Generalized synchronization in directionally coupled systems with identical individual dynamics

A simple chaotic flow is presented, which when driven by an identical copy of itself, for certain initial conditions, is able to display generalized synchronization instead of identical synchronization. Being that the drive and the response are observed in exactly the same coordinate system, generalized synchronization is demonstrated by means of the auxiliary system approach and by the conditional Lyapunov spectrum. This is interpreted in terms of changes in the structure of the system stationary points, caused by the coupling, which modify its global behavior.

Developmental constraints on vertebrate genome evolution.

Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on genome evolution in vertebrates. We used gene expression data from two vertebrates: zebrafish, using a microarray experiment spanning 14 stages of development, and mouse, using EST counts for 26 stages of development. We show that, in both species, genes expressed early in development (1) have a more dramatic effect of knock-out or mutation and (2) are more likely to revert to single copy after whole genome duplication, relative to genes expressed late. This supports high constraints on early stages of vertebrate development, making them less open to innovations (gene gain or gene loss). Results are robust to different sources of data -- gene expression from microarrays, ESTs, or in situ hybridizations; and mutants from directed KO, transgenic insertions, point mutations, or morpholinos. We determine the pattern of these constraints, which differs from the model used to describe vertebrate morphological conservation ("hourglass" model). While morphological constraints reach a maximum at mid-development (the "phylotypic" stage), genomic constraints appear to decrease in a monotonous manner over developmental time.

SiMR: A simulator for learning computer architecture

This paper presents SiMR, a simulator of the Rudimentary Machine designed to be used in a first course of computer architecture of Software Engineering and Computer Engineering programmes. The Rudimentary Machine contains all the basic elements in a RISC computer, and SiMR allows editing, assembling and executing programmes for this processor. SiMR is used at the Universitat Oberta de Catalunya as one of the most important resources in the Virtual Computing Architecture and Organisation Laboratory, since students work at home with the simulator and reports containing their work are automatically generated to be evaluated by lecturers. The results obtained from a survey show that most of the students consider SiMR as a highly necessary or even an indispensable resource to learn the basic concepts about computer architecture.

Apertium Advanced Web Interface : A first step towards interactivity and language tools convergence

This documents sums up a projectaimed at building a new web interfaceto the Apertium machine translationplatform, including pre-editing andpost-editing environments. It containsa description of the accomplished workon this project, as well as an overviewof possible evolutions.

Real-time quantitative PCR assay for measurement of bird telomeres

We present the application of a real-time quantitative PCR assay, previously developed to measure relative telomere length in humans and mice, to two bird species, the zebra finch Taeniopygia guttata and the Alpine swift Apus melba. This technique is based on the PCR amplification of telomeric (TTAGGG)(n) sequences using specific oligonucleotide primers. Relative telomere length is expressed as the ratio (T/S) of telomere repeat copy number (T) to control single gene copy number (S). This method is particularly useful for comparisons of individuals within species, or where the same individuals are followed longitudinally. We used glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a single control gene. In both species, we validated our PCR measurements of relative telomere length against absolute measurements of telomere length determined by the conventional method of quantifying telomere terminal restriction fragment (TRF) lengths using both the traditional Southern blot analysis (Alpine swifts) and in gel hybridization (zebra finches). As found in humans and mice, telomere lengths in the same sample measured by TRF and PCR were well correlated in both the Alpine swift and the zebra finch.. Hence, this PCR assay for measurement of bird telomeres, which is fast and requires only small amounts of genomic DNA, should open new avenues in the study of environmental factors influencing variation in telomere length, and how this variation translates into variation in cellular and whole organism senescence.

Concentration of Airborne Staphylococcus aureus (MRSA and MSSA), Total Bacteria, and Endotoxins in Pig Farms.

Pigs are very often colonized by Staphylococcus aureus and transmission of such pig-associated S. aureus to humans can cause serious medical, hygiene, and economic problems. The transmission route of zoonotic pathogens colonizing farm animals to humans is not well established and bioaerosols could play an important role. The aim of this study was to assess the potential occupational risk of working with S. aureus-colonized pigs in Switzerland. We estimated the airborne contamination by S. aureus in 37 pig farms (20 nursery and 17 fattening units; 25 in summer, 12 in winter). Quantification of total airborne bacterial DNA, airborne Staphylococcus sp. DNA, fungi, and airborne endotoxins was also performed. In this experiment, the presence of cultivable airborne methicillin-resistant S. aureus (MRSA) CC398 in a pig farm in Switzerland was reported for the first time. Airborne methicillin-sensitive S. aureus (MSSA) was found in ~30% of farms. The average airborne concentration of DNA copy number of total bacteria and Staphylococcus sp. measured by quantitative polymerase chain reaction was very high, respectively reaching values of 75 (± 28) × 10(7) and 35 (± 9.8) × 10(5) copy numbers m(-3) in summer and 96 (± 19) × 10(8) and 40 (± 12) × 10(6) copy numbers m(-3) in winter. Total mean airborne concentrations of endotoxins (1298 units of endotoxin m(-3)) and fungi (5707 colony-forming units m(-3)) exceeded the Swiss recommended values and were higher in winter than in summer. In conclusion, Swiss pig farmers will have to tackle a new emerging occupational risk, which could also have a strong impact on public health. The need to inform pig farmers about biological occupational risks is therefore crucial.

Results of An International Study of Quantitative BCR/ABL Assays Using Defined RNA Samples

Molecular monitoring of BCR/ABL transcripts by real time quantitative reverse transcription PCR (qRT-PCR) is an essential technique for clinical management of patients with BCR/ABL-positive CML and ALL. Though quantitative BCR/ABL assays are performed in hundreds of laboratories worldwide, results among these laboratories cannot be reliably compared due to heterogeneity in test methods, data analysis, reporting, and lack of quantitative standards. Recent efforts towards standardization have been limited in scope. Aliquots of RNA were sent to clinical test centers worldwide in order to evaluate methods and reporting for e1a2, b2a2, and b3a2 transcript levels using their own qRT-PCR assays. Total RNA was isolated from tissue culture cells that expressed each of the different BCR/ABL transcripts. Serial log dilutions were prepared, ranging from 100 to 10-5, in RNA isolated from HL60 cells. Laboratories performed 5 independent qRT-PCR reactions for each sample type at each dilution. In addition, 15 qRT-PCR reactions of the 10-3 b3a2 RNA dilution were run to assess reproducibility within and between laboratories. Participants were asked to run the samples following their standard protocols and to report cycle threshold (Ct), quantitative values for BCR/ABL and housekeeping genes, and ratios of BCR/ABL to housekeeping genes for each sample RNA. Thirty-seven (n=37) participants have submitted qRT-PCR results for analysis (36, 37, and 34 labs generated data for b2a2, b3a2, and e1a2, respectively). The limit of detection for this study was defined as the lowest dilution that a Ct value could be detected for all 5 replicates. For b2a2, 15, 16, 4, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. For b3a2, 20, 13, and 4 labs showed a limit of detection at the 10-5, 10-4, and 10-3 dilutions, respectively. For e1a2, 10, 21, 2, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. Log %BCR/ABL ratio values provided a method for comparing results between the different laboratories for each BCR/ABL dilution series. Linear regression analysis revealed concordance among the majority of participant data over the 10-1 to 10-4 dilutions. The overall slope values showed comparable results among the majority of b2a2 (mean=0.939; median=0.9627; range (0.399 - 1.1872)), b3a2 (mean=0.925; median=0.922; range (0.625 - 1.140)), and e1a2 (mean=0.897; median=0.909; range (0.5174 - 1.138)) laboratory results (Fig. 1-3)). Thirty-four (n=34) out of the 37 laboratories reported Ct values for all 15 replicates and only those with a complete data set were included in the inter-lab calculations. Eleven laboratories either did not report their copy number data or used other reporting units such as nanograms or cell numbers; therefore, only 26 laboratories were included in the overall analysis of copy numbers. The median copy number was 348.4, with a range from 15.6 to 547,000 copies (approximately a 4.5 log difference); the median intra-lab %CV was 19.2% with a range from 4.2% to 82.6%. While our international performance evaluation using serially diluted RNA samples has reinforced the fact that heterogeneity exists among clinical laboratories, it has also demonstrated that performance within a laboratory is overall very consistent. Accordingly, the availability of defined BCR/ABL RNAs may facilitate the validation of all phases of quantitative BCR/ABL analysis and may be extremely useful as a tool for monitoring assay performance. Ongoing analyses of these materials, along with the development of additional control materials, may solidify consensus around their application in routine laboratory testing and possible integration in worldwide efforts to standardize quantitative BCR/ABL testing.

A functional microsatellite of the macrophage migration inhibitory factor gene associated with meningococcal disease.

Macrophage migration inhibitory factor (MIF) is an abundantly expressed proinflammatory cytokine playing a critical role in innate immunity and sepsis and other inflammatory diseases. We examined whether functional MIF gene polymorphisms (-794 CATT(5-8) microsatellite and -173 G/C SNP) were associated with the occurrence and outcome of meningococcal disease in children. The CATT(5) allele was associated with the probability of death predicted by the Pediatric Index of Mortality 2 (P=0.001), which increased in correlation with the CATT(5) copy number (P=0.04). The CATT(5) allele, but not the -173 G/C alleles, was also associated with the actual mortality from meningoccal sepsis [OR 2.72 (1.2-6.4), P=0.02]. A family-based association test (i.e., transmission disequilibrium test) performed in 240 trios with 1 afflicted offspring indicated that CATT(5) was a protective allele (P=0.02) for the occurrence of meningococcal disease. At baseline and after stimulation with Neisseria meningitidis in THP-1 monocytic cells or in a whole-blood assay, CATT(5) was found to be a low-expression MIF allele (P=0.005 and P=0.04 for transcriptional activity; P=0.09 and P=0.09 for MIF production). Taken together, these data suggest that polymorphisms of the MIF gene affecting MIF expression are associated with the occurrence, severity, and outcome of meningococcal disease in children.

Regulation of the vitellogenin gene B1 promoter after transfer into hepatocytes in primary cultures.

The estrogen-dependent and tissue-specific regulation of the Xenopus laevis vitellogenin gene B1 promoter has been studied by lipid-mediated DNA transfer into Xenopus hepatocytes in primary culture. Hepatocytes achieve an efficient hormonal control of this promoter through a functional interaction between the estrogen responsive elements and a promoter proximal region upstream of the TATA box, which is characterized by a high density of binding sites for the transcription factors CTF/NF-1, C/EBP and HNF3. DNA accessibility to restriction enzymes within the chromosomal copy of the vitellogenin gene B1 promoter shows that the estrogen responsive unit and the promoter proximal region are sensitive to digestion in uninduced and estrogen-induced hepatocytes but not in erythrocyte nuclei. Together, these findings support the notion that chromatin configuration as well as the interplay of promoter elements mediate proper hormone-dependent and tissue-specific expression of the B1 vitellogenin gene.

Drying of Ink in Inkjet Printing

Tämän diplomityön tavoitteena oli saada perustietoa tekijöistä, jotka vaikuttavat musteen kuivumiseen erilaisilla paperipinnoilla inkjet tulostuksessa. Tavoitteena oli saada tietoa erilaisista musteista, joita käytetään yleisimmissä inkjet tulostustekniikoissa, miten paperit vaikuttavat musteen kuivumiseen ja minkälaisia menetelmiä on olemassa musteen kuivumistekijöiden määrittämiseen. Lisäksi tarkoituksena oli varmistaa, voidaanko inkjetmusteiden absorptioajan määrittämiseen käytettävää DIGAT-laitetta käyttää määrittämään ja ennustamaan erilaisten musteiden kuivumista erilaisilla paperipinnoilla sekä etsiä korrelaatioita musteen absorptioajan ja teknisten paperiominaisuuksien sekä inkjet tulostuksen laadun välillä. Kirjallisuusosassa tarkasteltiin erilaisia inkjet tulostusmenetelmiä, niissä käytettäviä musteita ja musteiden koostumuksia. Tutkittiin myös paperin ja musteen välisiä vuorovaikutuksia sekä inkjet tulostuksen laatua. Kokeellisessa osassa tutkittiin musteenabsorboitumista paperiin DIGAT-laitteen avulla. kuudella eri musteella. Paperinäytteistä määritettiin teknisiä paperiominaisuuksia sekä ominaisuuksia, jotka liittyvät inkjet tulostuksen laatuun. Inkjet tulostuksen laatua tarkasteltiin tulostamalla testikuva kolmella eri tulostimella, jotka olivat Canon Bubble Jet i950, HP DeskJet Cxi970 ja Epson Stylus C46. Havaittiin, että DIGAT-laite ei sovellu määrittämään musteen absorptioaikoja kiiltäville näytteille.Tässä tutkimuksessa näyte, jonka kiilto oli 65 %, oli liian kiiltävä mitattavaksi DIGAT-laitteella. Lisäksi absorptiomäärityksissä havaittiin, että erilaiset musteet asettuvat erilailla paperin pintaan ja että pigmenttipohjaisella musteella asettumisaika oli kaikista pisin. Musteiden absorptioajat olivat nopeimpia erikoisinkjetpaperilla ja hitaimpia päällystetyillä, tiiviillä papereilla. Musteen absorptioajan ja teknisten paperiominaisuuksien ja inkjet tulostuksen laadun välisiä korrelaatioita oli vaikea havaita. Voidaan sanoa, että tulokset olivat muste- ja printterikohtaisia. Havaittiin vain muutamia teknisiä paperiominaisuuksia, jotka korreloivat hyvin musteen absorboitumisen kanssa. Nämäolivat Gurley-Hill huokoisuus, paperin tuhka- sekä kalsiumkarbonaattipitoisuus ja K&N värinabsorptio. Myöskään inkjet tulostuksen laadun ja musteen absorption välisiä korrelaatioita ei löytynyt kuin muutama; densiteetti, mottling sekä bleeding. Tämän tutkimuksen perusteella voidaan todeta DIGAT-laitteen soveltuvan hyvin kuvaamaan inkjet tulostuksen laatuominaisuuksista densiteettia, mottlingia sekä bleedingiä. DIGAT-laitetta voidaan siis käyttää avuksi ennustettaessa kuivumisaikaa ja sen vaikutusta edellä mainittuihin ominaisuuksiin. Läpipainatusominaisuuksia DIGAT-laitteen avulla ei voida tutkia, sillä ne ovat enemmän riippuvaisia paperin neliömassasta, paksuudesta ja huokoisuudesta kuinmusteen absorptioajasta. Teknisistä paperiominaisuuksista Gurley-Hill huokoisuus, paperin tuhka-sekä CaCO3-pitoisuus ja K&N värinabsorptio kuvaavat hyvin musteen imeytymisaikaa paperiin, kun taas ominaisuudet Cobb, HST ja polaari- sekädispersiokomponentit eivät kuvaa. Näyttää siltä, että testikuva, joka on tällä hetkellä käytössä UPM Tutkimus-keskuksessa, ei sovellu suurtehotulostuksen laadun tarkkailuun. Testikuva toimii hyvin pöytätulostimilla ja perinteisillä kopiopapereilla ja inkjetpapereilla, jotka on tarkoitettu tulostettaviksi hitaasti. Tulostusnopeuden ja musteen kuivumisnopeuden välisiä ilmiöitä seei tuo esille, joten se ei sovellu kuvaamaan suurtehotulostusta.

Abnormal social behaviors and altered gene expression rates in a mouse model for Potocki-Lupski syndrome.

The Potocki-Lupski syndrome (PTLS) is associated with a microduplication of 17p11.2. Clinical features include multiple congenital and neurobehavioral abnormalities and autistic features. We have generated a PTLS mouse model, Dp(11)17/+, that recapitulates some of the physical and neurobehavioral phenotypes present in patients. Here, we investigated the social behavior and gene expression pattern of this mouse model in a pure C57BL/6-Tyr(c-Brd) genetic background. Dp(11)17/+ male mice displayed normal home-cage behavior but increased anxiety and increased dominant behavior in specific tests. A subtle impairment in the preference for a social target versus an inanimate target and abnormal preference for social novelty (the preference to explore an unfamiliar mouse versus a familiar one) was also observed. Our results indicate that these animals could provide a valuable model to identify the specific gene(s) that confer abnormal social behaviors and that map within this delimited genomic deletion interval. In a first attempt to identify candidate genes and for elucidating the mechanisms of regulation of these important phenotypes, we directly assessed the relative transcription of genes within and around this genomic interval. In this mouse model, we found that candidates genes include not only most of the duplicated genes, but also normal-copy genes that flank the engineered interval; both categories of genes showed altered expression levels in the hippocampus of Dp(11)17/+ mice.

Genetic aberrations in pediatric follicular lymphoma

Background: Pediatric follicular lymphoma (FL) is a rare disease that differs from its adult counterpart both genetically and clinically. Excluding pediatric FL with IRF4-translocation, the genetic events associated with pediatric FL have not yet been defined. Objectives: The aim of this study was to perform a complete genetic characterization of IRF4-translocation negative pediatric follicular lymphomas to elucidate the genetic profile of these rare pediatric cases and determine common genetic alterations that could be associated to this phenotype. Design/Methods: We applied array-comparative genomic hybridization and molecular inversion probe assay adapted to formalin-fixed paraffin-embedded tissues from 18 patients aged £18 years diagnosed with FL. With the exception of one case with only focal involvement by lymphoma, the tumor cell content exceeded 50% in the evaluable samples. Eleven of 18 patients were treated according to NHL-BFM group multicenter trials whereas the remaining according to different protocols. All lacked t(14;18) translocation. Mutational analysis of TNFRSF14 gene was performed in 17 cases. Results: Only six pediatric cases displayed chromosomal imbalances, with gain/amplification of 6pter-p24.3 (including IRF4) and deletion/ copy number neutral-loss of heterozygosity in 1p36 (including TNFRSF14) being the most frequent alterations. Sequencing of the candidate gene TNFRSF14 at 1p36.32 showed nine mutations in seven cases. Conclusion: Combination of molecular and genetic features differentiated a recurrent pattern of genomic imbalances as well as of TNFRSF14 mutations in pediatric FL which together with other genetic alterations distinguishes two subsets of pediatric follicular lymphomas. The first group shows genomic aberrations and is associated with more aggressive histopathologic and clinical features. The second group lacks genetic alterations detectable with the present approaches and is associated with a more limited disease. Despite the absence of genomic aberrations, these cases resembled FL by their histopathological features.

Developing a web portal for managing marketing campaign information

Diplomityö liittyy Accenturen projektiin, jossa kehitettiin asiakkaalle CMS Web-portaali, jonka tarkoitus on tarjota mekanismi tuote- ja kampanjainformaation luontiin ja hallintaan sekä hallita niihin liittyviä budjettiprosesseja yrityksen Intranetissä. Työn tavoitteena on kuvata CMS-portaalin kehitysprosessia ja koota projektin aikana saadut opit ja parannusehdotukset. Tavoitteena on myös esittää ideoita havaittujen ongelmien ehkäisemiseksi tulevissa projekteissa. Portaalin kehitysprojektinsuurimmat haasteet liittyivät tietojärjestelmien kehitysympäristöihin, portaali- ja sisällönhallintapuolen yhdistämiseen sekä tiimikehitykseen. Kun portaaliprojekti tehdään asiakkaan tiloissa, ei täyttä kontrollia kehitysympäristöistä voi saada. Jos kehitysympäristöjen kanssa on ongelmia, niistä on syytä kommunikoida selkeästi ja ammattimaisesti asiakkaan kehitysympäristöistä vastaavalle taholle. Yhteistyö ja hyvät henkilökohtaiset suhteet asiakkaan kanssaovat tärkeitä. Jos portaalin sisällönhallintatarpeet eivät ole erittäin rajoittuneet, on suositeltavaa käyttää erillistä sisällönhallintaohjelmistoa portaalin sisällön hallitsemiseksi. Pienemmillekin projekteille tämä mahdollistaa paremmat laajennusmahdollisuudet. Portaali- ja sisällönhallintapuolenyhdistäminen kannattaa tehdä ohjelmistojen tarjoajien ohjeiden mukaan ja yleisiä menettelytapoja noudattaen. Yleisillä menettelytavoilla tarkoitetaan portaalinja sisällönhallinnan yhdistämisessä sitä, että portaali vastaanottaa sisältöä sisällönhallintajärjestelmältä, mutta kaikki sisällön muokkaustoimenpiteet tehdään sisällönhallintajärjestelmän käyttöliittymän kautta. Jos mukautettuja menettelytapoja on käytettävä, näiden kehittämiselle on varattava niiden vaatima aika. Tällöin Web-palveluiden käyttöä kannattaa harkita, koska Web-palvelut auttavat ohjelmistojen yhdistämisessä etenkin, kun yhdistäminen tehdään mukautetusti. Kun portaali tehdään käyttäen tiimikehitystyötä, on käytettävä myös versionhallintajärjestelmää, jolla estetään päällekkäisten muutosten mahdollisuus. Kehitysprosessin yhdenmukaistamiseksi on erittäin suositeltavaa tehdä yleinen kehitysohjedokumentti. Lisäksi on huolehdittava siitä, että kaikki kehittäjät noudattavat yleisiä kehitysohjeita, jotta yhdenmukaisuuden mukanaan tuomat edut saavutetaan mahdollisimman hyvin.

Aging preferentially affects molecular pathways implicated in development and disease of myelinating glial cells

The central and peripheral nervous systems are involved in multiple age-dependent neurological deficits that are often attributed to alterations in function of myelinating glial cells. However, the molecular events that underlie the age-related decline of glial cell function are unknown. We used Schwann cells as a model to study biological processes affected in glial cells by aging. We comprehensively profiled gene expression of the Schwann cellrich mouse sciatic nerve throughout life, from day of birth until senescence (840 days of age). We combined the aging data with the microarray transcriptional data obtained using nerves isolated from Schwann cell-specific neuropathy-inducing mutants MPZCre/+/Lpin1fE2−3/fE2−3 , MPZCre/+/ScapfE1/fE1 and Pmp22-null mice. The majority of age related transcripts were also affected in the analyzed mouse models of neuropathy (54.4%) and in development (59.5%) indicating a high level of overlapping in implicated molecular pathways. We observed that compared to peripheral nerve development, dynamically changing expression profiles in aging have opposite (anticorrelated) orientation while they copy the orientation of transcriptional changes observed in analyzed neuropathy models. Subsequent clustering and biological annotation of dynamically changing transcripts revealed that the processes most significantly deregulated in aging include inflammatory/immune response and lipid biosynthesis/metabolism. Importantly, the changes in these pathways were also observed in myelinated oligodendrocyte-rich optic nerves of aged mice, albeit with lower magnitude. This observation suggests that similar biological processes are affected in aging glial cells in central and peripheral nervous systems, however with different dynamics. Our data, which provide the first comprehensive comparison of molecular changes in glial cells in three distinct biological conditions comprising development, aging and disease, provide not only a new inside into the molecular alterations underlying neural system aging but also identify target pathways for potential therapeutic approaches to prevent or delay complications associated with age-related and inherited forms of neuropathies. *Current address: Department of Physiology, UCSF, San Francisco, CA, USA.

Acyl-CoA synthetase 3 promotes lipid droplet biogenesis in ER microdomains.

Control of lipid droplet (LD) nucleation and copy number are critical, yet poorly understood, processes. We use model peptides that shift from the endoplasmic reticulum (ER) to LDs in response to fatty acids to characterize the initial steps of LD formation occurring in lipid-starved cells. Initially, arriving lipids are rapidly packed in LDs that are resistant to starvation (pre-LDs). Pre-LDs are restricted ER microdomains with a stable core of neutral lipids. Subsequently, a first round of"emerging" LDs is nucleated, providing additional lipid storage capacity. Finally, in proportion to lipid concentration, new rounds of LDs progressively assemble. Confocal microscopy and electron tomography suggest that emerging LDs are nucleated in a limited number of ER microdomains after a synchronized stepwise process of protein gathering, lipid packaging, and recognition by Plin3 and Plin2. A comparative analysis demonstrates that the acyl-CoA synthetase 3 is recruited early to the assembly sites, where it is required for efficient LD nucleation and lipid storage.