%, 11/72) of patients, livedo reticularis lesions (2.8%, 2/72) and petechiae (1.4%, 1/72). Majority of lesions were localized on the trunk (66.7%, 50/72), however, 19.4% (14/72) of patients experienced cutaneous manifestations in the hands and feet. Skin lesion development occurred before the onset of respiratory symptoms or COVID-19 diagnosis in 12.5% (9/72) of the patients, and lesions spontaneously healed in all patients within 10 days. Majority of the studies reported no correlation between COVID-19 severity and skin lesions. Conclusion: Infection with COVID-19 may result in dermatological manifestations with various clinical presentations, which may aid in the timely diagnosis of this infection

Factorised Steady States in Mass Transport Models

We study a class of mass transport models where mass is transported in a preferred direction around a one-dimensional periodic lattice and is globally conserved. The model encompasses both discrete and continuous masses and parallel and random sequential dynamics and includes models such as the Zero-range process and Asymmetric random average process as special cases. We derive a necessary and sufficient condition for the steady state to factorise, which takes a rather simple form.Comment: 6 page

On the suitability of suffix arrays for lempel-ziv data compression

Lossless compression algorithms of the Lempel-Ziv (LZ) family are widely used nowadays. Regarding time and memory requirements, LZ encoding is much more demanding than decoding. In order to speed up the encoding process, efficient data structures, like suffix trees, have been used. In this paper, we explore the use of suffix arrays to hold the dictionary of the LZ encoder, and propose an algorithm to search over it. We show that the resulting encoder attains roughly the same compression ratios as those based on suffix trees. However, the amount of memory required by the suffix array is fixed, and much lower than the variable amount of memory used by encoders based on suffix trees (which depends on the text to encode). We conclude that suffix arrays, when compared to suffix trees in terms of the trade-off among time, memory, and compression ratio, may be preferable in scenarios (e.g., embedded systems) where memory is at a premium and high speed is not critical

Fingerprints in Compressed Strings

The Karp-Rabin fingerprint of a string is a type of hash value that due to its strong properties has been used in many string algorithms. In this paper we show how to construct a data structure for a string S of size N compressed by a context-free grammar of size n that answers fingerprint queries. That is, given indices i and j, the answer to a query is the fingerprint of the substring S[i,j]. We present the first O(n) space data structures that answer fingerprint queries without decompressing any characters. For Straight Line Programs (SLP) we get O(logN) query time, and for Linear SLPs (an SLP derivative that captures LZ78 compression and its variations) we get O(log log N) query time. Hence, our data structures has the same time and space complexity as for random access in SLPs. We utilize the fingerprint data structures to solve the longest common extension problem in query time O(log N log l) and O(log l log log l + log log N) for SLPs and Linear SLPs, respectively. Here, l denotes the length of the LCE

Instability of Myelin Tubes under Dehydration: deswelling of layered cylindrical structures

We report experimental observations of an undulational instability of myelin figures. Motivated by this, we examine theoretically the deformation and possible instability of concentric, cylindrical, multi-lamellar membrane structures. Under conditions of osmotic stress (swelling or dehydration), we find a stable, deformed state in which the layer deformation is given by \delta R ~ r^{\sqrt{B_A/(hB)}}, where B_A is the area compression modulus, B is the inter-layer compression modulus, and h is the repeat distance of layers. Also, above a finite threshold of dehydration (or osmotic stress), we find that the system becomes unstable to undulations, first with a characteristic wavelength of order \sqrt{xi d_0}, where xi is the standard smectic penetration depth and d_0 is the thickness of dehydrated region.Comment: 5 pages + 3 figures [revtex 4