Database construction and Peptide identification strategies for proteogenomic studies on sequenced genomes.

Since the advent of high-throughput DNA sequencing technologies, the ever-increasing rate at which genomes have been published has generated new challenges notably at the level of genome annotation. Even if gene predictors and annotation softwares are more and more efficient, the ultimate validation is still in the observation of predicted gene product( s). Mass-spectrometry based proteomics provides the necessary high throughput technology to show evidences of protein presence and, from the identified sequences, confirmation or invalidation of predicted annotations. We review here different strategies used to perform a MS-based proteogenomics experiment with a bottom-up approach. We start from the strengths and weaknesses of the different database construction strategies, based on different genomic information (whole genome, ORF, cDNA, EST or RNA-Seq data), which are then used for matching mass spectra to peptides and proteins. We also review the important points to be considered for a correct statistical assessment of the peptide identifications. Finally, we provide references for tools used to map and visualize the peptide identifications back to the original genomic information.

Characterization of a new clinical yeast species, Candida tunisiensis sp. nov., isolated from a strain collection from Tunisian hospitals.

From a collection of yeast isolates isolated from patients in Tunisian hospitals between September 2006 and July 2010, the yeast strain JEY63 (CBS 12513), isolated from a 50-year-old male that suffered from oral thrush, could not be identified to the species level using conventional methods used in clinical laboratories. These methods include matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), germ tube formation, and the use of CHROMagar Candida and metabolic galleries. Sequence analysis of the nuclear rRNA (18S rRNA, 5.8S rRNA, and 26S rRNA) and internal transcribed spacer regions (ITS1 and ITS2) indicated that the ribosomal DNA sequences of this species were not yet reported. Multiple gene phylogenic analyses suggested that this isolate clustered at the base of the Dipodascaceae (Saccharomycetales, Saccharomycetes, and Ascomycota). JEY63 was named Candida tunisiensis sp. nov. according to several phenotypic criteria and its geographical origin. C. tunisiensis was able to grow at 42°C and does not form chlamydospores and hyphae but could grow as yeast and pseudohyphal forms. C. tunisiensis exhibited most probably a haploid genome with an estimated size of 10 Mb on at least three chromosomes. Using European Committee for Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) Candida albicans susceptibility breakpoints as a reference, C. tunisiensis was resistant to fluconazole (MIC = 8 μg/ml), voriconazole (MIC = 0.5 μg/ml), itraconazole (MIC = 16 μg/ml), and amphotericin B (MIC = 4 μg/ml) but still susceptible to posaconazole (MIC = 0.008 μg/ml) and caspofungin (MIC = 0.5 μg/ml). In conclusion, MALDI-TOF MS permitted the early selection of an unusual isolate, which was still unreported in molecular databases but could not be unambiguously classified based on phylogenetic approaches.

ViralZone: a knowledge resource to understand virus diversity.

The molecular diversity of viruses complicates the interpretation of viral genomic and proteomic data. To make sense of viral gene functions, investigators must be familiar with the virus host range, replication cycle and virion structure. Our aim is to provide a comprehensive resource bridging together textbook knowledge with genomic and proteomic sequences. ViralZone web resource (www.expasy.org/viralzone/) provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.

Electronic Payments for Driver's Licensing Transactions,December 31, 2008

House File 2196 required the Department of Transportation (DOT) to study the acceptance of electronic payments at its customer service sites and sites operated by county treasurers. Specifically the legislation requires the following: “The department of transportation shall review the current methods the department employs for the collection of fees and other revenues at sites operated by county treasurers under chapter 321M and at customer service sites operated by the department. In conducting its review, the department, in cooperation with the treasurer of state, shall consider providing an electronic payment option for all of its customers. The department shall report its findings and recommendations by December 31, 2008, to the senate and house standing committees on transportation regarding the advantages and disadvantages of implementing one or more electronic payment systems.” This review focused on estimating the costs of providing an electronic payment option for customers of the DOT driver’s license stations and those of the 81 county treasurers. Customers at these sites engage in three primary financial transactions for which acceptance of electronic payments was studied: paying for a driver’s license (DL), paying for a non-operator identification card (ID), and paying certain civil penalties. Both consumer credit cards and PIN-based debit cards were reviewed as electronic payment options. It was assumed that most transactions would be made using a consumer credit card. Credit card companies charge a fee for each transaction for which they are used. The amount of these fees varies among credit card companies. The estimates for credit card fees used in this study were based on the State Treasurer of Iowa’s current credit card contract, which is due to expire in September 2009. Since credit card companies adjust their fees each year, estimates were based on the 2008 fee schedule. There is also a fee for the use of PIN-based debit cards. The estimates for PIN-based debit card transactions were based on information provided by Wells Fargo Merchant Services for current fees charged by debit card networks. Credit and debit card transactions would be processed through vendor-provided hardware and software. The costs would be determined through the competitive bidding process since several vendors provide this function; therefore, these costs are not reflected in this document.

The pricing of academic journals: A two-sided market perspective

More and more academic journals adopt an open-access policy, by which articlesare accessible free of charge, while publication costs are recovered through authorfees. We study the consequences of this open access policy on a journal s qualitystandard. If the journal s objective was to maximize social welfare, open accesswould be optimal as long as the positive externalities generated by its diffusionexceed the marginal cost of distribution. However, we show that if an open accessjournal has a different objective (such as maximizing readers payoffs, the impactof the journal or its profit), it tends to choose a quality standard below the sociallyefficient level.

Electronic titling: Potential and risks

Initiatives in electronic conveyancing and registration show the potential of new technologies to transform such systems, reducing costs and enhancing legal security. However,they also incur substantial risks of transferring costs and risks among registries, conveyancersand rightholders, instead of reducing them; entrenching the private interests of conveyancers,instead of increasing competition and disintermediating them; modifying the allocation of tasksin a way that leads in the long term to the debasement of registries of rights with indefeasibletitle into mere recordings of deeds; and empowering conveyancers instead of transactors andrightholders, which increases costs and reduces security. Fulfilling the promise of newtechnologies in both costs and security requires strengthening registries incentives andempowering rightholders in their interaction with registries.

Vertical distributions of plankton in the upper 35m of the peruvian upwelling zone - application of a shipboard electronic plankton counting system

Analiza el proyecto ICANE y suma modificaciones para estudiar la distribución de zooplancton pequeño

How quickly should we titrate antihypertensive medication? Systematic review modelling blood pressure response from trial data.

Context There are no evidence syntheses available to guide clinicians on when to titrate antihypertensive medication after initiation. Objective To model the blood pressure (BP) response after initiating antihypertensive medication. Data sources electronic databases including Medline, Embase, Cochrane Register and reference lists up to December 2009. Study selection Trials that initiated antihypertensive medication as single therapy in hypertensive patients who were either drug naive or had a placebo washout from previous drugs. Data extraction Office BP measurements at a minimum of two weekly intervals for a minimum of 4 weeks. An asymptotic approach model of BP response was assumed and non-linear mixed effects modelling used to calculate model parameters. Results and conclusions Eighteen trials that recruited 4168 patients met inclusion criteria. The time to reach 50% of the maximum estimated BP lowering effect was 1 week (systolic 0.91 weeks, 95% CI 0.74 to 1.10; diastolic 0.95, 0.75 to 1.15). Models incorporating drug class as a source of variability did not improve fit of the data. Incorporating the presence of a titration schedule improved model fit for both systolic and diastolic pressure. Titration increased both the predicted maximum effect and the time taken to reach 50% of the maximum (systolic 1.2 vs 0.7 weeks; diastolic 1.4 vs 0.7 weeks). Conclusions Estimates of the maximum efficacy of antihypertensive agents can be made early after starting therapy. This knowledge will guide clinicians in deciding when a newly started antihypertensive agent is likely to be effective or not at controlling BP.

Registries in rheumatological and musculoskeletal conditions. Paediatric Behçet's disease: an international cohort study of 110 patients. One-year follow-up data.

OBJECTIVE: To set-up an international cohort of patients suspected with Behçet's disease (BD). The cohort is aimed at defining an algorithm for definition of the disease in children. METHODS: International experts have defined the inclusion criteria as follows: recurrent oral aphthosis (ROA) plus one of following-genital ulceration, erythema nodosum, folliculitis, pustulous/acneiform lesions, positive pathergy test, uveitis, venous/arterial thrombosis and family history of BD. Onset of disease is <16 years, disease duration is ≤3 years, future follow-up duration is ≥4 years and informed consent is obtained. The expert committee has classified the included patients into: definite paediatric BD (PED-BD), probable PED-BD and no PED-BD. Statistical analysis is performed to compare the three groups of patients. Centres document their patients into a single database. RESULTS: At January 2010, 110 patients (56 males/54 females) have been included. Mean age at first symptom: 8.1 years (median 8.2 years). At inclusion, 38% had only one symptom associated with ROA, 31% had two and 31% had three or more symptoms. A total of 106 first evaluations have been done. Seventeen patients underwent the first-year evaluation, and 36 had no new symptoms, 12 had one and 9 had two. Experts have examined 48 files and classified 30 as definite and 18 as probable. Twenty-six patients classified as definite fulfilled the International Study Group criteria. Seventeen patients classified as probable did not meet the international criteria. CONCLUSION: The expert committee has classified the majority of patients in the BD group although they presented with few symptoms independently of BD classification criteria.

Towards storage and access of electronic theses: A proposal of its organisation for the Consortium of Catalan Libraries

Els objectius d'aquest informe són realitzar un estudi de la tècnica en la digitalització, l'emmagatzematge i l'accés a les tesis doctorals electròniques, per tal de fer una proposta d’organització al Consorci de Biblioteques Universitàries de Catalunya (CBUC). Actualment, tot i que existeixen diverses iniciatives a Europa, és als EUA on la digitalització de tesis doctorals s’ha desenvolupat més amb la creació de la Networked Digital Library for Theses and Dissertation (NDLTD), i ha estat qui ha definit els estàndards en aquest camp. En el següent informe es planteja i es recomana al CBUC l’adhesió institucional a l’NDLTD per poder gaudir de la seva experiència.

Nontraumatic spinal epidural hematoma during pregnancy: diagnosis and management concerns.

OBJECTIVE: Nontraumatic spinal epidural hematoma (SEH) during pregnancy is rare. Therefore, appropriate management of this occurrence is not well defined. The aim of this study was to extensively review the literature on this subject, to propose some novel treatment guidelines. METHODS: Electronic databases, manual reviews and conference proceedings up to December 2011 were systematically reviewed. Articles were deemed eligible for inclusion in this study if they dealt with nontraumatic SEH during pregnancy. Search protocols and data were independently assessed by two authors. RESULTS: In all, 23 case reports were found to be appropriate for review. The mean patient age was 28 years and gestational age was 33.2 weeks. Thirteen cases presented with acute interscapular pain. The clinical picture consisted of paraplegia, which occurred approximately 63 h after pain onset. Spinal cord decompression was performed within an average time of 20 h after neurological deficit onset. Fifteen patients had cesarean deliveries, even when the gestational age was less than 36 weeks. CONCLUSION: This review failed to identify articles, other than case reports, which could assist in the formation of new guidelines to treat SEH in pregnancy. However, we believe that SEH may be managed neurosurgically, without requiring prior, premature, cesarean section.

Paper 4: EUROCAT statistical monitoring: identification and investigation of ten year trends of congenital anomalies in Europe.

BACKGROUND: As part of EUROCAT's surveillance of congenital anomalies in Europe, a statistical monitoring system has been developed to detect recent clusters or long-term (10 year) time trends. The purpose of this article is to describe the system for the identification and investigation of 10-year time trends, conceived as a "screening" tool ultimately leading to the identification of trends which may be due to changing teratogenic factors.METHODS: The EUROCAT database consists of all cases of congenital anomalies including livebirths, fetal deaths from 20 weeks gestational age, and terminations of pregnancy for fetal anomaly. Monitoring of 10-year trends is performed for each registry for each of 96 non-independent EUROCAT congenital anomaly subgroups, while Pan-Europe analysis combines data from all registries. The monitoring results are reviewed, prioritized according to a prioritization strategy, and communicated to registries for investigation. Twenty-one registries covering over 4 million births, from 1999 to 2008, were included in monitoring in 2010.CONCLUSIONS: Significant increasing trends were detected for abdominal wall anomalies, gastroschisis, hypospadias, Trisomy 18 and renal dysplasia in the Pan-Europe analysis while 68 increasing trends were identified in individual registries. A decreasing trend was detected in over one-third of anomaly subgroups in the Pan-Europe analysis, and 16.9% of individual registry tests. Registry preliminary investigations indicated that many trends are due to changes in data quality, ascertainment, screening, or diagnostic methods. Some trends are inevitably chance phenomena related to multiple testing, while others seem to represent real and continuing change needing further investigation and response by regional/national public health authorities.

The Gene Ontology: enhancements for 2011.

The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.

Soft tissue sarcomas of the trunk wall (STS-TW): a study of 343 patients from the French Sarcoma Group (FSG) database.

BACKGROUND: Soft tissue sarcomas of the trunk wall (STS-TW) are usually studied together with soft tissue sarcomas of other locations. We report a study on STS-TW forming part of the French Sarcoma Group database. PATIENTS AND METHODS: Three hundred and forty-three adults were included. We carried out univariate and multivariate analysis for overall survival (OS), metastasis-free survival (MFS) and local recurrence-free survival (LRFS). RESULTS: Tumor locations were as follows: thoracic wall, 82.5%; abdominal wall, 12.3% and pelvic wall, 5.2%. Median tumor size was 6.0 cm. The most frequent tumor types were unclassified sarcoma (27.7%) and myogenic sarcoma (19.2%). A total of 44.6% of cases were grade 3. In all, 21.9% of patients had a previous medical history of radiotherapy (PHR). Median follow-up was 7.6 years. The 5-year OS, MFS and LRFS rates were 60.4%, 68.9% and 58.4%, respectively. Multivariate analysis retained PHR and grade for predicting LRFS and PHR, size and grade as prognostic factors of MFS. Factors influencing OS were age, size, PHR, depth, grade and surgical margins. The predictive factors of incomplete response were PHR, size and T3. CONCLUSIONS: Our results suggest similar classical prognostic factors as compared with sarcomas of other locations. However, a separate analysis of STS-TW revealed a significant poor prognosis subgroup of patients with PHR.

Sistemes logístics de codificació i identificació, i perspectives de futur

Comptar amb sistemes sofisticats de gestió o programes ERP (Enterprise Resource Planning) no és suficient per a les organitzacions. Per a què aquests recursos donin resultats adequats i actualitzats, la informació d’entrada ha de llegir-se de forma automàtica, per aconseguir estalviar en recursos, eliminació d’errors i assegurar el compliment de la qualitat. Per aquest motiu és important comptar amb eines i serveis d’identificació automàtica i col•lecció de dades. Els principals objectius a assolir (a partir de la introducció al lector de la importància dels sistemes logístics d’identificació en un entorn global d’alta competitivitat), són conèixer i comprendre el funcionament de les tres principals tecnologies existents al mercat (codis de barres lineals, codis de barres bidimensionals i sistemes RFID), veure en quin estat d’implantació es troba cadascuna i les seves principals aplicacions. Un cop realitzat aquest primer estudi es pretén comparar les tres tecnologies per o poder obtenir perspectives de futur en l’àmbit de l’autoidentificació. A partir de la situació actual i de les necessitats de les empreses, juntament amb el meravellós món que sembla obrir la tecnologia RFID (Radio Frequency Identification), la principal conclusió a la que s’arribarà és que malgrat les limitacions tècniques dels codis de barres lineals, aquests es troben completament integrats a tota la cadena logística gràcies a l’estandarització i la utilització d’un llenguatge comú, sota el nom de simbologies GTIN (Global Trade Item Number), durant tota la cadena de subministres que garanteixen total traçabilitat dels productes gràcies en part a la gestió de les bases de dades i del flux d’informació. La tecnologia RFUD amb l’EPC (Electronic Product Code) supera aquestes limitacions, convertint-se en el màxim candidat per a substituir els limitats codis de barres. Tot i això, RFID, amb l’EPC, no serà un adequat identificador logístic fins que es superin importants barreres, com són la falta d’estandarització i l’elevat cost d’implantació.