A comprehensive evaluation of alignment algorithms in the context of RNA-seq.

Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events. In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic sequences. Although the FM-index based aligner Bowtie has become a de facto standard within mapping pipelines, a much larger number of possible alignment algorithms have been developed also including other variants of FM-index based aligners. Accordingly, developers and users of RNA-seq mapping pipelines have the choice among a large number of available alignment algorithms. To provide guidance in the choice of alignment algorithms for these purposes, we evaluated the performance of 14 widely used alignment programs from three different algorithmic classes: algorithms using either hashing of the reference transcriptome, hashing of reads, or a compressed FM-index representation of the genome. Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read. Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete

Characterising the ‘Txt2Stop’ Smoking Cessation Text Messaging Intervention in Terms of Behaviour Change Techniques

The ‘Txt2Stop’ SMS messaging programme has been found to double smokers’ chances of stopping. It is important to characterise the content of this information in terms of specific behaviour change techniques (BCTs) for the purpose of future development. This study aimed to (i) extend a proven system for coding BCTs to text messaging and (ii) characterise Txt2Stop using this system. A taxonomy previously used to specify BCTs in face-to-face behavioural support for smoking cessation was adapted for the Txt2Stop messages and inter-rater reliability for the adapted system assessed. The system was then applied to all the messages in the Txt2Stop programme to determine its profile in terms of BCTs used. The text message taxonomy comprised 34 BCTs. Inter-rater reliability was moderate, reaching a ceiling of 61% for the core program messages with all discrepancies readily resolved. Of 899 texts delivering BCTs, 218 aimed to maintain motivation to remain abstinent, 870 to enhance self-regulatory capacity or skills, 39 to promote use of adjuvant behaviours such as using stop-smoking medication, 552 to maintain engagement with the intervention and 24 were general communication techniques. The content of Txt2Stop focuses on helping smokers with self-regulation and maintaining engagement with the intervention. The intervention focuses to a lesser extent on boosting motivation to remain abstinent; little attention is given to promoting effective use of adjuvant behaviours such as use of nicotine replacement therapy. As new interventions of this kind are developed it will be possible to compare their effectiveness and relate this to standardised descriptions of their content using this system.</jats:p

The Economic Significance of Insignificant Rules

We know relatively little about the economic impacts of "minor" or "insignificant" rules because they are not typically analyzed. Yet, these rules could be important, particularly when we consider their aggregate impacts. We provide an economic analysis of one proposed rule to control hazardous air pollutants, which is not considered to be economically significant. This rule is of particular interest because it is likely to be the first in a long series of rules that EPA will use to address residual risk from hazardous air pollutants over the next several years. We find that the proposed controls that EPA considers are not likely to pass a benefit-cost test. Furthermore, we suggest that agencies consider applying a rule of thumb that would specify a threshold level of risk reduction that needs to be achieved before some kinds of regulation are considered. We believe that it is important to consider the impact of small rules more carefully at all levels of government. One way of addressing the problem would be to choose a list of small rules at random and examine their economic consequences. This research could provide insights into the potential economic importance of such rules. It could also provide information on how to utilize analysis more effectively to improve regulatory policy.

Cross-sectional Analysis of Sound Levels in the Neonatal Intensive Care Unit (NICU) at Thomas Jefferson University Hospital

Introduction . Infants in the NICU are considered at greater risk of developmental delay. It is now known that excessively loud noise can have a negative impact on parameters such as blood pressure, breathing, heart beat and oxygen saturation. Previous research has concluded that the optimal decibel (dB) level for proper growth of neonate hair cells rests around 45dB. Consequently, the American Academy of Pediatrics recommends that noise levels in the NICU be maintained to a maximum of 45dBA. However, little research has focused on designing new noise-altering products and their impact on neonatal outcomes. Methods. This was a cross sectional study. The NICU at Thomas Jefferson University Hospital was observed for room arrangements and general workflow. Additionally, decibel levels around empty neonatal incubators were measured. A decibel analyzer (REED Instruments SD-4023, Wilmington, NC) was used to record sound levels, both inside and outside of isolettes during various routine activities, including patient rounds, provider-parent conversations and vital monitoring alarms. Results. 30 discrete data points were surveyed, in addition to a 24-hour continuous decibel recording. Across all discrete data points, decibel levels had a mean of 65.6dB (SD ± 10.3). Ambient noise alone in a patient room was measured at 50dB. Noise levels in an open and closed isolette were measured at 58 and 57dB, respectively. Isolette side door opening and closing had a mean of 80.2dB (SD ± 7.60). With medical devices active in the patient room, noise levels had a mean of 62.7dB (SD ± 7.74). Conclusions. All data points were above the recommended safe noise level of 45dB. This data supports our development of a noise reduction product for use within neonatal isolettes. Our design will incorporate sterilizable, sound-absorbent materials and diffusion technologies to decrease ambient noise within neonatal incubators

Transportation Futures: Policy Scenarios for Achieving Greenhouse Gas Reduction Targets, MNTRC Report 12-11

It is well established that GHG emissions must be reduced by 50% to 80% by 2050 in order to limit global temperature increase to 2°C. Achieving reductions of this magnitude in the transportation sector is a challenge and requires a multitude of policies and technology options. The research presented here analyzes three scenarios: changes in the perceived price of travel, land-use intensification, and increases in transit. Elasticity estimates are derived using an activity-based travel model for the state of California and broadly representative of the U.S. The VISION model is used to forecast changes in technology and fuel options that are currently forecast to occur in the U.S., providing a life cycle GHG forecast for the road transportation sector. Results suggest that aggressive policy action is needed, especially pricing policies, but also more on the technology side. Medium- and heavy-duty vehicles are in particular need of additional fuel or technology-based GHG reductions

The State of Sustainable Research Software: Results from the Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE5.1)

This article summarizes motivations, organization, and activities of the Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE5.1) held in Manchester, UK in September 2017. The WSSSPE series promotes sustainable research software by positively impacting principles and best practices, careers, learning, and credit. This article discusses the Code of Conduct, idea papers, position papers, experience papers, demos, and lightning talks presented during the workshop. The main part of the article discusses the speed-blogging groups that formed during the meeting, along with the outputs of those sessions

Engaging low skilled employees in workplace learning

This report sets out the findings of a study into the motivators and barriers to participation in workplace learning by low skilled employees. Low skilled in the UK is usually considered to be below NVQ level 2 qualifications. The study was carried out by the Employment Research Institute at Edinburgh Napier University on behalf of the UK Commission for Employment and Skills. The report presents the results of a survey of both employee and employer views on participation in workplace learning in the care sector in north east England and the hotel sector in Yorkshire and the Humber region. The hotels and catering sector has the highest relative and absolute skill gaps in low skilled occupations, with some 63 per cent of staff suffering skills gaps. In contrast, the care sector has an apparent strong training culture, with care staff expected to progress to NVQ level 3 and only five per cent of low skilled staff suffered a skills gap

Tratamiento del juego patológico: un estudio controlado

This paper discusses the efficacy of a cognitive and behavioral treatment for pathological gambling. Pathological gamblers were randomly assigned to treamlent or wait-list control. The treatment included four components: 1) Cognitive correction of erroneous perceptions about gambling, 2) problem solving training, 3) Social-skills training and 4) relapse prevention. The dependent variables were the South Oaks Gambling Screen, perception of control, frequency of gambling, perceived self-efficacy, desire to gamble, and number of DSM-111-R criteria met by participants. Results indicated highly significant changes in the treatment group on all outcome measures and analysis of data from six and twelve month follow-ups revealed maintenance of the rapeutic gains. It is recommended that cognitive and behavioral therapy include cognitive correction of erroneous perceptions in gambling.Este trabajo discute la eficacia de un tratamiento cognitivo-conductual para el juego patológico. Los jugadores patológicos fueron asignados de forma aleatorizada a tratamiento o a lista de espera. El tratamiento incluyó cuatro componentes: 1) Corrección cognitiva de las percepciones erróneas sobre el juego, 2) entrenamiento en solución de problemas, 3) entrenamiento en habilidades sociales y 4) prevención de recaídas. Las variables dependientes fueron el South Oaks Gambling Screen, la percepción de control, frecuencia de juego, percepción de autoeficacia, deseo de jugar y número de criterios diagnósticos DSM-III-R cumplidos. Los resultados indicaron cambios significativos en el grupo de tratamiento en todas las medidas, y el análisis de los datos a los seis y docemeses de seguimiento informó del mantenimiento de los éxitos terapéuticos. Se recomienda que la terapia cognitiva y conductual incluya la corrección de las percepciones erróneas sobre el juego