Computational approaches for RNA structure ensemble deconvolution from structure probing data

RNA structure probing experiments have emerged over the last decade as a straightforward way to determine the structure of RNA molecules in a number of different contexts. Although powerful, the ability of RNA to dynamically interconvert between, and to simultaneously populate, alternative structural configurations, poses a nontrivial challenge to the interpretation of data derived from these experiments. Recent efforts aimed at developing computational methods for the reconstruction of coexisting alternative RNA conformations from structure probing data are paving the way to the study of RNA structure ensembles, even in the context of living cells. In this review, we critically discuss these methods, their limitations and possible future improvements

Optimizing Memory Efficiency for Convolution Kernels on Kepler GPUs

Convolution is a fundamental operation in many applications, such as computer vision, natural language processing, image processing, etc. Recent successes of convolutional neural networks in various deep learning applications put even higher demand on fast convolution. The high computation throughput and memory bandwidth of graphics processing units (GPUs) make GPUs a natural choice for accelerating convolution operations. However, maximally exploiting the available memory bandwidth of GPUs for convolution is a challenging task. This paper introduces a general model to address the mismatch between the memory bank width of GPUs and computation data width of threads. Based on this model, we develop two convolution kernels, one for the general case and the other for a special case with one input channel. By carefully optimizing memory access patterns and computation patterns, we design a communication-optimized kernel for the special case and a communication-reduced kernel for the general case. Experimental data based on implementations on Kepler GPUs show that our kernels achieve 5.16X and 35.5% average performance improvement over the latest cuDNN library, for the special case and the general case, respectively

Workplace aggression experiences and responses of Victorian nurses, midwives and care personnel

Background: Workplace aggression is a major work health and safety, and public health concern. To date, there has been limited investigation of population level exposure and responses to workplace aggression from all sources, and little evidence on the experiences, reporting and support-seeking behaviour of nurses, midwives and care personnel in Australian settings. Aim: To determine the 12-month prevalence of aggression experienced by nurses, midwives and care personnel from sources external and internal to the organisation, and the reporting behaviours and support sought from employers, health services, Trade Unions, work health and safety agencies, police and legal services. Methods: An online survey of the membership of the Australian Nursing and Midwifery Federation – Victorian Branch was conducted between 1 st May and 30th June 2017. Findings: In the previous 12 months, 96.5% of respondents experienced workplace aggression, with 90.9% experiencing aggression from external sources and 72.3% from internal sources. A majority indicated they just accepted incidents of aggression, and most rarely or never took time off work, sought medical or psychological treatment, or sought organisational or other institutional support, advice or action. Levels of satisfaction with institutional services were mostly neutral to poor. Discussion: Victorian nurses, midwives and care personnel work in aggressive and violent workplaces. The incivility endemic in health care likely sets the climate for the generation of and exposure to so much explicit aggression and violence. It appears that any systems or processes instituted to protect health care personnel from harm are failing. Conclusion: More targeted and effectively operationalised legislation, incentives and penalties are likely required. Further research may elaborate the extent of the impact of exposure to workplace aggression over time

Heterologous Hybridization of Cotton Microarrays with Velvetleaf (Abutilon theophrasti) Reveals Physiological Responses Due to Corn Competition

Microarray analysis was used to identify changes in gene expression in velvetleaf that result from competition with corn. The plants were grown in field plots under adequate N (addition of 220 kg N ha21 ) to minimize stress and sampled at the V6 growth stage of corn (late June). Leaf area, dry weight, and N and P concentration were similar in velvetleaf plants grown alone or with corn. Competition, however, did influence velvetleaf gene expression. Genes involved in carbon utilization, photosynthesis, red light signaling, and cell division were preferentially expressed when velvetleaf was grown in competition with corn. A less clear picture of the physiological impact of growth in monoculture was provided by the data. However, several genes involved in secondary metabolism and a gene preferentially expressed in response to phosphate availability were induced. No differences were observed in genes responsive to water stress or sequestering/transporting micronutrients

Heterologous Hybridization of Cotton Microarrays with Velvetleaf (Abutilon theophrasti) Reveals Physiological Responses Due to Corn Competition

Microarray analysis was used to identify changes in gene expression in velvetleaf that result from competition with corn. The plants were grown in field plots under adequate N (addition of 220 kg N ha−1) to minimize stress and sampled at the V6 growth stage of corn (late June). Leaf area, dry weight, and N and P concentration were similar in velvetleaf plants grown alone or with corn. Competition, however, did influence velvetleaf gene expression. Genes involved in carbon utilization, photosynthesis, red light signaling, and cell division were preferentially expressed when velvetleaf was grown in competition with corn. A less clear picture of the physiological impact of growth in monoculture was provided by the data. However, several genes involved in secondary metabolism and a gene preferentially expressed in response to phosphate availability were induced. No differences were observed in genes responsive to water stress or sequestering/transporting micronutrients

Research & Communication Skills (RCS) Weekly sessions (2013/14)

Slides and materials from each weeks session in one handy locatio

Estimación de la Huella Ecológica en el campus de la Universidad Peruana Unión, aplicando el método componente modificado

La estimación de la Huella Ecológica (HE) permite medir el consumo de recursos, la generación de residuos y emisiones asociadas a una población u organización específica, relacionándolas con la capacidad regenerativa de la biosfera. El presente artículo, tuvo como objetivo estimar la HE de la Universidad Peruana Unión(UpeU) en el año académico 2019 empleando el método componente propuesto por Simmons y modificado por López, mediante el proceso de datos obtenidos directa e indirectamente sobre el consumo anual de recursos para la realización de las actividades académicas. Del análisis preliminar se obtuvo que la UPeU requiere 1511.26 hectáreas globales (hag) para capturar el CO2 producido por sus actividades. Se estimó que la HE en la UPeU para 13670 personas, fue de 0.11 ha/persona/año durante el año académico 2019; valor que está por encima de la huella ecología calculada para la UPeU, durante el periodo 2017 que es de 0.08 ha/persona/año.Trabajo de investigaciónLIMAEscuela Profesional de Ingeniería AmbientalBiodiversidad y calidad ambienta