The roles of plant dsRNA-binding proteins in RNAi-like pathways

Dicers are associated with double-stranded RNA-binding proteins (dsRBPs) in animals. In the plant, Arabidopsis, there are four dicer-like (DCL) proteins and five potential dsRBPs. These DCLs act redundantly and hierarchically. However, we show there is little or no redundancy or hierarchy amongst the DRBs in their DCL interactions. DCL1 operates exclusively with DRB1 to produce micro (mi)RNAs, DCL4 operates exclusively with DRB4 to produce trans-acting (ta) siRNAs and 21nt siRNAs from viral RNA. DCL2 and DCL3 produce viral siRNAs without requiring assistance from any dsRBP. DRB2, DRB3 and DRB5 appear unnecessary for mi-, tasi-, viral si-, or heterochromatinising siRNA production but act redundantly in a developmental pathway. © 2008 Federation of European Biochemical Societies.

High-throughput vectors for efficient gene silencing in plants

A major challenge in the post-genome era of plant biology is to determine the functions of all genes in the plant genome. A straightforward approach to this problem is to reduce or knockout expression of a gene with the hope of seeing a phenotype that is suggestive of its function. Insertional mutagenesis is a useful tool for this type of study but is limited by gene redundancy, lethal knockouts, non-tagged mutants, and the inability to target the inserted element to a specific gene. The efficacy of gene silencing in plants using inverted-repeat transgene constructs that encode a hairpin RNA (hpRNA) has been demonstrated by a number of groups, and has several advantages over insertional mutagenesis. In this paper we describe two improved pHellsgate vectors that facilitate rapid generation of hpRNA-encoding constructs, pHellsgate 4 allows the production of an hpRNA construct in a single step from a single polymerase chain reaction product, while pHellsgate 8 requires a two-step process via an intermediate vector. We show that these vectors are effective at silencing three endogenous genes in Arabidopsis, FLOWERING LOCUS C, PHYTOENE DESATURASE and ETHYLENE INSENSITIVE 2. We also show that a construct of sequences from two genes silences both genes.

Interestingness Measures for Multi-Level Association Rules

Association rule mining is one technique that is widely used when querying databases, especially those that are transactional, in order to obtain useful associations or correlations among sets of items. Much work has been done focusing on efficiency, effectiveness and redundancy. There has also been a focusing on the quality of rules from single level datasets with many interestingness measures proposed. However, with multi-level datasets now being common there is a lack of interestingness measures developed for multi-level and cross-level rules. Single level measures do not take into account the hierarchy found in a multi-level dataset. This leaves the Support-Confidence approach, which does not consider the hierarchy anyway and has other drawbacks, as one of the few measures available. In this chapter we propose two approaches which measure multi-level association rules to help evaluate their interestingness by considering the database’s underlying taxonomy. These measures of diversity and peculiarity can be used to help identify those rules from multi-level datasets that are potentially useful.

Development of hospital disaster resilience : conceptual framework and potential measurement

Objective Despite ‘hospital resilience’ gaining prominence in recent years, it remains poorly defined. This article aims to define hospital resilience, build a preliminary conceptual framework and highlight possible approaches to measurement. Methods Searches were conducted of the commonly used health databases to identify relevant literature and reports. Search terms included ‘resilience and framework or model’ or ‘evaluation or assess or measure and hospital and disaster or emergency or mass casualty and resilience or capacity or preparedness or response or safety’. Articles were retrieved that focussed on disaster resilience frameworks and the evaluation of various hospital capacities. Result A total of 1480 potentially eligible publications were retrieved initially but the final analysis was conducted on 47 articles, which appeared to contribute to the study objectives. Four disaster resilience frameworks and 11 evaluation instruments of hospital disaster capacity were included. Discussion and conclusion Hospital resilience is a comprehensive concept derived from existing disaster resilience frameworks. It has four key domains: hospital safety; disaster preparedness and resources; continuity of essential medical services; recovery and adaptation. These domains were categorised according to four criteria, namely, robustness, redundancy, resourcefulness and rapidity. A conceptual understanding of hospital resilience is essential for an intellectual basis for an integrated approach to system development. This article (1) defines hospital resilience; (2) constructs conceptual framework (including key domains); (3) proposes comprehensive measures for possible inclusion in an evaluation instrument, and; (4) develops a matrix of critical issues to enhance hospital resilience to cope with future disasters.

Acquired differential regulation of caspase-8 in cisplatin-resistant non-small-cell lung cancer

Failure to efficiently induce apoptosis contributes to cisplatin resistance in non-small-cell lung cancer (NSCLC). Although BCL-2-associated X protein (BAX) and BCL-2 antagonist killer (BAK) are critical regulators of the mitochondrial apoptosis pathway, their requirement has not been robustly established in relation to cisplatin. Here, we show that cisplatin can efficiently bypass mitochondrial apoptosis block caused by loss of BAX and BAK, via activation of the extrinsic death receptor pathway in some model cell lines. Apoptosis resistance following cisplatin can only be observed when both extrinsic and intrinsic pathways are blocked, consistent with redundancy between mitochondrial and death receptor pathways in cisplatin-induced apoptosis. In H460 NSCLC cells, caspase-8 cleavage was shown to be induced by cisplatin and is dependent on death receptor 4, death receptor 5, Fas-associated protein with death domain, acid sphingomyelinase and ceramide synthesis. In contrast, cisplatin-resistant cells fail to activate caspase-8 via this pathway despite conserving sensitivity to death ligand-driven activation. Accordingly, caspase-8 activation block acquired during cisplatin resistance, can be bypassed by death receptor agonism.

Revisiting sub-topic retrieval in the ImageCLEF 2009 photo retrieval task

Ranking documents according to the Probability Ranking Principle has been theoretically shown to guarantee optimal retrieval effectiveness in tasks such as ad hoc document retrieval. This ranking strategy assumes independence among document relevance assessments. This assumption, however, often does not hold, for example in the scenarios where redundancy in retrieved documents is of major concern, as it is the case in the sub–topic retrieval task. In this chapter, we propose a new ranking strategy for sub–topic retrieval that builds upon the interdependent document relevance and topic–oriented models. With respect to the topic– oriented model, we investigate both static and dynamic clustering techniques, aiming to group topically similar documents. Evidence from clusters is then combined with information about document dependencies to form a new document ranking. We compare and contrast the proposed method against state–of–the–art approaches, such as Maximal Marginal Relevance, Portfolio Theory for Information Retrieval, and standard cluster–based diversification strategies. The empirical investigation is performed on the ImageCLEF 2009 Photo Retrieval collection, where images are assessed with respect to sub–topics of a more general query topic. The experimental results show that our approaches outperform the state–of–the–art strategies with respect to a number of diversity measures.

Is intent-aware expected reciprocal rank sufficient to evaluate diversity?

In this paper we define two models of users that require diversity in search results; these models are theoretically grounded in the notion of intrinsic and extrinsic diversity. We then examine Intent-Aware Expected Reciprocal Rank (ERR-IA), one of the official measures used to assess diversity in TREC 2011-12, with respect to the proposed user models. By analyzing ranking preferences as expressed by the user models and those estimated by ERR-IA, we investigate whether ERR-IA assesses document rankings according to the requirements of the diversity retrieval task expressed by the two models. Empirical results demonstrate that ERR-IA neglects query-intents coverage by attributing excessive importance to redundant relevant documents. ERR-IA behavior is contrary to the user models that require measures to first assess diversity through the coverage of intents, and then assess the redundancy of relevant intents. Furthermore, diversity should be considered separately from document relevance and the documents positions in the ranking.

Consolidation of business process model collections

This thesis presents novel techniques for addressing the problems of continuous change and inconsistencies in large process model collections. The developed techniques treat process models as a collection of fragments and facilitate version control, standardization and automated process model discovery using fragment-based concepts. Experimental results show that the presented techniques are beneficial in consolidating large process model collections, specifically when there is a high degree of redundancy.

Phenotypic changes associated with RNA interference silencing of chalcone synthase in apple (Malus × domestica)

We have identified in apple (Malus × domestica) three chalcone synthase (CHS) genes. In order to understand the functional redundancy of this gene family RNA interference knockout lines were generated where all three of these genes were down-regulated. These lines had no detectable anthocyanins and radically reduced concentrations of dihydrochalcones and flavonoids. Surprisingly, down-regulation of CHS also led to major changes in plant development, resulting in plants with shortened internode lengths, smaller leaves and a greatly reduced growth rate. Microscopic analysis revealed that these phenotypic changes extended down to the cellular level, with CHS-silenced lines showing aberrant cellular organisation in the leaves. Fruit collected from one CHS-silenced line was smaller than the 'Royal Gala' controls, lacked flavonoids in the skin and flesh and also had changes in cell morphology. Auxin transport experiments showed increased rates of auxin transport in a CHS-silenced line compared with the 'Royal Gala' control. As flavonoids are well known to be key modulators of auxin transport, we hypothesise that the removal of almost all flavonoids from the plant by CHS silencing creates a vastly altered environment for auxin transport to occur and results in the observed changes in growth and development.

Capacity of fatty acid profiles and substrate utilization patterns to describe differences in soil microbial communities associated with increased salinity or alkalinity at three locations in South Australia

Fatty acid methyl ester (FAME) profiles, together with Biolog substrate utilization patterns, were used in conjunction with measurements of other soil chemical and microbiological properties to describe differences in soil microbial communities induced by increased salinity and alkalinity in grass/legume pastures at three sites in SE South Australia. Total ester-linked FAMEs (EL-FAMEs) and phospholipid-linked FAMEs (PL-FAMEs), were also compared for their ability to detect differences between the soil microbial communities. The level of salinity and alkalinity in affected areas of the pastures showed seasonal variation, being greater in summer than in winter. At the time of sampling for the chemical and microbiological measurements (winter) only the affected soil at site 1 was significantly saline. The affected soils at all three sites had lower organic C and total N concentrations than the corresponding non-affected soils. At site 1 microbial biomass, CO 2-C respiration and the rate of cellulose decomposition was also lower in the affected soil compared to the non-affected soil. Biomarker fatty acids present in both the EL- and PL-FAME profiles indicated a lower ratio of fungal to bacterial fatty acids in the saline affected soil at site 1. Analysis of Biolog substrate utilization patterns indicated that the bacterial community in the affected soil at site 1 utilized fewer carbon substrates and had lower functional diversity than the corresponding community in the non-affected soil. In contrast, increased alkalinity, of major importance at sites 2 and 3, had no effect on microbial biomass, the rate of cellulose decomposition or functional diversity but was associated with significant differences in the relative amounts of several fatty acids in the PL-FAME profiles indicative of a shift towards a bacterial dominated community. Despite differences in the number and relative amounts of fatty acids detected, principal component analysis of the EL- and PL-FAME profiles were equally capable of separating the affected and non-affected soils at all three sites. Redundancy analysis of the FAME data showed that organic C, microbial biomass, electrical conductivity and bicarbonate-extractable P were significantly correlated with variation in the EL-FAME profiles, whereas pH, electrical conductivity, NH 4-N, CO 2-C respiration and the microbial quotient were significantly correlated with variation in the PL-FAME profiles. Redundancy analysis of the Biolog data indicated that cation exchange capacity and bicarbonate-extractable K were significantly correlated with the variation in Biolog substrate utilization patterns.

Исследования и испытания алгоритмов автоматической пилотажно-навигационной системы малогабаритного беспилотного летательного аппарата = Research and testing of automatic navigation management system’s algorithms for small unmanned aerial vehicle

В статье представлено развитие принципа построения автоматической пилотажно-навигационной системы (АПНС) для беспилотного летательного аппарата (БЛА). Принцип заключается в синтезе комплексных систем управления БПЛА не только на основе использования алгоритмов БИНС, но и алгоритмов, объединяющих в себе решение задач формирования и отработки сформированной траектории резервированной системой управления и навигации. Приведены результаты аналитического исследования и данные летных экспериментов разработанных алгоритмов АПНС БЛА, обеспечивающих дополнительное резервирование алгоритмов навигации и наделяющих БЛА новым функциональной способностью по выходу в заданную точку пространства с заданной скоростью в заданный момент времени с учетом атмосферных ветровых возмущений. Предложена и испытана методика идентификации параметров воздушной атмосферы: направления и скорости W ветра. Данные летных испытаний полученного решения задачи терминальной навигации демонстрируют устойчивую работу синтезированных алгоритмов управления в различных метеоусловиях. The article presents a progress in principle of development of automatic navigation management system (ANMS) for small unmanned aerial vehicle (UAV). The principle defines a development of integrated control systems for UAV based on tight coupling of strap down inertial navigation system algorithms and algorithms of redundant flight management system to form and control flight trajectory. The results of the research and flight testing of the developed ANMS UAV algorithms are presented. The system demonstrates advanced functional redundancy of UAV guidance. The system enables new UAV capability to perform autonomous multidimensional navigation along waypoints with controlled speed and time of arrival taking into account wind. The paper describes the technique for real-time identification of atmosphere parameters such as wind direction and wind speed. The flight test results demonstrate robustness of the algorithms in diverse meteorological conditions.

Modulation and control of three-phase paralleled Z-source inverters for distributed generation applications

This paper presents a modulation and controller design method for paralleled Z-source inverter systems applicable for alternative energy sources like solar cells, fuel cells, or variablespeed wind turbines with front-end diode rectifiers. A modulation scheme is designed based on simple shoot-through principle with interleaved carriers to give enhanced ripple reduction in the system. Subsequently, a control method is proposed to equalize the amount of power injected by the inverters in the grid-connected mode and also to provide reliable supply to sensitive loads onsite in the islanding mode. The modulation and controlling methods are proposed to have modular independence so that redundancy, maintainability, and improved reliability of supply can be achieved. The performance of the proposed paralleled Z-source inverter configuration is validated with simulations carried out using Matlab/Simulink/Powersim. Moreover, a prototype is built in the laboratory to obtain the experimental verifications.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent

Proposing and developing the definition and conceptual framework for healthcare resilience to cope with disasters

Building healthcare resilience is an important step towards creating more resilient communities to better cope with future disasters. To date, however, there appears to be little literature on how the concept of healthcare resilience should be defined and operationalized with a conceptual framework. This article aims to build a comprehensive healthcare disaster management approach guided by the concept of resilience. Methods: Google and major health electronic databases were searched to retrieve critical relevant publications. A total of 61 related publications were included, to provide a comprehensive overview of theories and definitions relevant to disaster resilience. Results and Discussions: Resilience is an inherent and adaptive capacity to cope with future uncertainty, through multiple strategies with all hazards approaches, in an attempt to achieve a positive outcome with linkage and cooperation. Healthcare resilience can be defined as the capability of healthcare organisations to resist, absorb, and respond to the shock of disasters while maintaining the most essential functions, then recover to their original state or adapt to a new state. It can be assessed by criteria, namely: robustness, redundancy, resourcefulness; and a complex of key dimensions, namely: vulnerability and safety, disaster resources and preparedness, continuity of essential health services, recovery and adaptation. Conclusions: This new concept places healthcare organisations’ disaster capabilities, management tasks, activities and disaster outcomes together into a comprehensive whole view, using an integrated approach and establishing achievable goals.

Autotransporters of Escherichia coli : a sequence-based characterization

Autotransporter (AT) proteins are found in all Escherichia coli pathotypes and are often associated with virulence. In this study we took advantage of the large number of available E. coli genome sequences to perform an in-depth bioinformatic analysis of AT-encoding genes. Twenty-eight E. coli genome sequences were probed using an iterative approach, which revealed a total of 215 AT-encoding sequences that represented three major groups of distinct domain architecture: (i) serine protease AT proteins, (ii) trimeric AT adhesins and (iii) AIDA-I-type AT proteins. A number of subgroups were identified within each broad category, and most subgroups contained at least one characterized AT protein; however, seven subgroups contained no previously described proteins. The AIDA-I-type AT proteins represented the largest and most diverse group, with up to 16 subgroups identified from sequence-based comparisons. Nine of the AIDA-I-type AT protein subgroups contained at least one protein that possessed functional properties associated with aggregation and/or biofilm formation, suggesting a high degree of redundancy for this phenotype. The Ag43, YfaL/EhaC, EhaB/UpaC and UpaG subgroups were found in nearly all E. coli strains. Among the remaining subgroups, there was a tendency for AT proteins to be associated with individual E. coli pathotypes, suggesting that they contribute to tissue tropism or symptoms specific to different disease outcomes.