Alvira : comparative genomics of viral strains

The Alvira tool is a general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. This new tool has been devised specifically to address the problem of the simultaneous analysis of a large number of viral strains. The multiple alignment is embedded in a graph that can be explored at different levels of resolution

Anomaly detection and mode identification in multimode processes using the field Kalman filter

A process plant can have multiple modes of operation due to varying demand, availability of resources or the fundamental design of a process. Each of these modes is considered as normal operation. Anomalies in the process are characterised as deviations away from normal operation. Such anomalies can be indicative of developing faults which, if left unresolved, can lead to failures and unplanned downtime. The Field Kalman Filter (FKF) is a model-based approach, which is adopted in this paper for monitoring a multimode process. Previously, the FKF has been applied in process monitoring to differentiate normal operation from known faulty modes of operation. This paper extends the FKF so that it may detect occurrences of anomalies and differentiate them from the various normal modes of operation. A method is proposed for offline training an FKF monitoring model and on-line monitoring. The off-line part comprises training an FKF model based on Multivariate Autoregressive State-Space (MARSS) models fitted to historical process data. A monitoring indicator is also introduced. On-line monitoring, on the basis of the FKF for anomaly detection and mode identification, is demonstrated using a simulated multimode process. The performance of the proposed method is also demonstrated using data obtained from a pilot scale multiphase flow facility. The results show that the method can be applied successfully for anomaly detection and mode identification

Non equilibrium anisotropic excitons in atomically thin ReS2_2

We present a systematic investigation of the electronic properties of bulk and few layer ReS$_2$ van der Waals crystals using low temperature optical spectroscopy. Weak photoluminescence emission is observed from two non-degenerate band edge excitonic transitions separated by $\sim$ 20 meV. The comparable emission intensity of both excitonic transitions is incompatible with a fully thermalized (Boltzmann) distribution of excitons, indicating the hot nature of the emission. While DFT calculations predict bilayer ReS$_2$ to have a direct fundamental band gap, our optical data suggests that the fundamental gap is indirect in all cases

The Instrument Set for Generating Fast Adiabatic Passage

The design and construction of a high-performance, low-cost, and easy to assemble adiabatic extension set for homebuilt and commercial spectrometers is described. Described apparatus set was designed for the fast adiabatic passage generation and is based on direct digital synthesizer DDS. This solution gives generator high signal to noise ratio, phase stability even during frequency change which is only possible in expansive commercial high-end hardware. Critical synchronization and timing issues are considered and solutions are discussed. Different experimental conditions and techniques for the measurements are briefly discussed. The proposed system is very flexible and might be used for the measurement of low-frequency nuclear magnetic resonance

Association of parenting practices to encourage or discourage physical activity with Hispanic preschool children's objectively measured physical activity

Oral Session - Determinants of physical activity in children and adolescents: no. O.002Conference Theme: Promoting Healthy Eating and Activity WorldwidePURPOSE: Assess the association of parenting practices (PP) to encourage or discourage physical activity (PA) with Hispanic 3-5 year old children’s objectively measured PA METHOD: Cross-sectional study of Hispanic parent-child dyads (n= 84) who reported their demographics and frequency of using PP that encourage (structure/encouragement) or discourage (promote inactive transport, promote screen time, psychological control, and safety concerns) child PA using verified scales. Children wore Actigraph GT3X accelerometers recording 15 second epochs for 7 days. Allowing for re-wears …postprin

Psychometrics of new scales of parenting practices to encourage or discourage Hispanic preschool children's physical activity

Conference Theme: Promoting Healthy Eating and activity worldwidePoster - Personal and environmental determinants of physical activity in children and adolescents: abstract P077PURPOSE: Develop and assess the psychometrics of a new instrument for parenting practices (PP) that encourage or discourage physical activity (PA) in Hispanic preschool children. METHOD: Cross--‐sectional study of 240 Hispanic parents who reported their demographics and frequency of using PP that encourage (structure and encouragement) or discourage (promoting inactivity, psychological control, safety …postprin

Identification of Novel sRNAs in Mycobacterial Species

Bacterial small RNAs (sRNAs) are short transcripts that typically do not encode proteins and often act as regulators of gene expression through a variety of mechanisms. Regulatory sRNAs have been identified in many species, including Mycobacterium tuberculosis, the causative agent of tuberculosis. Here, we use a computational algorithm to predict sRNA candidates in the mycobacterial species M. smegmatis and M. bovis BCG and confirmed the expression of many sRNAs using Northern blotting. Thus, we have identified 17 and 23 novel sRNAs in M. smegmatis and M. bovis BCG, respectively. We have also applied a high-throughput technique (Deep-RACE) to map the 5′ and 3′ ends of many of these sRNAs and identified potential regulators of sRNAs by analysis of existing ChIP-seq datasets. The sRNAs identified in this work likely contribute to the unique biology of mycobacteria

Measuring diet in primary school children aged 8-11 years: validation of the Child and Diet Evaluation Tool (CADET) with an emphasis on fruit and vegetable intake.

Background/Objectives:The Child And Diet Evaluation Tool (CADET) is a 24-h food diary that measures the nutrition intake of children aged 3-7 years, with a focus on fruit and vegetable consumption. Until now CADET has not been used to measure nutrient intake of children aged 8-11 years. To ensure that newly assigned portion sizes for this older age group were valid, participants were asked to complete the CADET diary (the school and home food diary) concurrently with a 1-day weighed record. Subjects/Methods:A total of 67 children with a mean age of 9.3 years (s.d.: ± 1.4, 51% girls) participated in the study. Total fruit and vegetable intake in grams and other nutrients were extracted to compare the mean intakes from the CADET diary and Weighed record using t-tests and Pearson's r correlations. Bland-Altman analysis was also conducted to assess the agreement between the two methods. Results: Correlations comparing the CADET diary to the weighed record were high for fruit, vegetables and combined fruit and vegetables (r=0.7). The results from the Bland-Altman plots revealed a mean difference of 54 g (95% confidence interval: -88, 152) for combined fruit and vegetables intake. CADET is the only tool recommended by the National Obesity Observatory that has been validated in a UK population and provides nutrient level data on children's diets. Conclusions:The results from this study conclude that CADET can provide high-quality nutrient data suitable for evaluating intervention studies now for children aged 3-11 years with a focus on fruit and vegetable intake

I2N: image to nutrients, a sensor guided semi-automated tool for annotation of images for nutrition analysis of eating episodes

INTRODUCTION: Dietary assessment is important for understanding nutritional status. Traditional methods of monitoring food intake through self-report such as diet diaries, 24-hour dietary recall, and food frequency questionnaires may be subject to errors and can be time-consuming for the user. METHODS: This paper presents a semi-automatic dietary assessment tool we developed - a desktop application called Image to Nutrients (I2N) - to process sensor-detected eating events and images captured during these eating events by a wearable sensor. I2N has the capacity to offer multiple food and nutrient databases (e.g., USDA-SR, FNDDS, USDA Global Branded Food Products Database) for annotating eating episodes and food items. I2N estimates energy intake, nutritional content, and the amount consumed. The components of I2N are three-fold: 1) sensor-guided image review, 2) annotation of food images for nutritional analysis, and 3) access to multiple food databases. Two studies were used to evaluate the feasibility and usefulness of I2N: 1) a US-based study with 30 participants and a total of 60 days of data and 2) a Ghana-based study with 41 participants and a total of 41 days of data). RESULTS: In both studies, a total of 314 eating episodes were annotated using at least three food databases. Using I2N's sensor-guided image review, the number of images that needed to be reviewed was reduced by 93% and 85% for the two studies, respectively, compared to reviewing all the images. DISCUSSION: I2N is a unique tool that allows for simultaneous viewing of food images, sensor-guided image review, and access to multiple databases in one tool, making nutritional analysis of food images efficient. The tool is flexible, allowing for nutritional analysis of images if sensor signals aren't available