RNA processing and Arabidopsis flowering time control.

Plants control their flowering time in order to ensure that they reproduce under favourable conditions. The components involved in this complex process have been identified using a molecular genetic approach in Arabidopsis and classified into genetically separable pathways. The autonomous pathway controls the level of mRNA encoding a floral repressor, FLC, and comprises three RNA-binding proteins, FCA, FPA and FLK. FCA interacts with the 3'-end RNA-processing factor FY to autoregulate its own expression post-transcriptionally and to control FLC. Other components of the autonomous pathway, FVE and FLD, regulate FLC epigenetically. This combination of epigenetic and post-transcriptional control gives precision to the control of FLC expression and flowering time.

Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning.

Small RNAs have several important biological functions. MicroRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) regulate mRNA stability and translation, and siRNAs cause post-transcriptional gene silencing of transposons, viruses and transgenes and are important in both the establishment and maintenance of cytosine DNA methylation. Here, we study the role of the four Arabidopsis thaliana DICER-LIKE genes (DCL1-DCL4) in these processes. Sequencing of small RNAs from a dcl2 dcl3 dcl4 triple mutant showed markedly reduced tasiRNA and siRNA production and indicated that DCL1, in addition to its role as the major enzyme for processing miRNAs, has a previously unknown role in the production of small RNAs from endogenous inverted repeats. DCL2, DCL3 and DCL4 showed functional redundancy in siRNA and tasiRNA production and in the establishment and maintenance of DNA methylation. Our studies also suggest that asymmetric DNA methylation can be maintained by pathways that do not require siRNAs.

Village level processing techniques

The agar-bearing seaweeds Gracilaria and Gelidium grow abundantly in the Asia-Pacific region. Production and post-harvest techniques and methods for processing Gracilaria to produce agar suitable for local market is necessary to increase the meager income of coastal dwellers. A flow diagram of a village level agar production is provided. A guide is also given for the quality of dried seaweeds, which are divided into 3 classes.

The post-processed Galerkin method applied to non-linear shell vibrations

We present the results of a computational study of the post-processed Galerkin methods put forward by Garcia-Archilla et al. applied to the non-linear von Karman equations governing the dynamic response of a thin cylindrical panel periodically forced by a transverse point load. We spatially discretize the shell using finite differences to produce a large system of ordinary differential equations (ODEs). By analogy with spectral non-linear Galerkin methods we split this large system into a 'slowly' contracting subsystem and a 'quickly' contracting subsystem. We then compare the accuracy and efficiency of (i) ignoring the dynamics of the 'quick' system (analogous to a traditional spectral Galerkin truncation and sometimes referred to as 'subspace dynamics' in the finite element community when applied to numerical eigenvectors), (ii) slaving the dynamics of the quick system to the slow system during numerical integration (analogous to a non-linear Galerkin method), and (iii) ignoring the influence of the dynamics of the quick system on the evolution of the slow system until we require some output, when we 'lift' the variables from the slow system to the quick using the same slaving rule as in (ii). This corresponds to the post-processing of Garcia-Archilla et al. We find that method (iii) produces essentially the same accuracy as method (ii) but requires only the computational power of method (i) and is thus more efficient than either. In contrast with spectral methods, this type of finite-difference technique can be applied to irregularly shaped domains. We feel that post-processing of this form is a valuable method that can be implemented in computational schemes for a wide variety of partial differential equations (PDEs) of practical importance.

Rapid entropy-based detection and properties measurement of concrete spalling with machine vision for post-earthquake safety assessments

The current procedures in post-earthquake safety and structural assessment are performed manually by a skilled triage team of structural engineers/certified inspectors. These procedures, and particularly the physical measurement of the damage properties, are time-consuming and qualitative in nature. This paper proposes a novel method that automatically detects spalled regions on the surface of reinforced concrete columns and measures their properties in image data. Spalling has been accepted as an important indicator of significant damage to structural elements during an earthquake. According to this method, the region of spalling is first isolated by way of a local entropy-based thresholding algorithm. Following this, the exposure of longitudinal reinforcement (depth of spalling into the column) and length of spalling along the column are measured using a novel global adaptive thresholding algorithm in conjunction with image processing methods in template matching and morphological operations. The method was tested on a database of damaged RC column images collected after the 2010 Haiti earthquake, and comparison of the results with manual measurements indicate the validity of the method.

Enhancement of conductivity and transmittance of ZnO films by post hydrogen plasma treatment

We studied the effects of hydrogen plasma treatment on the electrical and optical properties of ZnO films deposited by radio frequency magnetron sputtering. It is found that the ZnO H film is highly transparent with the average transmittance of 92% in the visible range. Both carrier concentration and mobility are increased after hydrogen plasma treatment, correspondingly, the resistivity of the ZnO H films achieves the order of 10(-3) cm. We suggest that the incorporated hydrogen not only passivates most of the defects and/or acceptors present, but also introduces shallow donor states such as the V-O-H complex and the interstitial hydrogen H-i. Moreover, the annealing data indicate that H-i is unstable in ZnO, while the V-O-H complex remains stable on the whole at 400 degrees C, and the latter diffuses out when the annealing temperature increases to 500 degrees C. These results make ZnO H more attractive for future applications as transparent conducting electrodes.

Structural properties of polycrystalline silicon films formed by pulsed rapid thermal processing

A novel pulsed rapid thermal processing (PRTP) method has been used for realizing solid-phese crystallization of amorphous silicon films prepared by plasma-enhanced chemical vapour deposit ion. The microstructure and surface morphology of the crystallized films were investigated using x-ray diffraction and atomic Force microscopy. The results indicate that PRTP is a suitable post-crystallization technique for fabricating large-area polycrystalline silicon films with good structural quality, such as large grain size, small lattice microstrain and smooth surface morphology on low-cost glass substrates.

Structural properties of polycrystalline silicon films formed by pulsed rapid thermal processing

A novel pulsed rapid thermal processing (PRTP) method has been used for realizing the solid-phase crystallization of amorphous silicon films prepared by PECVD. The microstructure and surface morphology of the crystallized films are investigated by X-ray diffraction (XRD) and atomic force microscopy (AFM). The results indicate that this PRTP is a suitable post-crystallization technique for fabricating large-area polycrystalline silicon films with good structural qualities such as large grain size, small lattice microstain and smooth surface morphology on low-cost substrate.

The implementation of a translational study involving a primary care based behavioral program to improve blood pressure control: The HTN-IMPROVE study protocol (01295).

BACKGROUND: Despite the impact of hypertension and widely accepted target values for blood pressure (BP), interventions to improve BP control have had limited success. OBJECTIVES: We describe the design of a 'translational' study that examines the implementation, impact, sustainability, and cost of an evidence-based nurse-delivered tailored behavioral self-management intervention to improve BP control as it moves from a research context to healthcare delivery. The study addresses four specific aims: assess the implementation of an evidence-based behavioral self-management intervention to improve BP levels; evaluate the clinical impact of the intervention as it is implemented; assess organizational factors associated with the sustainability of the intervention; and assess the cost of implementing and sustaining the intervention. METHODS: The project involves three geographically diverse VA intervention facilities and nine control sites. We first conduct an evaluation of barriers and facilitators for implementing the intervention at intervention sites. We examine the impact of the intervention by comparing 12-month pre/post changes in BP control between patients in intervention sites versus patients in the matched control sites. Next, we examine the sustainability of the intervention and organizational factors facilitating or hindering the sustained implementation. Finally, we examine the costs of intervention implementation. Key outcomes are acceptability and costs of the program, as well as changes in BP. Outcomes will be assessed using mixed methods (e.g., qualitative analyses--pattern matching; quantitative methods--linear mixed models). DISCUSSION: The study results will provide information about the challenges and costs to implement and sustain the intervention, and what clinical impact can be expected.

Functional neuroimaging of emotionally intense autobiographical memories in post-traumatic stress disorder.

Post-traumatic stress disorder (PTSD) affects regions that support autobiographical memory (AM) retrieval, such as the hippocampus, amygdala and ventral medial prefrontal cortex (PFC). However, it is not well understood how PTSD may impact the neural mechanisms of memory retrieval for the personal past. We used a generic cue method combined with parametric modulation analysis and functional MRI (fMRI) to investigate the neural mechanisms affected by PTSD symptoms during the retrieval of a large sample of emotionally intense AMs. There were three main results. First, the PTSD group showed greater recruitment of the amygdala/hippocampus during the construction of negative versus positive emotionally intense AMs, when compared to controls. Second, across both the construction and elaboration phases of retrieval the PTSD group showed greater recruitment of the ventral medial PFC for negatively intense memories, but less recruitment for positively intense memories. Third, the PTSD group showed greater functional coupling between the ventral medial PFC and the amygdala for negatively intense memories, but less coupling for positively intense memories. In sum, the fMRI data suggest that there was greater recruitment and coupling of emotional brain regions during the retrieval of negatively intense AMs in the PTSD group when compared to controls.

Ultra-fast processing of gigapixel Tissue MicroArray images using high performance computing.

BACKGROUND:
tissue MicroArrays (TMAs) are a valuable platform for tissue based translational research and the discovery of tissue biomarkers. The digitised TMA slides or TMA Virtual Slides, are ultra-large digital images, and can contain several hundred samples. The processing of such slides is time-consuming, bottlenecking a potentially high throughput platform.
METHODS:
a High Performance Computing (HPC) platform for the rapid analysis of TMA virtual slides is presented in this study. Using an HP high performance cluster and a centralised dynamic load balancing approach, the simultaneous analysis of multiple tissue-cores were established. This was evaluated on Non-Small Cell Lung Cancer TMAs for complex analysis of tissue pattern and immunohistochemical positivity.
RESULTS:
the automated processing of a single TMA virtual slide containing 230 patient samples can be significantly speeded up by a factor of circa 22, bringing the analysis time to one minute. Over 90 TMAs could also be analysed simultaneously, speeding up multiplex biomarker experiments enormously.
CONCLUSIONS:
the methodologies developed in this paper provide for the first time a genuine high throughput analysis platform for TMA biomarker discovery that will significantly enhance the reliability and speed for biomarker research. This will have widespread implications in translational tissue based research.

Post-slaughter changes in ATP metabolites, Reducing and phosphorylated sugars in chicken meat

The formation of ATP breakdown products in chicken M. pectoralis major post-slaughter is reported. The concentrations of metabolites were followed in chicken breast throughout the carcass processing post-slaughter and during chilled storage. The concentration of glucose remains similar throughout the period whilst that of glucose-6-phosphate decreases linearly. Glucose and glucose-6-phosphate concentrations were inversely related to the pHu of the breast meat throughout chilled storage. Rapid post-mortem glycolysis and high pHu values suggest the occurrence of stress at and pre-slaughter. Whilst ATP, ADP and AMP were rapidly broken down, the concentration of IMP rose rapidly and remained high. Concentrations of inosine, ribose and hypoxanthine increased gradually post-slaughter but an initial increase in ribose phosphate was not sustained. Most of the potential ribose present in chicken meat, believed to be important for flavor formation, remains bound in the form of inosine and IMP. There is evidence that additional breakdown pathways for ribose and ribose-5-phosphate may deplete the concentrations of these precursors.

A review of ADP processing software

Data processing is an essential part of Acoustic Doppler Profiler (ADP) surveys, which have become the standard tool in assessing flow characteristics at tidal power development sites. In most cases, further processing beyond the capabilities of the manufacturer provided software tools is required. These additional tasks are often implemented by every user in mathematical toolboxes like MATLAB, Octave or Python. This requires the transfer of the data from one system to another and thus increases the possibility of errors. The application of dedicated tools for visualisation of flow or geographic data is also often beneficial and a wide range of tools are freely available, though again problems arise from the necessity of transferring the data. Furthermore, almost exclusively PCs are supported directly by the ADP manufacturers, whereas small computing solutions like tablet computers, often running Android or Linux operating systems, seem better suited for online monitoring or data acquisition in field conditions. While many manufacturers offer support for developers, any solution is limited to a single device of a single manufacturer. A common data format for all ADP data would allow development of applications and quicker distribution of new post processing methodologies across the industry.

Synergism between high-pressure processing and active packaging against Listeria monocytogenes in ready-to-eat chicken breast

The effects of high-pressure processing (HPP) in conjunction with an essential oil-based active packaging on the surface of ready-to-eat (RTE) chicken breast were investigated as post-processing listericidal treatment. Three different treatments were used, and all samples were vacuum packed: (i) HPP at 500. MPa for 1. min (control), (ii) active packaging based on coriander essential oil, and (iii) active packaging and HPP. When applied individually, active packaging and pressurisation delayed the growth of Listeria monocytogenes. The combination of HPP and active packaging resulted in a synergistic effect reducing the counts of the pathogen below the detection limit throughout 60. days storage at 4. °C. However, when these samples were stored at 8. °C, growth did occur, but again a delay in growth was observed. The effects on colour and lipid oxidation were also studied during storage and were not significantly affected by the treatments. Active packaging followed by in-package pressure treatment could be a useful approach to reduce the risk of L. monocytogenes in cooked chicken without impairing its quality. Industrial relevance: Ready-to-eat products are of great economic importance to the industry. However, they have been implicated in several outbreaks of listeriosis. Therefore, effective ways to reduce the risk from this pathogenic microorganism can be very attractive for manufacturers. This study showed that the use of active packaging followed by HPP can enhance the listericidal efficiency of the treatment while using lower pressure levels, and thus having limited effects on colour and lipid oxidation of RTE chicken breast.