T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

Object-oriented development of client / server application: case study of service control software

Tässä työssä on esitetty sen ohjelmiston kehittämisen prosessi, joka on tarkoitettu annettavien palveluiden valvottavaksi käyttäen prototyyppimallia. Raportti sisältää vaatimusten, kohteisiin suunnatun analyysin ja suunnittelun, realisointiprosessien kuvauksen ja prototyypin testauksen. Ohjelmiston käyttöala – antavien palveluiden valvonta. Vaatimukset sovellukselle analysoitiin ohjelmistomarkkinoiden perusteella sekä ohjelmiston engineeringin periaatteiden mukaisesti. Ohjelmiston prototyyppi on realisoitu käyttäen asiakas-/palvelinhybridimallia sekä ralaatiokantaa. Kehitetty ohjelmisto on tarkoitettu venäläisille tietokonekerhoille, jotka erikoistuvat pelipalvelinten antamiseen.

Kolmannen sukupolven matkaviestinverkon puhelunohjaus MSC Server –konseptilla

Tietoliikenneala elää muutosten aikaa. Vanhat piirikytketyt kapeakaistaiset verkot ovat väistymässä seuraavan sukupolven verkkojen tieltä. GPRS-verkot tekevät tuloaan ja 3G-verkkojen kehitystyö on kiivaimmillaan laitetoimittajien ratkoessa verkoille asetettuja haasteita. Jää nähtäväksi, kykenevätkö 3G-verkot vastaamaan näihin haasteisiin. Työssä käsitellään 3G-verkon arkkitehtuuria, toimintaa ja puhelunohjausta MSC Server -konseptissa, sekä käydään läpi muutamia puheluesimerkkejä. 3G-verkon arkkitehtuuri, jossa puhelunohjaus on erotettu mediakerroksesta, esitetään ja uudet verkkoelementit ja niiden toiminta käsitellään. Esitelty teoria perustuu kirjallisuuteen sekä yleisesti hyväksyttyihin 3G- verkon standardeihin. Näitä standardeja julkaisevat muun muassa ITU-T ja 3GPP yhdessä yhteistyöyritystensä kanssa. Standardointityö on monin osin vielä kesken ja se on vaikeuttanut 3G-verkkojen suunnittelutyötä merkittävästi. Työn tarkoituksena on selvittää puhelunohjausta 3G-verkossa ja sen toteuttamista MSC Server –konseptilla. MSC Serverin toteutusvaihtoehtoja arvioidaan ja niistä valitaan yksi 3G-verkon puhelunohjauksen toteutusmalliksi. Työtä jatketaan tämän diplomityön jälkeen tarkemman toteutuksen suunnittelulla, päämääränä rakentaa 3G-verkko.

Investigation of interface between Multimedia IP Network and Call Processing Server in 3G IP Telephony Core Network

The thesis presents an overview of third generation of IP telephony. The architecture of 3G IP Telephony and its components are described. The main goal of the thesis is to investigate the interface between the Call Processing Server and Multimedia IP Networks. The interface functionality, proposed protocol stack and a general description are presented in the thesis. To provide useful services, 3G IP Telephony requires a set of control protocols for connection establishment, capabilities exchange and conference control. The Session Initiation Protocol (SIP) and the H.323 are two protocols that meet these needs. In the thesis these two protocols are investigated and compared in terms of Complexity, Extensibility, Scalability, Services, Resource Utilization and Management.

Fmoc-2-Mercaptobenzothiazole (MBT), for the Introduction of the Fmoc Moiety Free of Side-Reactions

A double side-reaction, consisting in the formation of Fmoc--Ala-OH and Fmoc--Ala-AA-OH, during the preparation of Fmoc protected amino acids (Fmoc-AA-OH) with Fmoc-OSu is discussed. Furthermore, the new Fmoc-2-MBT reagent is proposed for avoiding these side-reactions as well as the formation of the Fmoc-dipeptides (Fmoc-AA-AA-OH) and even tripeptides, which is another important side-reaction when chloroformates such as Fmoc-Cl is used for the protection of the -amino function of the amino acids.

Server Virtualization

Virtualisoinnin ideana on kuvata tietotekniikkaan liittyvät laiteresurssit ryhminä. Kun jonkin tehtävän suoritukseen tarvitaan resursseja, ne kerätään erikseen jokaisesta ryhmästä. Virtualisoinnin yksi osa-alue on palvelimen tai palvelinten virtualisointi, jossa pyritään hyödyntämään palvelinlaitteisto mahdollisimman tehokkaasti. Tehokkuus saavutetaan käyttämällä erillisiä instansseja, joita kutsutaan virtuaalikoneiksi. Tässä diplomityössä esitellään ja verrataan erilaisia palvelinten virtualisointimalleja ja tekniikoita, joita voidaan käyttää IA-32 arkkitehtuurin kanssa. Eroa virtualisoinnin ja eri partitiointitekniikoiden välillä tarkastellaan erikseen. Lisäksi muutoksia, joita palvelinten virtualisointi aiheuttaa infrastruktuuriin, ympäristöön ja laitteistoon käsitellään yleisellä tasolla. Teorian oikeellisuutta todistettiin suorittamalla useita testejä käyttäen kahta eri virtualisointiohjelmistoa. Testien perusteella palvelinten virtualisointi vähentää suorituskykyä ja luo ympäristön, jonka hallitseminen on vaikeampaa verrattuna perinteiseen ympäristöön. Myös tietoturvaa on katsottava uudesta näkökulmasta, sillä fyysistä eristystä ei virtuaalikoneille voida toteuttaa. Jotta virtualisoinnista saataisiin mahdollisimman suuri hyöty tuotantoympäristössä, vaaditaan tarkkaa harkintaa ja suunnitelmallisuutta. Parhaat käyttökohteet ovat erilaiset testiympäristöt, joissa vaatimukset suorituskyvyn ja turvallisuuden suhteen eivät ole niin tarkat.

Marked increase in incidence for bloodstream infections due to Escherichia coli, a side effect of previous antibiotic therapy in the elderly.

We conducted a survey including 3334 bloodstream infections (BSIs) due to E. coli diagnosed in 2005-2014 at a stable cohort of hospitals. Marked increases in incidence were observed for community-acquired (CA) BSIs in patients aged >75 years, CA-BSIs of digestive origin in patients aged 60-74 years, healthcare-associated BSIs, and BSIs associated with ESBL (extended-spectrum B-lactamase)-producing E. coli (ESBLEc). Using MLST, we studied the genetic diversity of 412 BSI isolates recovered during the 2014 survey: 7 major sequence type complexes (STCs) were revealed in phylogenetic group B2, 3 in group A/B1 and 2 in group D. Among the 31 ESBLEc isolates, 1/3 belonged to STC 131. We searched for possible associations between clonal groups, clinical determinants and characteristics of BSIs: isolates from groups B2 (except STC 131) and D were susceptible to antibiotics and associated with BSIs of urinary origin in patients <60 years. STC 131 and group A/B1 isolates were multi-drug resistant and associated with CA-BSIs of digestive origin in patients aged 60-74 with a recent history of antibiotic treatment. STC 131 isolates were associated with HCA-BSIs in patients with recent/present hospitalization in a long-stay unit. We provide a unique population-based picture of the epidemiology of E. coli BSI. The aging nature of the population led to an increase in the number of cases caused by the B2 and D isolates generally implicated in BSIs. In addition, the association of a trend toward increasing rates of gut colonization with multi drug-resistant isolates revealed by the rise in the incidence of BSIs of digestive origin caused by STC 131 and A/B1 (STCs 10, 23, and 155) isolates, and a significant increase in the frequency of BSIs in elderly patients with recent antibiotic treatment suggested that antibiotic use may have contributed to the growing incidence of BSI.

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

Background Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser. Results BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin. Conclusions BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper webcite.

Radiothérapie « flash » à très haut débit de dose : un moyen d'augmenter l'indice thérapeutique par minimisation des dommages aux tissus sains [Ultrahigh dose-rate, "flash" irradiation minimizes the side-effects of radiotherapy].

PURPOSE: Pencil beam scanning and filter free techniques may involve dose-rates considerably higher than those used in conventional external-beam radiotherapy. Our purpose was to investigate normal tissue and tumour responses in vivo to short pulses of radiation. MATERIAL AND METHODS: C57BL/6J mice were exposed to bilateral thorax irradiation using pulsed (at least 40Gy/s, flash) or conventional dose-rate irradiation (0.03Gy/s or less) in single dose. Immunohistochemical and histological methods were used to compare early radio-induced apoptosis and the development of lung fibrosis in the two situations. The response of two human (HBCx-12A, HEp-2) tumour xenografts in nude mice and one syngeneic, orthotopic lung carcinoma in C57BL/6J mice (TC-1 Luc+), was monitored in both radiation modes. RESULTS: A 17Gy conventional irradiation induced pulmonary fibrosis and activation of the TGF-beta cascade in 100% of the animals 24-36 weeks post-treatment, as expected, whereas no animal developed complications below 23Gy flash irradiation, and a 30Gy flash irradiation was required to induce the same extent of fibrosis as 17Gy conventional irradiation. Cutaneous lesions were also reduced in severity. Flash irradiation protected vascular and bronchial smooth muscle cells as well as epithelial cells of bronchi against acute apoptosis as shown by analysis of caspase-3 activation and TUNEL staining. In contrast, the antitumour effectiveness of flash irradiation was maintained and not different from that of conventional irradiation. CONCLUSION: Flash irradiation shifted by a large factor the threshold dose required to initiate lung fibrosis without loss of the antitumour efficiency, suggesting that the method might be used to advantage to minimize the complications of radiotherapy.

Brief report : Academic amotivation in light of the dark side of identity formation

The study intended to determine motivational profiles of first-year undergraduates and aimed their characterization in terms of identity processes. First, a cluster analysis revealed five motivational profiles: combined (i.e., high quantity of motivation, low amotivation); intrinsic (i.e., high intrinsic, low introjected and external regulation, low amotivation); "demotivated" (i.e., very low quantity of motivation and amotivation); extrinsic (i.e., high extrinsic and identified regulation and low intrinsic and amotivation); and "amotivated" (i.e., low intrinsic and identified, very high amotivation). Second, using Lebart's (2000) methodology, the most characteristic identity processes were listed for each motivational cluster. Demotivated and amotivated profiles were refined in terms of adaptive and maladaptive forms of exploration. Notably, exploration in breadth and in depth were underrepresented in demotivated students compared to the total sample; commitment and ruminative exploration were under and overrepresented respectively in amotivated students. Educational and clinical implications are proposedand future research is suggested.

Treatment-related renal side-effects in pediatric cancer patients

Background: The long-term side-effects of cancer treatments are of growing importance, since the number of pediatric cancer survivors has considerably increased. Renal side-effects should be noted early to prevent further deterioration. Renal dysfunction may also develop long after cancer treatment. Easy and reliable methods for assessing renal function are needed. Aims: The aims were to find the mechanisms behind methotrexate-induced renal damage by studying renal tubular cells (LLC-PK1cells), and to evaluate the usefulness of laboratory tests in assessing glomerular function in pediatric cancer patients by comparing an isotope clearance method with alternative methods. The aim was also to study the long-term effects of bone marrow transplantation (BMT) and high-dose methotrexate (HD-MTX) treatment in renal function. Results: Methotrexate induced time-dependent renal tubular cell swelling and cell death. In patients treated with HD-MTX a significant decrease in GFR was noted after a follow-up time of one to ten years. One year after BMTthe GFR was reduced, especially in patients treated with total body irradiation (TBI). GFR recovered slightly but remained stable thereafter. In glomerular function assessment the serum cystatin C (cysC) concentration showed a significant association with GFR measured by the isotope method. Conclusions: Methotrexate induced acute damage in renal tubular cells. In assessing GFR the isotope method still remains the method of choice, but the assay of cystatin C was the most reliable of other alternatives. Long-term follow-up of renal function is needed in BMT patients and patients treated with HD-MTX.

Kuormitustestausvälineen valinta Microsoft Office SharePoint Server 2007 – toteutuksessa

Kuormitustestaus on osa web-sovellusten kehitystä ja käyttöönottoa. Sillä varmistetaan sovellusten toimivuus ennalta määrätyn kuorman alla. Microsoft Office SharePoint Server 2007 (MOSS) on palvelintuote nykyaikaisten web-sovellusten luontiin ja ylläpitoon. Työssä vertaillaan kahta eri uormitustestaustyökalua: SilkPerformer 2008 ja Visual Studio Team System 2008 Test Edition ja valitaan MOSS – web-sovelluksille paremmin sopiva työkalu. Työssä vertaillaan työkaluja niiden ominaisuuksien perusteella sekä suorittamalla kuormitustestausta testausta varten luodulle MOSS – web-sovellukselle. Vaikuttavien tekijöiden perusteella työkaluja arvioidaan ja tämän perusteella saadaan tulos vertailulle. Työn tuloksena Visual Studio Team System 2008 Test Edition sopii paremmin MOSS – web-sovelluksen kuormitustestausvälineeksi. Vertailussa kuitenkin havaittiin, että työkalut ovat melko tasavertaisia, ja käytännön tilanteesta riippuu, kumpi sopii paremmin. Tämä työ auttaa valinnan teossa.