A 35.7 kb DNA fragment from the Bacillus subtilis chromosome containing a putative 12.3 kb operon involved in hexuronate catabolism and a perfectly symmetrical hypothetical catabolite-responsive element.

The Bacillus subtilis strain 168 chromosomal region extending from 109 degrees to 112 degrees has been sequenced. Among the 35 ORFs identified, cotT and rapA were the only genes that had been previously mapped and sequenced. Out of ten ORFs belonging to a single putative transcription unit, seven are probably involved in hexuronate catabolism. Their sequences are homologous to Escherichia coli genes exuT, uidB, uxaA, uxaB, uxaC, uxuA and uxuB, which are all required for the uptake of free D-glucuronate, D-galacturonate and beta-glucuronide, and their transformation into glyceraldehyde 3-phosphate and pyruvate via 2-keto-3-deoxygluconate. The remaining three ORFs encode two dehydrogenases and a transcriptional regulator. The operon is preceded by a putative catabolite-responsive element (CRE), located between a hypothetical promoter and the RBS of the first gene. This element, the longest and the only so far described that is fully symmetrical, consists of a 26 bp palindrome matching the theoretical B. subtilis CRE sequence. The remaining predicted amino acid sequences that share homologies with other proteins comprise: a cytochrome P-450, a glycosyltransferase, an ATP-binding cassette transporter, a protein similar to the formate dehydrogenase alpha-subunit (FdhA), protein similar to NADH dehydrogenases, and three homologues of polypeptides that have undefined functions.

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience.

The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online.

Impact of neoadjuvant chemoradiotherapy on postoperative outcomes after esophageal cancer resection: results of a European multicenter study.

OBJECTIVES: To assess the impact of neoadjuvant chemoradiotherapy (NCRT) on anastomotic leakage (AL) and other postoperative outcomes after esophageal cancer (EC) resection. BACKGROUND: Conflicting data have emerged from randomized studies regarding the impact of NCRT on AL. METHODS: Among 2944 consecutive patients operated on for EC between 2000 and 2010 in 30 European centers, patients treated by NCRT after surgery (n = 593) were compared with those treated by primary surgery (n = 1487). Multivariable analyses and propensity score matching were used to compensate for the differences in some baseline characteristics. RESULTS: Patients in the NCRT group were younger, with a higher prevalence of male sex, malnutrition, advanced tumor stage, squamous cell carcinoma, and surgery after 2005 when compared with the primary surgery group. Postoperative AL rates were 8.8% versus 10.6% (P = 0.220), and 90-day postoperative mortality and morbidity rates were 9.3% versus 7.2% (P = 0.110) and 33.4% versus 32.1% (P = 0.564), respectively. Pulmonary complication rates did not differ between groups (24.6% vs 22.5%; P = 0.291), whereas chylothorax (2.5% vs 1.2%; P = 0.020), cardiovascular complications (8.6% vs 0.1%; P = 0.037), and thromboembolic events (8.6% vs 6.0%; P = 0.037) were higher in the NCRT group. After propensity score matching, AL rates were 8.8% versus 11.3% (P = 0.228), with more chylothorax (2.5% vs 0.7%; P = 0.030) and trend toward more cardiovascular and thromboembolic events in the NCRT group (P = 0.069). Predictors of AL were high American Society of Anesthesiologists scores, supracarinal tumoral location, and cervical anastomosis, but not NCRT. CONCLUSIONS: Neoadjuvant chemoradiotherapy does not have an impact on the AL rate after EC resection (NCT 01927016).

Generación de interfaces para aplicaciones por línea de comandos

Generación dinámica de interfaces web basadas en ficheros descriptivos XML para el control de la parametrización compleja y ejecución de programas por línea de comandos. La necesidad surge con la aplicación mlcoalsim, utilizada por investigadores de la UAB, cuya parametrización requiere la edición manual de un fichero de texto la sintaxis del cual es complicada y pesada. Con la generación de interfaces web se pretende ayudar a los usuarios en la correcta parametrización y ejecución de aplicaciones como mlcoalsim.

Non-tuberculous mycobacteria I: one year clinical isolates identification in Tertiary Hospital Aids Reference Center, Rio de Janeiro, Brazil, in pre highly active antiretroviral therapy era

The aim of this study was to determine the prevalence of non-tuberculous mycobacteria (NTM) isolates at University Hospital, Reference Center for Aids in Rio de Janeiro, Brazil, during one year. We used standard biochemical tests for species identification and IS1245 PCR amplification was applied as a Mycobacterium avium specific identification marker. Four hundred and four specimens from 233 patients yielded acid-fast bacilli growth. M. tuberculosis was identified in 85% of the patients and NTM in 15%. NTM disseminated infection was a common event correlated with human immunodeficiency virus (HIV) infected patients and only in HIV negative patients the source of NTM was non sterile site. M. avium complex (MAC) was biochemically identified in 57.8% (49/83) of NTM isolates, most of them from sterile sites (75.5%), and in 94% (46/49) the IS 1245 marker specific for M. avium was present. Twenty NTM strains showed a MAC biochemical pattern with the exception of a urease-positive (99% of MAC are urease-negative), however IS1245 was detected in 96% of the strains leading to their identification as M. avium. In this group differences in NTM source was not significant. The second most frequently isolated NTM was identified as M. scrofulaceum (7.2%), followed by M. terrae (3.6%), M. gordonae (2.4%), M. chelonae (1.2%), M. fortuitum (1.2%) and one strain which could not be identified. All were IS1245 negative except for one strain identified as M. scrofulaceum. It is interesting to note that non-sterile sites were the major source of these isolates (92.8%). Our finding indicated that M. avium is still the major atypical species among in the MAC isolates recovered from Brazilian Aids patients without highty active antiretroviral therapy schema. Some discrepancies were seen between the identification methods and further investigations must be done to better characterize NTM isolates using other phenotypic and genotypic methods.

Desenvolupament d'un memetracker - rastrejador de notícies

El projecte es centra en el desenvolupament d'un recol·lector de notícies publicades a una llarga llista de blocs ampliada contínuament pel desenvolupador i pels usuaris, afegint els seus blocs preferits. L'aplicació desenvolupada realitza una recol·lecció contínua de notícies consultant les possibles novetats que apareguin en cada un dels blocs inscrits a l'aplicació. Se'ls hi aplica un classificador per idioma i per temàtica i es relaciona amb les altres notícies existents si aquestes parlen sobre el mateix tema. En l'aplicació desenvolupada hi ha la possibilitat d'escollir entre les temàtiques ofertes i en l'idioma que ha estat publicada la notícia. Pel desenvolupament del projecte s'ha desitjat que la plataforma sigui el més compatible possible amb la tecnologia actual fent servir diversos llenguatges de programació que han permès desenvolupar cada un dels algorismes necessaris pel desenvolupament global de l'aplicació; en ordre d'ús he fet servir Php, Matlab, Html, MySql, CSS3, Javascript i XML. s'ha de destacar que el projecte aporta una comoditat per tots aquells lectors de blocs que es troben tantes vegades amb notícies ja llegides en els diferents blocs que consulten.

Targetting of the ventro-intermediate nucleus using ultra-high field (7T) MRI for gamma knife surgery purposes: A pilot in vivo study on healthy subjects.

INTRODUCTION: Gamma Knife surgery (GKS) is a non-invasive neurosurgical stereotactic procedure, increasingly used as an alternative to open functional procedures. This includes targeting of the ventro-intermediate nucleus of the thalamus (e.g. Vim) for tremor. We currently perform an indirect targeting, as the Vim is not visible on current 3Tesla MRI acquisitions. Our objective was to enhance anatomic imaging (aiming at refining the precision of anatomic target selection by direct visualisation) in patients treated for tremor with Vim GKS, by using high field 7T MRI. MATERIALS AND METHODSH: Five young healthy subjects were scanned on 3 (T1-w and diffusion tensor imaging) and 7T (high-resolution susceptibility weighted images (SWI)) MRI in Lausanne. All images were further integrated for the first time into the Gamma Plan Software(®) (Elekta Instruments, AB, Sweden) and co-registered (with T1 was a reference). A simulation of targeting of the Vim was done using various methods on the 3T images. Furthermore, a correlation with the position of the found target with the 7T SWI was performed. The atlas of Morel et al. (Zurich, CH) was used to confirm the findings on a detailed analysis inside/outside the Gamma Plan. RESULTS: The use of SWI provided us with a superior resolution and an improved image contrast within the basal ganglia. This allowed visualization and direct delineation of some subgroups of thalamic nuclei in vivo, including the Vim. The position of the target, as assessed on 3T, perfectly matched with the supposed one of the Vim on the SWI. Furthermore, a 3-dimensional model of the Vim-target area was created on the basis of the obtained images. CONCLUSION: This is the first report of the integration of SWI high field MRI into the LGP, aiming at the improvement of targeting validation of the Vim in tremor. The anatomical correlation between the direct visualization on 7T and the current targeting methods on 3T (e.g. quadrilatere of Guyot, histological atlases) seems to show a very good anatomical matching. Further studies are needed to validate this technique, both by improving the accuracy of the targeting of the Vim (potentially also other thalamic nuclei) and to perform clinical assessment.

Tissue-specific and SRSF1-dependent splicing of fibronectin, a matrix protein that controls host cell invasion.

Cell invasion targets specific tissues in physiological placental implantation and pathological metastasis, which raises questions about how this process is controlled. We compare dermis and endometrium capacities to support trophoblast invasion, using matching sets of human primary fibroblasts in a coculture assay with human placental explants. Substituting endometrium, the natural trophoblast target, with dermis dramatically reduces trophoblast interstitial invasion. Our data reveal that endometrium expresses a higher rate of the fibronectin (FN) extra type III domain A+ (EDA+) splicing isoform, which displays stronger matrix incorporation capacity. We demonstrate that the high FN content of the endometrium matrix, and not specifically the EDA domain, supports trophoblast invasion by showing that forced incorporation of plasma FN (EDA-) promotes efficient trophoblast invasion. We further show that the serine/arginine-rich protein serine/arginine-rich splicing factor 1 (SRSF1) is more highly expressed in endometrium and, using RNA interference, that it is involved in the higher EDA exon inclusion rate in endometrium. Our data therefore show a mechanism by which tissues can be distinguished, for their capacity to support invasion, by their different rates of EDA inclusion, linked to their SRSF1 protein levels. In the broader context of cancer pathology, the results suggest that SRSF1 might play a central role not only in the tumor cells, but also in the surrounding stroma.

Aplicación para la transformación y estudio de archivos log

La aplicación Log2XML tiene como objeto principal la transformación de archivos log en formato texto con separador de campos a un formato XML estandarizado. Para permitir que la aplicación pueda trabajar con logs de diferentes sistemas o aplicaciones, dispone de un sistema de plantillas (indicación de orden de campos y carácter separador) que permite definir la estructura mínima para poder extraer la información de cualquier tipo de log que se base en separadores de campo. Por último, la aplicación permite el procesamiento de la información extraída para la generación de informes y estadísticas.Por otro lado, en el proyecto se profundiza en la tecnología Grails.

Aplicaciones Web para trabajo colaborativo: Diseño y prototipo de un sofware para la replicación de ficheros en sistemas de trabajo en grupo P2P

Aplicación para trabajar en un entorno colaborativo con el fin de compartir ficheros xml. Dicho entorno colaborativo se basa en una red peer to peer.

Servei de recerca automatitzada de continguts

Aquest projecte se centra en el disseny i implementació d'un servei de recerca automatitzada de continguts web, fent servir les fonts d'informació disponibles en format RSS i Atom, dues especificacions basades en XML que serveixen per sindicar tot tipus de dades. Un cop llegits els continguts es poden definir regles de selecció automàtica que s'encarreguen de seleccionar la informació que més ens interessa en funció dels valors dels diferents atributs disponibles.

Missing value imputation in longitudinal measures of alcohol consumption

Attrition in longitudinal studies can lead to biased results. The study is motivated by the unexpected observation that alcohol consumption decreased despite increased availability, which may be due to sample attrition of heavy drinkers. Several imputation methods have been proposed, but rarely compared in longitudinal studies of alcohol consumption. The imputation of consumption level measurements is computationally particularly challenging due to alcohol consumption being a semi-continuous variable (dichotomous drinking status and continuous volume among drinkers), and the non-normality of data in the continuous part. Data come from a longitudinal study in Denmark with four waves (2003-2006) and 1771 individuals at baseline. Five techniques for missing data are compared: Last value carried forward (LVCF) was used as a single, and Hotdeck, Heckman modelling, multivariate imputation by chained equations (MICE), and a Bayesian approach as multiple imputation methods. Predictive mean matching was used to account for non-normality, where instead of imputing regression estimates, "real" observed values from similar cases are imputed. Methods were also compared by means of a simulated dataset. The simulation showed that the Bayesian approach yielded the most unbiased estimates for imputation. The finding of no increase in consumption levels despite a higher availability remained unaltered. Copyright (C) 2011 John Wiley & Sons, Ltd.

PHA urges 'freshers' to be smart and know their alcohol limits

As 'fresher's week' commences, the Public Health Agency is encouraging students across Northern Ireland to avoid binge drinking and to know their limits if they do choose to drink alcohol.Enjoying new freedoms, at college or university, means taking care of yourself and others and, if you choose to drink, staying within safe alcohol limits. Owen O'Neill, PHA Health and Social Wellbeing Improvement Manager for drugs and alcohol, said: "Some young people may drink more when they leave home, or join their friends in college or university for the first time. They might think that, as young people, they don't have to take care with alcohol, but staying within the safe drinking limits is important for everyone who drinks. Excessive and binge drinking can have lasting effects on health, such as damage to the liver, heart, brain and stomach. Drinking too much can also increase the risk of accidents and antisocial behaviour as well as sexually transmitted infections and unplanned pregnancy"."We would also strongly advise against drinking games. Although they are regarded as a 'bit of fun', in reality they can be very dangerous. As an extreme form of binge drinking, where large quantities of alcohol are consumed in a very short time, drinking games can result in alcohol poisoning, leading to brain damage, coma or death. The PHA encourages students to enjoy their new student life, but urges them to be aware of their alcohol intake and drink responsibly, especially throughout fresher's week, with the many cheap drink promotions currently available."Daily alcohol limits are recommended by the government in order to avoid the risks of excessive and binge drinking in any one session. These are:Men: No more than 3 to 4 units of alcohol a day and no more than 21 units over the course of the week.Women: No more than 2 to 3 units of alcohol a day and no more than 14 units over the course of the week.Examples of units:Can of extra strong lager - 4 unitsBottle of lager - 1.5 unitsPint of standard lager - 2.5 unitsPint of premium larger - 3 unitsSmall pub bottle of wine - 2.25 units70cl bottle of wine - 7 to 10 unitsStandard 275ml of alcopops - 1.5 to 1.8 units70cl bottle of alcopops - 3.75 to 4.5 unitsPub measure of spirits - 1.5 unitsPint of cider - 3 unitsPint of stout - 2.5 unitsIf you do choose to drink alcohol:DON'T:Ever drink and driveDrink on an empty stomachMix alcohol with other drugsDrink in rounds as this may speed up your drinkingLeave your drinks unattendedDO:Take sips rather than gulpsAlternate each alcoholic drink with a non alcoholic drink e.g. water or a soft drinkSet yourself a limit and try to stick to it (refer to daily alcohol limits) Take frequent breaks from drinking to give your body time to recoverTell friends and family where you are going and who you will be withRemember, that for each unit you drink over the daily limit, the risk to your health increases. It's important to spread the units throughout the week - you can't 'save up' your units for the weekend or your holiday. It is also important to drink plenty of water, ideally matching the amount of alcohol you have consumed.So students make smart choices this term - drink sensibly and know your limits!For further information on sensible drinking and alcohol units visit the Public Health Agency's website www.knowyourlimits.info

PHA reinforce sensible drinking in Alcohol Awareness Week

Recent health figures show that 20% of adults surveyed admitted to drinking over the weekly alcohol limits (1)so the Public Health Agency is using Alcohol Awareness Week (14-20th November) to reinforce the importance of drinking sensibly and staying within safe alcohol limits.Government guidelines on safe drinking are 21 units per week for males and 14 units per week for females. Staying within these limits is important as excessive and binge drinking can lead, in the short term, to increased risk of accidents, antisocial behaviour, impact on relationships, unplanned pregnancy. Longer term it can damage the liver, heart, brain and stomach, not to mention the other human costs, and costs to the economy and society as a whole.Owen O'Neill, PHA Health and Social Wellbeing Improvement Manager and Drugs and Alcohol Lead, said: "The Department of Health, Social Services and Public Safety's drinking limits are in place to encourage the public to develop safe and sensible drinking habits. However, these recent figures highlight that not everyone is adhering to these limits. It is crucial that those who do decide to have a drink do so in moderation and stick to the recommended limits to prevent any long or short term damages".The message is clear, if you drink, remember to be smart and enjoy alcohol within safe limits. People should follow the recommended daily alcohol intake. These are:Men: No more than 3 to 4 units of alcohol a day and no more than 21 units over the course of the week.Women: No more than 2 to 3 units of alcohol a day and no more than 14 units over the course of the week.Examples of units:Can of extra strong lager - 4 unitsBottle of lager - 1.5 unitsPint of standard lager - 2.5 unitsPint of premium larger - 3 unitsSmall pub bottle of wine - 2.25 unitsPub measure of spirits - 1.5 unitsPint of cider - 3 unitsPint of stout - 2.5 units. Remember, that for each unit you drink over the daily limit, the risk to your health increases. It's important to spread the units throughout the week - you can't 'save up' your units for the weekend or an upcoming holiday. It is also important to drink plenty of water, ideally matching the amount of alcohol you have consumed.For further information on sensible drinking and alcohol units visit the Public Health Agency's website www.knowyourlimits.infoReference(1) Health Survey Northern Ireland: first results from the 2010/2011 survey (2011) DHSSPS, http://dhsspsni.giv/index/stats_research/stats-public-health.htm

A New Year's Resolution - be smart about your drinking!

Now 2012 has arrived, the Public Health Agency is encouraging people to make a New Year's resolution to know their limits when it comes to alcohol, not to drink excessively and to cut back for a while, especially if the festive period led to a little too much consumption.Owen O'Neill, PHA Health and Social Wellbeing Improvement Manager and drugs and alcohol lead, explained: "The New Year is a great opportunity for us to be positive about our health, making resolutions that make us look and feel better. If people choose to drink, staying within the safe drinking limits is important. Excessive and binge drinking can have lasting effects on health, such as damage to the liver, heart, brain and stomach. Drinking too much can also increase the risk of accidents and antisocial behaviour as well as sexually transmitted infections and unplanned pregnancy. And it doesn't have to be drinking to extremes - regularly drinking over the recommended limits can have a damaging effect."Remember that for each unit you drink over the daily limit, the risk to your health increases. It's important to spread the units throughout the week and not 'save' them for the weekend and to drink plenty of water, ideally matching the amount of alcohol you have consumed."For those who have consumed a lot of alcohol over the festive season, cutting back in the New Year and being careful can have immediate, positive effects particularly on helping you to look and feel better, being less tired during the day, feeling fitter and perhaps losing weight. Longer term, the benefits include improved mood, sleep, memory and general health, particularly improving liver function, immunity to illness and preventing any damage caused by any excessive drinking getting any worse."Daily alcohol limits are recommended by the government to avoid the dangers of excessive and binge drinking in any one session. These are:MenNo more than 3 to 4 units of alcohol a day and no more than 21 units over the course of the week.WomenNo more than 2 to 3 units of alcohol a day and no more than 14 units over the course of the week.Examples of units:Can of extra strong lager - 4 unitsBottle of lager - 1.5 unitsSmall pub bottle of wine - 2.25 unitsPub measure of spirits - 1.5 unitsPint of stout - 2.5 unitsPint of cider - 3 unitsFor further information on sensible drinking and alcohol units visit the Public Health Agency's website www.knowyourlimits.info