ViralZone: recent updates to the virus knowledge resource.

ViralZone (http://viralzone.expasy.org) is a knowledge repository that allows users to learn about viruses including their virion structure, replication cycle and host-virus interactions. The information is divided into viral fact sheets that describe virion shape, molecular biology and epidemiology for each viral genus, with links to the corresponding annotated proteomes of UniProtKB. Each viral genus page contains detailed illustrations, text and PubMed references. This new update provides a linked view of viral molecular biology through 133 new viral ontology pages that describe common steps of viral replication cycles shared by several viral genera. This viral cell-cycle ontology is also represented in UniProtKB in the form of annotated keywords. In this way, users can navigate from the description of a replication-cycle event, to the viral genus concerned, and the associated UniProtKB protein records.

Caregiver's interpret infants' early gestures based on shared knowledge about referents

Gestures are the first forms of conventional communication that young children develop in order to intentionally convey a specific message. However, at first, infants rarely communicate successfully with their gestures, prompting caregivers to interpret them. Although the role of caregivers in early communication development has been examined, little is known about how caregivers attribute a specific communicative function to infants' gestures. In this study, we argue that caregivers rely on the knowledge about the referent that is shared with infants in order to interpret what communicative function infants wish to convey with their gestures. We videotaped interactions from six caregiver-infant dyads playing with toys when infants were 8, 10, 12, 14, and 16 months old. We coded infants' gesture production and we determined whether caregivers interpreted those gestures as conveying a clear communicative function or not; we also coded whether infants used objects according to their conventions of use as a measure of shared knowledge about the referent. Results revealed an association between infants' increasing knowledge of object use and maternal interpretations of infants' gestures as conveying a clear communicative function. Our findings emphasize the importance of shared knowledge in shaping infants' emergent communicative skills.

Use of DNA profiles for investigation using a simulated national DNA database: Part I. Partial SGM Plus profiles.

In traditional criminal investigation, uncertainties are often dealt with using a combination of common sense, practical considerations and experience, but rarely with tailored statistical models. For example, in some countries, in order to search for a given profile in the national DNA database, it must have allelic information for six or more of the ten SGM Plus loci for a simple trace. If the profile does not have this amount of information then it cannot be searched in the national DNA database (NDNAD). This requirement (of a result at six or more loci) is not based on a statistical approach, but rather on the feeling that six or more would be sufficient. A statistical approach, however, could be more rigorous and objective and would take into consideration factors such as the probability of adventitious matches relative to the actual database size and/or investigator's requirements in a sensible way. Therefore, this research was undertaken to establish scientific foundations pertaining to the use of partial SGM Plus loci profiles (or similar) for investigation.

Angiotensinergic innervation of the kidney: present knowledge and its significance.

Intrarenal neurotransmission implies the co-release of neuropeptides at the neuro-effector junction with direct influence on parameters of kidney function. The presence of an angiotensin (Ang) II-containing phenotype in catecholaminergic postganglionic and sensory fibers of the kidney, based on immunocytological investigations, has only recently been reported. These angiotensinergic fibers display a distinct morphology and intrarenal distribution, suggesting anatomical and functional subspecialization linked to neuronal Ang II-expression. This review discusses the present knowledge concerning these fibers, and their significance for renal physiology and the pathogenesis of hypertension in light of established mechanisms. The data suggest a new role of Ang II as a co-transmitter stimulating renal target cells or modulating nerve traffic from or to the kidney. Neuronal Ang II is likely to be an independent source of intrarenal Ang II. Further physiological experimentation will have to explore the role of the angiotensinergic renal innervation and integrate it into existing concepts.

Which prior knowledge? Quantification of in vivo brain 13C MR spectra following 13C glucose infusion using AMARES.

The recent developments in high magnetic field 13C magnetic resonance spectroscopy with improved localization and shimming techniques have led to important gains in sensitivity and spectral resolution of 13C in vivo spectra in the rodent brain, enabling the separation of several 13C isotopomers of glutamate and glutamine. In this context, the assumptions used in spectral quantification might have a significant impact on the determination of the 13C concentrations and the related metabolic fluxes. In this study, the time domain spectral quantification algorithm AMARES (advanced method for accurate, robust and efficient spectral fitting) was applied to 13 C magnetic resonance spectroscopy spectra acquired in the rat brain at 9.4 T, following infusion of [1,6-(13)C2 ] glucose. Using both Monte Carlo simulations and in vivo data, the goal of this work was: (1) to validate the quantification of in vivo 13C isotopomers using AMARES; (2) to assess the impact of the prior knowledge on the quantification of in vivo 13C isotopomers using AMARES; (3) to compare AMARES and LCModel (linear combination of model spectra) for the quantification of in vivo 13C spectra. AMARES led to accurate and reliable 13C spectral quantification similar to those obtained using LCModel, when the frequency shifts, J-coupling constants and phase patterns of the different 13C isotopomers were included as prior knowledge in the analysis.

Is MDCT enough reliable for the evaluation of acute colitis including the underlying etiology? : correlation with colonoscopy and pathology : P2

Purpose: 1. To assess the diagnostic value of MDCT for acute colitis of various origin confirmed by colonoscopy and histology. 2. To evaluate the accuracy of MDCT of making the correct differential diagnosis. Methods and materials: The electronic hospital database from January 2006 to August 2008 revealed 351 patients with acute colitis of any origin wdetected by colonoscopy. In 85 out of these patients MDCT had been simultaneously performed (delay 3.1 days). Two radiologists jointly reviewed their corresponding CT features without knowledge of pathology and correlated them with the final histological diagnosis. Results: Eighty patients were finally included (46 women, mean age 63.4). Colitis was of ischemic (n = 35, 44%) or infectious (n = 15, 19%) origin. 18 patients (23%) had acute ulcerative colitis or Crohn's disease, in 10 patients (12%) another inflammatory cause and in two patients (2%) post radiation colitis was proven. MDCT was positive in 63 patients (78.9%). In 11 out of the 17 negative MDCT, the examination had been performed without large bowel distention. Ischemic colitis was responsible for 47.1% of the negative MDCT. Correct differential diagnosis was made in 32 (50.7%) out of the 63 positive MDCT. Among the different etiologies, the ischemic colitis was the most often misdiagnosed cause (n = 17, 58.6%). Conclusion: Large bowel distension is mandatory for reliable MDCT detection of acute colitis of any origin. Among the different aetiologies the ischemic cause is the most often associated with false negative MDCT findings and, in case of positive features, the most difficult to recognize as such.

A Modulated Closed Form solution for Quantitative Susceptibility Mapping - A thorough evaluation and comparison to iterative methods based on edge prior knowledge.

The aim of this study is to perform a thorough comparison of quantitative susceptibility mapping (QSM) techniques and their dependence on the assumptions made. The compared methodologies were: two iterative single orientation methodologies minimizing the l2, l1TV norm of the prior knowledge of the edges of the object, one over-determined multiple orientation method (COSMOS) and anewly proposed modulated closed-form solution (MCF). The performance of these methods was compared using a numerical phantom and in-vivo high resolution (0.65mm isotropic) brain data acquired at 7T using a new coil combination method. For all QSM methods, the relevant regularization and prior-knowledge parameters were systematically changed in order to evaluate the optimal reconstruction in the presence and absence of a ground truth. Additionally, the QSM contrast was compared to conventional gradient recalled echo (GRE) magnitude and R2* maps obtained from the same dataset. The QSM reconstruction results of the single orientation methods show comparable performance. The MCF method has the highest correlation (corrMCF=0.95, r(2)MCF =0.97) with the state of the art method (COSMOS) with additional advantage of extreme fast computation time. The l-curve method gave the visually most satisfactory balance between reduction of streaking artifacts and over-regularization with the latter being overemphasized when the using the COSMOS susceptibility maps as ground-truth. R2* and susceptibility maps, when calculated from the same datasets, although based on distinct features of the data, have a comparable ability to distinguish deep gray matter structures.

The eukaryotic promoter database (EPD).

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes a description of the initiation site mapping data, exhaustive cross-references to the EMBL nucleotide sequence database, SWISS-PROT, TRANSFAC and other databases, as well as bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. WWW-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria, and to navigate to related databases exploiting different cross-references. The EPD web site also features yearly updated base frequency matrices for major eukaryotic promoter elements. EPD can be accessed at http://www.epd.isb-sib.ch

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1,000,000 hits from 462,500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk.

Prevalence at Birth of Cleft Lip With or Without Cleft Palate: Data From the International Perinatal Database of Typical Oral Clefts (IPDTOC).

As part of a collaborative project on the epidemiology of craniofacial anomalies, funded by the National Institutes for Dental and Craniofacial Research and channeled through the Human Genetics Programme of the World Health Organization, the International Perinatal Database of Typical Orofacial Clefts (IPDTOC) was established in 2003. IPDTOC is collecting case-by-case information on cleft lip with or without cleft palate and on cleft palate alone from birth defects registries contributing to at least one of three collaborative organizations: European Surveillance Systems of Congenital Anomalies (EUROCAT) in Europe, National Birth Defects Prevention Network (NBDPN) in the United States, and International Clearinghouse for Birth Defects Surveillance and Research (ICBDSR) worldwide. Analysis of the collected information is performed centrally at the ICBDSR Centre in Rome, Italy, to maximize the comparability of results. The present paper, the first of a series, reports data on the prevalence of cleft lip with or without cleft palate from 54 registries in 30 countries over at least 1 complete year during the period 2000 to 2005. Thus, the denominator comprises more than 7.5 million births. A total of 7704 cases of cleft lip with or without cleft palate (7141 livebirths, 237 stillbirths, 301 terminations of pregnancy, and 25 with pregnancy outcome unknown) were available. The overall prevalence of cleft lip with or without cleft palate was 9.92 per 10,000. The prevalence of cleft lip was 3.28 per 10,000, and that of cleft lip and palate was 6.64 per 10,000. There were 5918 cases (76.8%) that were isolated, 1224 (15.9%) had malformations in other systems, and 562 (7.3%) occurred as part of recognized syndromes. Cases with greater dysmorphological severity of cleft lip with or without cleft palate were more likely to include malformations of other systems.

The relationship between HRM practices and organizational commitment of knowledge workers. Facts obtained from Swiss SMEs

This paper explores the effects of human resource management (HRM) practices in Swiss small -to-medium enterprises (SMEs). More specifically, the main objective of this study is to assess the impacts of HRM practices developed in Swiss SMEs upon the commitment of knowledge workers. Using data from a survey of over 198 knowledge workers, this study shows the importance of looking closer at HRM practices and, furthermore, to really investigate the impacts of the different HRM practices on employees' commitment. Results show, for example, that organisational support, procedural justice and the reputation of the organisation may clearly influence knowledge workers' commitment, whereas other HRM practices such as involvement in the decision-making, skills management or even the degree of satisfaction with pay do not have any impact on knowledge workers' commitment.

Knowledge of Glasgow coma scale by air-rescue physicians.

OBJECTIVE: To assess the theoretical and practical knowledge of the Glasgow Coma Scale (GCS) by trained Air-rescue physicians in Switzerland. METHODS: Prospective anonymous observational study with a specially designed questionnaire. General knowledge of the GCS and its use in a clinical case were assessed. RESULTS: From 130 questionnaires send out, 103 were returned (response rate of 79.2%) and analyzed. Theoretical knowledge of the GCS was consistent for registrars, fellows, consultants and private practitioners active in physician-staffed helicopters. The clinical case was wrongly scored by 38 participants (36.9%). Wrong evaluation of the motor component occurred in 28 questionnaires (27.2%), and 19 errors were made for the verbal score (18.5%). Errors were made most frequently by registrars (47.5%, p = 0.09), followed by fellows (31.6%, p = 0.67) and private practitioners (18.4%, p = 1.00). Consultants made significantly less errors than the rest of the participating physicians (0%, p < 0.05). No statistically significant differences were shown between anesthetists, general practitioners, internal medicine trainees or others. CONCLUSION: Although the theoretical knowledge of the GCS by out-of-hospital physicians is correct, significant errors were made in scoring a clinical case. Less experienced physicians had a higher rate of errors. Further emphasis on teaching the GCS is mandatory.