Learning Unions of k-Testable Languages

A classical problem in grammatical inference is to identify a language from a set of examples. In this paper, we address the problem of identifying a union of languages from examples that belong to several different unknown languages. Indeed, decomposing a language into smaller pieces that are easier to represent should make learning easier than aiming for a too generalized language. In particular, we consider k-testable languages in the strict sense (k-TSS). These are defined by a set of allowed prefixes, infixes (sub-strings) and suffixes that words in the language may contain. We establish a Galois connection between the lattice of all languages over alphabet {\Sigma}, and the lattice of k-TSS languages over {\Sigma}. We also define a simple metric on k-TSS languages. The Galois connection and the metric allow us to derive an efficient algorithm to learn the union of k-TSS languages. We evaluate our algorithm on an industrial dataset and thus demonstrate the relevance of our approach

L-systems in Geometric Modeling

We show that parametric context-sensitive L-systems with affine geometry interpretation provide a succinct description of some of the most fundamental algorithms of geometric modeling of curves. Examples include the Lane-Riesenfeld algorithm for generating B-splines, the de Casteljau algorithm for generating Bezier curves, and their extensions to rational curves. Our results generalize the previously reported geometric-modeling applications of L-systems, which were limited to subdivision curves.Comment: In Proceedings DCFS 2010, arXiv:1008.127

Role of Ucp1 enhancer methylation and chromatin remodelling in the control of Ucp1 expression in murine adipose tissue

Aims/hypothesis Increasing the expression of the brown adipose tissue-specific gene uncoupling protein-1 (Ucp1) is a potential target for treating obesity. We investigated the role of DNA methylation and histone modification in Ucp1 expression in adipose cell lines and ex vivo murine adipose tissues. Methods Methylation state of the Ucp1 enhancer was studied using bisulphite mapping in murine adipose cell lines, and tissue taken from cold-stressed mice, coupled with functional assays of the effects of methylation and demethylation of the Ucp1 promoter on gene expression and nuclear protein binding. Results We show that demethylation of the Ucp1 promoter by 5-aza-deoxycytidine increases Ucp1 expression while methylation of Ucp1 promoter–reporter constructs decreases expression. Brown adipose tissue-specific Ucp1 expression is associated with decreased CpG dinucleotide methylation of the Ucp1 enhancer. The lowest CpG dinucleotide methylation state was found in two cyclic AMP response elements (CRE3, CRE2) in the Ucp1 promoter and methylation of the CpG in CRE2, but not CRE3 decreased nuclear protein binding. Chromatin immunoprecipitation assays revealed the presence of the silencing DiMethH3K9 modification on the Ucp1 enhancer in white adipose tissue and the appearance of the active TriMethH3K4 mark at the Ucp1 promoter in brown adipose tissue in response to a cold environment. Conclusions/interpretation The results demonstrate that CpG dinucleotide methylation of the Ucp1 enhancer exhibits tissue-specific patterns in murine tissue and cell lines and suggest that adipose tissue-specific Ucp1 expression involves demethylation of CpG dinucleotides found in regulatory CREs in the Ucp1 enhancer, as well as modification of histone tails

IgTM: An algorithm to predict transmembrane domains and topology in proteins

<p>Abstract</p> <p>Background</p> <p>Due to their role of receptors or transporters, membrane proteins play a key role in many important biological functions. In our work we used Grammatical Inference (GI) to localize transmembrane segments. Our GI process is based specifically on the inference of Even Linear Languages.</p> <p>Results</p> <p>We obtained values close to 80% in both specificity and sensitivity. Six datasets have been used for the experiments, considering different encodings for the input sequences. An encoding that includes the topology changes in the sequence (from inside and outside the membrane to it and vice versa) allowed us to obtain the best results. This software is publicly available at: <url>http://www.dsic.upv.es/users/tlcc/bio/bio.html</url></p> <p>Conclusion</p> <p>We compared our results with other well-known methods, that obtain a slightly better precision. However, this work shows that it is possible to apply Grammatical Inference techniques in an effective way to bioinformatics problems.</p

Has the liver and other visceral organs migrated to its normal position in children with giant omphalocele? A follow-up study with ultrasonography

Contains fulltext : 88428.pdf (publisher's version ) (Closed access)This study evaluates whether, on the long run, in patients born with a giant omphalocele, the liver and other solid organs reach their normal position, shape, and size. Seventeen former patients with a giant omphalocele, treated between 1970 and 2004, were included. Physical examination was supplemented with ultrasonography for ventral hernia and precise description of the liver, spleen, and kidneys. The findings were compared with 17 controls matched for age, gender, and body mass index. We found an abnormal position of the liver, spleen, left kidney, and right kidney in eight, six, five, and four patients, respectively. An unprotected liver was present in all 17 patients and in 11 controls, the difference being statistically significant (p = 0.04). In ten of the 11 patients with an incisional hernia, the liver was located underneath the abdominal defect. CONCLUSION: In all former patients with a giant omphalocele, an abnormal position of the liver and in the majority of them, an incisional hernia was also found. The liver and sometimes also the spleen and the kidneys do not migrate to their normal position. Exact documentation and good information are important for both the patient and their caretakers in order to avoid liver trauma.1 mei 201

Endothelin-1 enhances fibrogenic gene expression, but does not promote DNA synthesis or apoptosis in hepatic stellate cells

BACKGROUND: In liver injury, the pool of hepatic stellate cell (HSC) increases and produces extracellular matrix proteins, decreasing during the resolution of fibrosis. The profibrogenic role of endothelin-1 (ET-1) in liver fibrosis remains disputed. We therefore studied the effect of ET-1 on proliferation, apoptosis and profibrogenic gene expression of HSCs. RESULTS: First passage HSC predominantly expressed endothelin A receptor (ETAR) mRNA and 4th passage HSC predominantly expressed the endothelin B receptor (ETBR) mRNA. ET-1 had no effect on DNA synthesis in 1st passage HSC, but reduced DNA synthesis in 4th passage HSC by more than 50%. Inhibition of proliferation by endothelin-1 was abrogated by ETBR specific antagonist BQ788, indicating a prominent role of ETBR in growth inhibition. ET-1 did not prevent apoptosis induced by serum deprivation or Fas ligand in 1st or 4th passage HSC. However, ET-1 increased procollagen α1(I), transforming growth factor β-1 and matrix metalloproteinase (MMP)-2 mRNA transcripts in a concentration-dependent manner in 1st, but not in 4th passage HSC. Profibrogenic gene expression was abrogated by ETAR antagonist BQ123. Both BQ123 and BQ788 attenuated the increase of MMP-2 expression by ET-1. CONCLUSION: We show that ET-1 stimulates fibrogenic gene expression for 1st passage HSC and it inhibits HSC proliferation for 4th passage HSC. These data indicate the profibrogenic and antifibrogenic action of ET-1 for HSC are involved in the process of liver fibrosis

Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotype

<p>Abstract</p> <p>Background</p> <p>A finite state machine manipulating information-carrying DNA strands can be used to perform autonomous molecular-scale computations at the cellular level.</p> <p>Results</p> <p>We propose a new finite state machine able to detect and correct aberrant molecular phenotype given by mutated genetic transcripts. The aberrant mutations trigger a cascade reaction: specific molecular markers as input are released and induce a spontaneous self-assembly of a wild type protein or peptide, while the mutational disease phenotype is silenced. We experimentally demostrated in <it>in vitro </it>translation system that a viable protein can be autonomously assembled.</p> <p>Conclusion</p> <p>Our work demostrates the basic principles of computational genes and particularly, their potential to detect mutations, and as a response thereafter administer an output that suppresses the aberrant disease phenotype and/or restores the lost physiological function.</p

Lymphocyte recruitment and homing to the liver in primary biliary cirrhosis and primary sclerosing cholangitis

The mechanisms operating in lymphocyte recruitment and homing to liver are reviewed. A literature review was performed on primary biliary cirrhosis (PBC), progressive sclerosing cholangitis (PSC), and homing mechanisms; a total of 130 papers were selected for discussion. Available data suggest that in addition to a specific role for CCL25 in PSC, the CC chemokines CCL21 and CCL28 and the CXC chemokines CXCL9 and CXCL10 are involved in the recruitment of T lymphocytes into the portal tract in PBC and PSC. Once entering the liver, lymphocytes localize to bile duct and retain by the combinatorial or sequential action of CXCL12, CXCL16, CX3CL1, and CCL28 and possibly CXCL9 and CXCL10. The relative importance of these chemokines in the recruitment or the retention of lymphocytes around the bile ducts remains unclear. The available data remain limited but underscore the importance of recruitment and homing

Effects of Time of Day and Sleep Deprivation on Motorcycle-Driving Performance

The aim of this study was to investigate whether motorcycle handling capabilities – measured by means of the efficiency of emergency manoeuvres – were dependent on prior sleep deprivation and time of day. Twelve male participants voluntarily took part in four test sessions, starting at 6 a.m., 10 a.m., 2 p.m., and 6 p.m., following a night either with or without sleep. Each test session comprised temperature and sleepiness measurements, before three different types of motorcycling tests were initiated: (1) stability in straight ahead riding at low speed (in “slow motion” mode and in “brakes and clutch” mode), (2) emergency braking and (3) crash avoidance tasks performed at 20 kph and 40 kph. The results indicate that motorcycle control at low speed depends on time of day, with an improvement in performance throughout the day. Emergency braking performance is affected at both speeds by time of day, with poorer performance (longer total stopping distance, reaction time and braking distance) in the morning, and also by sleep deprivation, from measurements obtained at 40 kph (incorrect initial speed). Except for a tendency observed after the sleepless night to deviate from the initial speed, it seems that crash avoidance capabilities are quite unaffected by the two disturbance factors. Consequently, some motorcycle handling capabilities (stability at low speed and emergency braking) change in the same way as the diurnal fluctuation observed in body temperature and sleepiness, whereas for others (crash avoidance) the participants were able to maintain their initial performance level despite the high levels of sleepiness recorded after a sleepless night. Motorcycle riders have to be aware that their handling capabilities are limited in the early morning and/or after sleep deprivation. Both these situations can increase the risk of falls and of being involved in a road accident