A really simple approximation of smallest grammar

In this paper we present a really simple linear-time algorithm constructing a context-free grammar of size O(g log (N/g)) for the input string, where N is the size of the input string and g the size of the optimal grammar generating this string. The algorithm works for arbitrary size alphabets, but the running time is linear assuming that the alphabet Sigma of the input string can be identified with numbers from 1,ldots, N^c for some constant c. Algorithms with such an approximation guarantee and running time are known, however all of them were non-trivial and their analyses were involved. The here presented algorithm computes the LZ77 factorisation and transforms it in phases to a grammar. In each phase it maintains an LZ77-like factorisation of the word with at most l factors as well as additional O(l) letters, where l was the size of the original LZ77 factorisation. In one phase in a greedy way (by a left-to-right sweep and a help of the factorisation) we choose a set of pairs of consecutive letters to be replaced with new symbols, i.e. nonterminals of the constructed grammar. We choose at least 2/3 of the letters in the word and there are O(l) many different pairs among them. Hence there are O(log N) phases, each of them introduces O(l) nonterminals to a grammar. A more precise analysis yields a bound O(l log(N/l)). As l \leq g, this yields the desired bound O(g log(N/g)).Comment: Accepted for CPM 201

On the maximal sum of exponents of runs in a string

A run is an inclusion maximal occurrence in a string (as a subinterval) of a repetition $v$ with a period $p$ such that $2p \le |v|$. The exponent of a run is defined as $|v|/p$ and is $\ge 2$. We show new bounds on the maximal sum of exponents of runs in a string of length $n$. Our upper bound of $4.1n$ is better than the best previously known proven bound of $5.6n$ by Crochemore & Ilie (2008). The lower bound of $2.035n$, obtained using a family of binary words, contradicts the conjecture of Kolpakov & Kucherov (1999) that the maximal sum of exponents of runs in a string of length $n$ is smaller than $2n$Comment: 7 pages, 1 figur

Online Self-Indexed Grammar Compression

Although several grammar-based self-indexes have been proposed thus far, their applicability is limited to offline settings where whole input texts are prepared, thus requiring to rebuild index structures for given additional inputs, which is often the case in the big data era. In this paper, we present the first online self-indexed grammar compression named OESP-index that can gradually build the index structure by reading input characters one-by-one. Such a property is another advantage which enables saving a working space for construction, because we do not need to store input texts in memory. We experimentally test OESP-index on the ability to build index structures and search query texts, and we show OESP-index's efficiency, especially space-efficiency for building index structures.Comment: To appear in the Proceedings of the 22nd edition of the International Symposium on String Processing and Information Retrieval (SPIRE2015

Syntactic View of Sigma-Tau Generation of Permutations

We give a syntactic view of the Sawada-Williams $(\sigma,\tau)$-generation of permutations. The corresponding sequence of $\sigma-\tau$-operations, of length $n!-1$ is shown to be highly compressible: it has $O(n^2\log n)$ bit description. Using this compact description we design fast algorithms for ranking and unranking permutations.Comment: accepted on LATA201

No association between the intake of marine n-3 PUFA during the second trimester of pregnancy and factors associated with cardiometabolic risk in the 20-year-old offspring.

To access publisher's full text version of this article click on the hyperlink at the bottom of the pageThe intake of marine n-3 PUFA has been shown to decrease the risk of CVD in a number of studies. Since the development of CVD is often a lifelong process, marine n-3 PUFA intake early in life may also affect the development of later CVD. The aim of the present study was to investigate the association between maternal intake of marine n-3 PUFA during the second trimester of pregnancy and factors associated with cardiometabolic risk in the 20-year-old offspring. The study was based on the follow-up of the offspring of a Danish pregnancy cohort who participated in a study conducted from 1988 to 1989. A total of 965 pregnant women were originally included in the cohort and detailed information about the intake of marine n-3 PUFA during the second trimester was collected. In 2008-9, the offspring were invited to participate in a clinical examination including anthropometric, blood pressure (BP) and short-term heart rate variability measurements. Also, a fasting venous blood sample was drawn from them. Multiple linear regression modelling, using the lowest quintile of marine n-3 PUFA intake as the reference, was used to estimate the association with all outcomes. A total of 443 offspring participated in the clinical examination. No association between the intake of marine n-3 PUFA during the second trimester of pregnancy and offspring adiposity, glucose metabolism, BP or lipid profile was found. In conclusion, no association between the intake of marine n-3 PUFA during the second trimester of pregnancy and the factors associated with cardiometabolic risk in the 20-year-old offspring could be detected.Danish Council for Strategic Research 09-067124 2101-07-0025 2101-06-000

Social, dietary and clinical correlates of oedema in children with severe acute malnutrition:a cross-sectional study

BACKGROUND: Severe acute malnutrition is a serious public health problem, and a challenge to clinicians. Why some children with malnutrition develop oedema (kwashiorkor) is not well understood. The objective of this study was to investigate socio-demographic, dietary and clinical correlates of oedema, in children hospitalised with severe acute malnutrition. METHODS: We recruited children with severe acute malnutrition admitted to Mulago Hospital, Uganda. Data was collected using questionnaires, clinical examination and measurement of blood haemoglobin, plasma c-reactive protein and α(1)-acid glycoprotein. Correlates of oedema were identified using multiple logistic regression analysis. RESULTS: Of 120 children included, 77 (64%) presented with oedematous malnutrition. Oedematous children were slightly older (17.7 vs. 15.0 months, p = 0.006). After adjustment for age and sex, oedematous children were less likely to be breastfed (odds ratio (OR): 0.19, 95%-confidence interval (CI): 0.06; 0.59), to be HIV-infected (OR: 0.10, CI: 0.03; 0.41), to report cough (OR: 0.33, CI: 0.13; 0.82) and fever (OR: 0.22, CI: 0.09; 0.51), and to have axillary temperature > 37.5°C (OR: 0.28 CI: 0.11; 0.68). Household dietary diversity score was lower in children with oedema (OR: 0.58, CI: 0.40; 85). No association was found with plasma levels of acute phase proteins, household food insecurity or birth weight. CONCLUSION: Children with oedematous malnutrition were less likely to be breastfed, less likely to have HIV infection and had fewer symptoms of other infections. Dietary diversity was lower in households of children who presented with oedema. Future research may confirm whether a causal relationship exists between these factors and nutritional oedema. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12887-015-0341-8) contains supplementary material, which is available to authorized users

Ischemic Preconditioning Improves Microvascular Endothelial Function in Remote Vasculature by Enhanced Prostacyclin Production.

BACKGROUND The mechanisms underlying the effect of preconditioning on remote microvasculature remains undisclosed. The primary objective was to document the remote effect of ischemic preconditioning on microvascular function in humans. The secondary objective was to test if exercise also induces remote microvascular effects. METHODS AND RESULTS A total of 12 healthy young men and women participated in 2 experimental days in a random counterbalanced order. On one day the participants underwent 4×5 minutes of forearm ischemic preconditioning, and on the other day they completed 4×5 minutes of hand-grip exercise. On both days, catheters were placed in the brachial and femoral artery and vein for infusion of acetylcholine, sodium nitroprusside, and epoprostenol. Vascular conductance was calculated from blood flow measurements with ultrasound Doppler and arterial and venous blood pressures. Ischemic preconditioning enhanced (P<0.05) the remote vasodilator response to intra-arterial acetylcholine in the leg at 5 and 90 minutes after application. The enhanced response was associated with a 6-fold increase (P<0.05) in femoral venous plasma prostacyclin levels and with a transient increase (P<0.05) in arterial plasma levels of brain-derived neurotrophic factor and vascular endothelial growth factor. In contrast, hand-grip exercise did not influence remote microvascular function. CONCLUSIONS These findings demonstrate that ischemic preconditioning of the forearm improves remote microvascular endothelial function and suggest that one of the underlying mechanisms is a humoral-mediated potentiation of prostacyclin formation

Prenatal Exposure to Perfluorooctanoate and Risk of Overweight at 20 Years of Age: A Prospective Cohort Study

Background: Perfluoroalkyl acids are persistent compounds used in various industrial -applications. Of these compounds, perfluorooctanoate (PFOA) is currently detected in humans worldwide. A recent study on low-dose developmental exposure to PFOA in mice reported increased weight and elevated biomarkers of adiposity in postpubertal female offspring

Rpair: Rescaling RePair with Rsync

Data compression is a powerful tool for managing massive but repetitive datasets, especially schemes such as grammar-based compression that support computation over the data without decompressing it. In the best case such a scheme takes a dataset so big that it must be stored on disk and shrinks it enough that it can be stored and processed in internal memory. Even then, however, the scheme is essentially useless unless it can be built on the original dataset reasonably quickly while keeping the dataset on disk. In this paper we show how we can preprocess such datasets with context-triggered piecewise hashing such that afterwards we can apply RePair and other grammar-based compressors more easily. We first give our algorithm, then show how a variant of it can be used to approximate the LZ77 parse, then leverage that to prove theoretical bounds on compression, and finally give experimental evidence that our approach is competitive in practice