Mapping of a gene coding for a major late structural polypeptide on the vaccinia virus genome.

Cell-free translation of total RNA isolated from vaccinia virus-infected cells late in infection results in a complex mixture of polypeptides. A monospecific antibody directed against one of the major structural proteins of the virus particle immunoprecipitated a single polypeptide with a molecular weight of 11,000 (11K) from this mixture. Immunoprecipitation was therefore used to identify the structural polypeptide among the in vitro translation products of RNA purified by hybridization selection to restriction fragments of the vaccinia virus genome. This allowed us to map the mRNA coding for the 11K polypeptide to the extreme left-hand end of the HindIII E fragment. Detailed transcriptional mapping of this region of the genome by nuclease S1 analysis revealed the presence of a late RNA transcribed from the rightward-reading strand. Its 5' end mapped at ca. 130 base pairs to the left of the HindIII site at the junction between the HindIII F and E fragments. The map position of this RNA coincided precisely with the map position of the late message coding for the 11K polypeptide.

Intramolecular basis set superposition error effects on the planarity of benzene and other aromatic molecules: A solution to the problem

Recently, the surprising result that ab initio calculations on benzene and other planar arenes at correlated MP2, MP3, configuration interaction with singles and doubles (CISD), and coupled cluster with singles and doubles levels of theory using standard Pople’s basis sets yield nonplanar minima has been reported. The planar optimized structures turn out to be transition states presenting one or more large imaginary frequencies, whereas single-determinant-based methods lead to the expected planar minima and no imaginary frequencies. It has been suggested that such anomalous behavior can be originated by two-electron basis set incompleteness error. In this work, we show that the reported pitfalls can be interpreted in terms of intramolecular basis set superposition error (BSSE) effects, mostly between the C–H moieties constituting the arenes. We have carried out counterpoise-corrected optimizations and frequency calculations at the Hartree–Fock, B3LYP, MP2, and CISD levels of theory with several basis sets for a number of arenes. In all cases, correcting for intramolecular BSSE fixes the anomalous behavior of the correlated methods, whereas no significant differences are observed in the single-determinant case. Consequently, all systems studied are planar at all levels of theory. The effect of different intramolecular fragment definitions and the particular case of charged species, namely, cyclopentadienyl and indenyl anions, respectively, are also discussed

Knowledge and attitude regarding standard precautions in a Brazilian public emergency service: a cross-sectional study

The purpose of this study was to assess the knowledge and attitude of health care professionals regarding their use of universal precaution measures at a public emergency service. The study also aimed to assess the rates of occupational accidents involving biological substances among those workers. This study was performed with 238 workers, from June to November 2006, using univariate and multivariate analysis. The chance of not adopting precaution measures was 20.7 (95% CI: 5.68 - 75.14) times greater among drivers compared to physicians. No significant association was found between adopting universal precaution measures. The occupational accident rate was 20.6% (40.8% involving sharp-edged objects). The risk of physicians having an occupational accident was 2.7(95% CI: 1.05 - 7.09) times higher than that of drivers. The fact that a staff member had adequate knowledge about universal precaution measures was insufficient to foster compatible attitudes towards reducing the risk of transmitting infectious agents and causing occupational accidents.

Small and long non-coding RNAs in cardiac homeostasis and regeneration

Cardiovascular diseases and in particular heart failure are major causes of morbidity and mortality in the Western world. Recently, the notion of promoting cardiac regeneration as a means to replace lost cardiomyocytes in the damaged heart has engendered considerable research interest. These studies envisage the utilization of both endogenous and exogenous cellular populations, which undergo highly specialized cell fate transitions to promote cardiomyocyte replenishment. Such transitions are under the control of regenerative gene regulatory networks, which are enacted by the integrated execution of specific transcriptional programs. In this context, it is emerging that the non-coding portion of the genome is dynamically transcribed generating thousands of regulatory small and long non-coding RNAs, which are central orchestrators of these networks. In this review, we discuss more particularly the biological roles of two classes of regulatory non-coding RNAs, i.e. microRNAs and long non-coding RNAs, with a particular emphasis on their known and putative roles in cardiac homeostasis and regeneration. Indeed, manipulating non-coding RNA-mediated regulatory networks could provide keys to unlock the dormant potential of the mammalian heart to regenerate. This should ultimately improve the effectiveness of current regenerative strategies and discover new avenues for repair. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Cardiac Pathways of Differentiation, Metabolism and Contraction.

Is there an advantage to be gained from adding digital image cytometry of brush cytology to a standard biopsy protocol in patients with Barrett's esophagus?

BACKGROUND AND STUDY AIMS: The current gold standard in Barrett's esophagus monitoring consists of four-quadrant biopsies every 1-2 cm in accordance with the Seattle protocol. Adding brush cytology processed by digital image cytometry (DICM) may further increase the detection of patients with Barrett's esophagus who are at risk of neoplasia. The aim of the present study was to assess the additional diagnostic value and accuracy of DICM when added to the standard histological analysis in a cross-sectional multicenter study of patients with Barrett's esophagus in Switzerland. METHODS: One hundred sixty-four patients with Barrett's esophagus underwent 239 endoscopies with biopsy and brush cytology. DICM was carried out on 239 cytology specimens. Measures of the test accuracy of DICM (relative risk, sensitivity, specificity, likelihood ratios) were obtained by dichotomizing the histopathology results (high-grade dysplasia or adenocarcinoma vs. all others) and DICM results (aneuploidy/intermediate pattern vs. diploidy). RESULTS: DICM revealed diploidy in 83% of 239 endoscopies, an intermediate pattern in 8.8%, and aneuploidy in 8.4%. An intermediate DICM result carried a relative risk (RR) of 12 and aneuploidy a RR of 27 for high-grade dysplasia/adenocarcinoma. Adding DICM to the standard biopsy protocol, a pathological cytometry result (aneuploid or intermediate) was found in 25 of 239 endoscopies (11%; 18 patients) with low-risk histology (no high-grade dysplasia or adenocarcinoma). During follow-up of 14 of these 18 patients, histological deterioration was seen in 3 (21%). CONCLUSION: DICM from brush cytology may add important information to a standard biopsy protocol by identifying a subgroup of BE-patients with high-risk cellular abnormalities.

Estimation of protein coding density in a corpus of DNA sequence data

A number of experimental methods have been reported for estimating the number of genes in a genome, or the closely related coding density of a genome, defined as the fraction of base pairs in codons. Recently, DNA sequence data representative of the genome as a whole have become available for several organisms, making the problem of estimating coding density amenable to sequence analytic methods. Estimates of coding density for a single genome vary widely, so that methods with characterized error bounds have become increasingly desirable. We present a method to estimate the protein coding density in a corpus of DNA sequence data, in which a ‘coding statistic’ is calculated for a large number of windows of the sequence under study, and the distribution of the statistic is decomposed into two normal distributions, assumed to be the distributions of the coding statistic in the coding and noncoding fractions of the sequence windows. The accuracy of the method is evaluated using known data and application is made to the yeast chromosome III sequence and to C.elegans cosmid sequences. It can also be applied to fragmentary data, for example a collection of short sequences determined in the course of STS mapping.

Identifying protein-coding genes in genomic sequences

The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets.

La néphrectomie partielle dans le cancer du rein: un nouveau standard [Partial nephrectomy in renal cancer: a new standard?]

Rising renal cell carcinoma incidence is in relationship with early diagnosis during radiological exams. Radical nephrectomy was the gold standard treatment for 30 years. Partial nephrectomy is nowadays a validated therapeutic option for renal cell carcinoma up to 7 cm with comparable oncological results associated with better life quality and survival. Partial nephrectomy is tricky and laparoscopic approach remains reserved for expert centers.

Updated survival data of the phase iii clinical trial of novottf-100a versus best standard chemotherapy for recurrent glioblastoma

NovoTTF-100A (TTF) is a portable device delivering low-intensity, intermediate-frequency, alternating electric fields using noninvasive, disposable scalp electrodes. TTF interferes with tumor cell division, and it has been approved by the US Food and Drug Administration (FDA) for the treatment of recurrent glioblastoma (rGBM) based on data from a phase III trial. This presentation describes the updated survival data 2 years after completing recruitment. Adults with rGBM (KPS ≥ 70) were randomized (stratified by surgery and center) to either continuous TTF (20-24 h/day, 7 days/week) or efficacious chemotherapy based on best physician choice (BPC). The primary endpoint was overall survival (OS), and secondary endpoints were PFS6, 1-year survival, and QOL. Patients were randomized (28 US and European centers) to either TTF alone (n ¼ 120) or BPC (n ¼ 117). Patient characteristics were balanced, median age was 54 years (range, 23-80 years), and median KPS was 80 (range, 50-100). One quarter of the patients had debulking surgery, and over half of the patients were at their second or later recurrence. OS in the intent-to-treat (ITT) population was equivalent in TTF versus BPC patients (median OS, 6.6vs. 6.0 months; n ¼ 237; p ¼ 0.26; HR ¼ 0.86). With a median follow-up of 33.6 months, long-term survival in the TTF group was higher than that in the BPC group at 2, 3, and 4 years of follow-up (9.3% vs. 6.6%; 8.4% vs. 1.4%; 8.4% vs. 0.0%, respectively). Analysis of patients who received at least one treatment course demonstrated a survival benefit for TTF patients compared to BPC patients (median OS, 7.8 vs. 6.0 months; n ¼ 93 vs. n ¼ 117; p ¼ 0.012; HR ¼ 0.69). In this group, 1-year survival was 28% vs. 20%, and PFS6 was 26.2% vs. 15.2% (p ¼ 0.034). TTF, a noninvasive, novel cancer treatment modality shows significant therapeutic efficacy with promising long-term survival results. The impact of TTF was more pronounced when comparing only patients who received the minimal treatment course. A large-scale phase III trial in newly diagnosed GBM is ongoing.

A Musically aware system for browsing and interacting with audio music collections

In the context of the CompMusic project we are developing methods to automatically describe/annotate audio music recordings pertaining to various music cultures. As away to demonstrate the usefulness of the methods we are also developing a system to browse and interact with specific audio collections. The system is an online web application that interfaces with all the data gathered (audio, scores plus contextual information) and all the descriptions that are automatically generated with the developed methods. In this paper we present the basic architecture of the proposed system, the types of data sources that it includes,and we mention some of the culture specific issues that we are working on for its development. The system is in a preliminary stage but it shows the potential that MIR technologies can have in browsing and interacting with musiccollections of various cultures.

Chimioradiothérapie postopératoire des cancers des voies aérodigestives : vers un nouveau standard [Post-operative radiochemotherapy of the head and neck: Towards new standards?]

Head and neck squamous cell carcinomas are frequently diagnosed at an advanced stage. Their treatment remains controversial, and has to be multidisciplinary. External beam radiotherapy is a recognized treatment option after radical curative surgery in order to improve local control. Different adjuvant treatment options have been studied in order to improve the outcome of these patients. We review in this paper the different prognostic factors indicating an adjuvant treatment and the interest of treatment intensification in bad prognostic patients.

Transcription, tagging and coding of bilingual corpora via LIDES

L'objectiu d'aquest informe és presentar l'aplicació d'una sèrie de propostes sobre transcripció, etiquetatge i codificació a dos corpus: el corpus bilingüe LC (La Canonja (Català-Espanyol)) i el corpus trilingüe CSCD (Code-switching as Communicative Design (Català-Espanyol-Anglès)). Aquestes propostes, que constitueixen l'aportació de l'equip IULA-LIPPS (Language Interaction in Plurilingual and Plurilectal Speakers) al manual de codificació del sistema LIDES (Language Interaction Database Exchange System), adoptat pel grup europeu LIPPS, poden ser útils per transcriure, etiquetar i codificar dades provinents de llengües tipològicament properes i distants.

The Regulatory Choice between a Label and a Minimum-Quality Standard, 2005

This paper revisits the issue of the regulatory choice between a mandatory label and a minimum-quality standard. When the cost of regulation is relatively low, we show that the socially optimal choice depends on the producers’ cost structure for complying with regulation and improving quality. Under a marginal cost for improving quality, the mandatory labeling is sufficient for reaching the socially optimal level of quality. Under a fixed cost for improving quality, we show that each instrument or the combination of both instruments may emerge at the equilibrium.

Induktiosilmukka kuulolaitteen käyttäjän apuvälineenä

Tämä insinöörityö tehtiin Kuulonhuoltoliitto ry:n Esteetön kuuntelu -projektille. Työ käsittelee kuulolaitteen käyttäjän apuvälineenä käytettäviä induktiosilmukkajärjestelmiä. Induktiivisen äänensiirtojärjestelmän avulla huonokuuloinen saa kuunteluympäristöstään paremman signaali-kohinasuhteen ilman tilan kaikua ja taustahälyä. Tämä helpottaa kuuntelua esimerkiksi puhetilaisuuksissa. Työn tarkoituksena oli päivittää aiempia tutkimuksia kokoamalla uusin tietous induktiosilmukoiden tekniikasta. Kirjallisuustutkimuksen lisäksi kartoitettiin nykyinen silmukkavahvistinkanta haastattelemalla maahantuojia ja jälleenmyyjiä. Silmukkavahvistimien hintakartoituksen tarkoituksena oli rakentaa perusteet sopivan tehoisen ja hintaisen vahvistimen hankintaa varten suunniteltaessa induktiivisella äänensiirtojärjestelmällä varustettavia tiloja. Työ tarkastelee induktiivisen äänensiirtojärjestelmän ensisijaisen kohderyhmän, kuulokojeita käyttävien huonokuuloisten keskeisiä tarpeita ja heidän käyttämäänsä apuvälinetekniikkaa. Työ käy läpi audiotekniikan perusteita, sähkömagneettisen induktioilmiön, induktiivisen äänensiirtojärjestelmän rakenteen, sen ylikuulumisongelmat ja häiriötekijät sekä IEC:n 60118-4 edition 2.0 standardin CDV-luonnoksen mukaiset periaatteelliset asennusja mittausohjeet. IEC:n tuleva standardi tekee työstä ajankohtaisen. Työn tuloksena saatua tietoa voidaan käyttää Kuulonhuoltoliitto ry:n opas- ja tiedotusmateriaalin uudistamisessa, pohjana hyvän kuunteluympäristön malliratkaisujen ja esteettömyyskriteerien soveltamisessa. Työstä on hyötyä erityisesti Kuulonhuoltoliitto ry:n vapaaehtoiskartoittajille kuten myös kenelle tahansa aiheesta syvemmin kiinnostuneelle.

Wörter stehen da einige. On nominal split topicalization in non-standard viennese german

This work investigates the syntactic, semantic, and pragmatic properties of nominal Split Topicalization (ST) constructions in Standard and non-Standard German. The topic phrase denotes a property, and the MF phrase either modifies this property or picks out a specific entity. Semantically, the topic phrase will be analysed as a property-denoting expression which restricts the denotation of the verbal predicate, while the MF phrase is composed either via specify or restrict (cf. Chung and Ladusaw, 2003). Syntactically, the base position of the topic phrase is the (incorporating) verb, and the MF phrase is generated independently as the complement of the verb containing an empty pronoun. Since predicates introduce abstract discourse referents, the topic phrase can be resumed via "pro" in the MF phrase.