Efficient Large-scale Trace Checking Using MapReduce

The problem of checking a logged event trace against a temporal logic specification arises in many practical cases. Unfortunately, known algorithms for an expressive logic like MTL (Metric Temporal Logic) do not scale with respect to two crucial dimensions: the length of the trace and the size of the time interval for which logged events must be buffered to check satisfaction of the specification. The former issue can be addressed by distributed and parallel trace checking algorithms that can take advantage of modern cloud computing and programming frameworks like MapReduce. Still, the latter issue remains open with current state-of-the-art approaches. In this paper we address this memory scalability issue by proposing a new semantics for MTL, called lazy semantics. This semantics can evaluate temporal formulae and boolean combinations of temporal-only formulae at any arbitrary time instant. We prove that lazy semantics is more expressive than standard point-based semantics and that it can be used as a basis for a correct parametric decomposition of any MTL formula into an equivalent one with smaller, bounded time intervals. We use lazy semantics to extend our previous distributed trace checking algorithm for MTL. We evaluate the proposed algorithm in terms of memory scalability and time/memory tradeoffs.Comment: 13 pages, 8 figure

Flaxseed Lignan Complex Administration in Older Human Type 2 Diabetics Manages Central Obesity and Prothrombosis—An Invitation to Further Investigation into Polypharmacy Reduction

Aim. Animal and human study evidence supports the hypothesis that flaxseed lignan complex (FLC) at a dose of 600 mg secoisolariciresinol diglucoside (SDG)/day for three months would combat hyperglycaemia, dyslipidemia, blood pressure, central obesity, prothrombotic state, inflammation, and low density lipoprotein (LDL) oxidation. Methods. Sixteen type 2 diabetic patients completed this double-blind, randomised crossover placebo-controlled study. A univariate repeated measures analysis of covariance (significance P<0.05) was followed by a mixed linear model effects analysis corrected for multiple comparisons (MCC). Results. Prior to MCC, FLC caused decreased fasting plasma glucose, A1c, inflammation (c-reactive protein (CRP) and interleukin-6 (IL-6)), and increased bleeding time. After correction for multiple comparisons, FLC induced a statistically significant increase in bleeding time and smaller waist circumference gain. No treatment effect occurred in the other variables before or after adjustment. Conclusions. It is concluded that FLC significantly increased bleeding time thus reducing the prothrombotic state, reduced central obesity gain as measured by waist circumference, and did not affect significantly the other dependent variables measured after adjustment for multiple comparisons. These findings, not yet published in human type 2 diabetes, suggest that this FLC dose over at least three months, may, subject to further investigation, reduce polypharmacy

THE ESTIMATION OF GENETIC DISTANCE BETWEEN GERMAN CATTLE BREEDS

Za budući izbor uzgoja potrebno je očuvanje genetske raznolikosti u životinja. U filogenetskim proučavanjima mikrosateliti su dokazani kao snažno sredstvo. (Bowcock et al. 1994.). Procjena genetskih udaljenosti što se temelji na učestalosti alela mikrosatelitskih markera pomoći će u procjeni veličine razlika između usko povezanih pasmina stoke. Pasmina Shorthom i Angler mogu se identificirati kao sporedne pasmine, pa je stoga razvoj programa očuvanja vrlo koristan. Prilagođenje pasmine Orginal Black Pied još nije jasno. Odredit će se dodatni markeri kako bi se povećala točnost procjene. Niti vrijednosti udaljenosti između Holsteina i mliječnog Red Pied niti slični uzgojni ciljevi čini se da nisu razuman razlog da se ove pasmine drže odijeljeno. Ovaj će rad biti od pomoći u odlučivanju o očuvanju pasmina u posebnim programima očuvanja konzervacijom in vivo i in vitro

Headache yesterday in Europe

BACKGROUND: Surveys enquiring about burden of headache over a prior period of time (eg, 3 months) are subject to recall bias. To eliminate this as far as possible, we focused on presence and impact of headache on the preceding day (“headache yesterday”). METHODS: Adults (18-65 years) were surveyed from the general populations of Germany, Italy, Lithuania, Luxembourg and the Netherlands, from a work-force population in Spain and from mostly non-headache patient populations of Austria, France and UK. A study of non-responders in some countries allowed detection of potential participation bias where initial participation rates were low. RESULTS: Participation rates varied between 11% and 59% (mean 27%). Non-responder studies suggested that, because of participation bias, headache prevalence might be overestimated in initial responders by up to 2% (absolute). Across all countries, 1,422 of 8,271 participants (15-17%, depending on correction for participation bias) had headache yesterday lasting on average for 6 hours. It was bad or very bad in 56% of cases and caused absence from work or school in 6%. Among those who worked despite headache, 20% reported productivity reduced by >50%. Social activities were lost by 24%. Women (21%) were more likely than men (12%) to have headache yesterday, but impact was similar in the two genders. CONCLUSIONS: With recall biases avoided, our findings indicate that headache costs at least 0.7% of working capacity in Europe. This calculation takes into account that most of those who missed work could make up for this later, which, however, means that leisure and social activities are even more influenced by headache

TRANSFAC(®) and its module TRANSCompel(®): transcriptional gene regulation in eukaryotes

The TRANSFAC(®) database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel(®) on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match™ and Patch™ provides increased functionality for TRANSFAC(®). The list of databases which are linked to the common GENE table of TRANSFAC(®) and TRANSCompel(®) has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD™ and TRANSPRO™. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel(®) contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC(®), in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC(®) 7.0 and TRANSCompel(®) 7.0, are accessible under

Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses

G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5'-LTR U3 region were completely conserved in primate lentiviruses. A G4 was also present in a cattle-infecting lentivirus. All other non-primate lentiviruses displayed hints of less stable G4s. In primate lentiviruses, the possibility to fold into G4s was highly conserved among strains. LTR G4 sequences were very similar among phylogenetically related primate viruses, while they increasingly differed in viruses that diverged early from a common ancestor. A strong correlation between primate lentivirus LTR G4s and Sp1/NF\u3baB binding sites was found. All LTR G4s folded: their complexity was assessed by polymerase stop assay. Our data support a role of the lentiviruses 5'-LTR G4 region as control centre of viral transcription, where folding/unfolding of G4s and multiple recruitment of factors based on both sequence and structure may take place

Release properties of UCx_x and molten U targets

The release properties of UC$_x$ and molten U thick targets associated with a Nier- Bernas ion source have been studied. Two experimental methods are used to extract the release time. Results are presented and discussed for Kr, Cd, I and Xe

The role of RelA (p65) threonine 505 phosphorylation in the regulation of cell growth, survival, and migration

The NF-κB family of transcription factors is a well-established regulator of the immune and inflammatory responses and also plays a key role in other cellular processes, including cell death, proliferation, and migration. Conserved residues in the trans-activation domain of RelA, which can be posttranslationally modified, regulate divergent NF-κB functions in response to different cellular stimuli. Using rela(−/−) mouse embryonic fibroblasts reconstituted with RelA, we find that mutation of the threonine 505 (T505) phospho site to alanine has wide-ranging effects on NF-κB function. These include previously described effects on chemotherapeutic drug-induced apoptosis, as well as new roles for this modification in autophagy, cell proliferation, and migration. This last effect was associated with alterations in the actin cytoskeleton and expression of cellular migration–associated genes such as WAVE3 and α-actinin 4. We also define a new component of cisplatin-induced, RelA T505–dependent apoptosis, involving induction of NOXA gene expression, an effect explained at least in part through induction of the p53 homologue, p73. Therefore, in contrast to other RelA phosphorylation events, which positively regulate NF-κB function, we identified RelA T505 phosphorylation as a negative regulator of its ability to induce diverse cellular processes such as apoptosis, autophagy, proliferation, and migration

Uncovering mechanisms of transcriptional regulations by systematic mining of cis regulatory elements with gene expression profiles

<p>Abstract</p> <p>Background</p> <p>Contrary to the traditional biology approach, where the expression patterns of a handful of genes are studied at a time, microarray experiments enable biologists to study the expression patterns of many genes simultaneously from gene expression profile data and decipher the underlying hidden biological mechanism from the observed gene expression changes. While the statistical significance of the gene expression data can be deduced by various methods, the biological interpretation of the data presents a challenge.</p> <p>Results</p> <p>A method, called CisTransMine, is proposed to help infer the underlying biological mechanisms for the observed gene expression changes in microarray experiments. Specifically, this method will predict potential cis-regulatory elements in promoter regions which could regulate gene expression changes. This approach builds on the MotifADE method published in 2004 and extends it with two modifications: up-regulated genes and down-regulated genes are tested separately and in addition, tests have been implemented to identify combinations of transcription factors that work synergistically. The method has been applied to a genome wide expression dataset intended to study myogenesis in a mouse C2C12 cell differentiation model. The results shown here both confirm the prior biological knowledge and facilitate the discovery of new biological insights.</p> <p>Conclusion</p> <p>The results validate that the CisTransMine approach is a robust method to uncover the hidden transcriptional regulatory mechanisms that can facilitate the discovery of mechanisms of transcriptional regulation.</p