Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

Epidemiologic Evaluation of Mandibular Fractures in the Rio de Janeiro High-Complexity Hospital

The aim of this study was to gather data on trauma etiology and mandibular fracture localization in patients who presented at the General Hospital of Nova Iguacu, Rio de Janeiro, Brazil. From March 2007 to December 2008, 95 patients with mandibular fracture were registered in a medical form, at the Bucomax-illofacial Surgery Department of the General Hospital of Nova Iguacu, Rio de Janeiro, Brazil. Concerning mandibular fracture etiology, 21.05% were caused by motorcycle accidents, followed by interpersonal violence without use of weapons (punches, kicks, bumps with the head, blows with the elbow, etc) (16.84%) and interpersonal violence with firearm (14.73%). It was found that 52.63% of the patients had a single fracture line. The most affected fracture area was the parasymphysis (26.02%), followed by the condyle (22.60%) and mandibular angle (18.49%). Concerning the injury area, 24.21% were directed to the mandibular symphysis, 22.17% of the patients did not remember the injury area, and 18.94% had multiple injuries. When the injury was directed to the symphysis, the result was more condyle fractures (11.64%), and injuries at the mandibular angle resulted in fractures at the angle itself (8.90%). The most common fracture cause was traffic accidents, mainly motorcycle accidents, and the most affected areas were the parasymphysis and the condyle. The mandible isolated fractures occurred in half of the cases. Motorcycle accidents resulted in more fractures in the parasymphysis area, and when the symphysis area is affected by injuries, the result is a higher percentage in condyle fractures.

O acesso aos exames de alta complexidade nos planos de saúde privados na perspectiva dos usuários

A dissertação trata do acesso aos serviços de alta complexidade, particularmente os exames diagnósticos e complementares, estudado entre usuários de planos de saúde privados que buscam atendimento e diagnóstico especializado. Desde a década de 80 o usuário do sistema público de saúde vem procurando a saúde suplementar. Contudo, afirmar que o acesso é garantido no domínio privado, através da contratação dos planos de saúde, é uma incerteza que rodeia a inspiração para esta pesquisa, que se justifica pela relevância de ações que possibilitem a melhora da qualidade regulatória dos planos de saúde, a partir do controle social de seus usuários. O objetivo geral é analisar as percepções do acesso aos exames de alta complexidade nos serviços de saúde privados entre usuários de planos de saúde. Os objetivos específicos são descrever as percepções dos usuários de planos de saúde acerca do acesso aos exames de alta complexidade; analisar as motivações dos usuários de planos de saúde privados para a realização de exames de alta complexidade através da rede privada de assistência; e analisar o nível de satisfação dos usuários de planos de saúde quanto ao acesso aos exames de alta complexidade. A metodologia é qualitativa-descritiva, onde a amostra foi de trinta usuários de planos de saúde, acima de 18 anos, selecionados no campo de estudo no ano de 2010. O cenário de estudo foi um laboratório privado de medicina diagnóstica no Rio de Janeiro. As técnicas de coleta de dados utilizadas foram formulário e entrevista individual estruturada. A análise do formulário foi realizada através de estatística descritiva, e as entrevistas através da análise de conteúdo temática-categorial. Os usuários de plano de saúde declararam que o acesso é garantido com facilidade para os exames de alta complexidade. Suas principais motivações para a realização desses exames na rede privada de assistência foram caracterizadas pela rapidez de atendimento, flexibilidade e facilidade de marcação pela internet, telefone ou pessoalmente no laboratório estudado, pronta entrega dos resultados, dificuldade e morosidade do atendimento do SUS, localização do prestador credenciado próxima de bairros residenciais ou do trabalho, resolutividade diagnóstica de imagem de excelência, possibilidade de escolha pelo usuário entre as modalidades aberta e fechada de ressonância magnética e tomografia computadorizada, além da densitometria óssea que foram facilmente acessíveis a todos os sujeitos da pesquisa. O nível de satisfação foi correspondido com a rapidez na realização dos exames em caráter eletivo e de urgência quase equiparados na escala de tempo de acordo com os usuários. Contudo, embora as notas de avaliação dos usuários quanto aos seus planos de saúde tenham sido altas, foram abordadas algumas dificuldades, tais como: prazos de validade dos pedidos médicos com datação prévia; solicitações de senhas de autorização pela operadora; burocracia nos procedimentos de agendamento; dificuldades de acesso para tratamentos como implantes, fisioterapia, RPG, pilates, home care, consultas de check up; negação de reembolsos; restrição de materiais cirúrgicos, em especial as próteses e órteses; e restrições específicas de grau para cirurgias de miopia. Conclui-se que o atendimento rápido dos exames de imagem de alto custo na amostra foi descrito como satisfatório, embora a percepção de rapidez possa variar em função do tipo de produto do plano de saúde privado contratado, com necessidade de melhoria regulatória em alguns aspectos pontuais da saúde suplementar.

Slice, mine and dice : complexity-aware automated discovery of business process models

Automated process discovery techniques aim at extracting models from information system logs in order to shed light into the business processes supported by these systems. Existing techniques in this space are effective when applied to relatively small or regular logs, but otherwise generate large and spaghetti-like models. In previous work, trace clustering has been applied in an attempt to reduce the size and complexity of automatically discovered process models. The idea is to split the log into clusters and to discover one model per cluster. The result is a collection of process models -- each one representing a variant of the business process -- as opposed to an all-encompassing model. Still, models produced in this way may exhibit unacceptably high complexity. In this setting, this paper presents a two-way divide-and-conquer process discovery technique, wherein the discovered process models are split on the one hand by variants and on the other hand hierarchically by means of subprocess extraction. The proposed technique allows users to set a desired bound for the complexity of the produced models. Experiments on real-life logs show that the technique produces collections of models that are up to 64% smaller than those extracted under the same complexity bounds by applying existing trace clustering techniques.

A test rig for the condition-based maintenance application on the traction chain of very high speed trains

The preventive maintenance of traction equipment for Very High Speed Trains (VHST) nowadays is becoming very expensive owing to the high complexity and quality of these components that require high reliability. An efficient maintenance approach like the Condition-Based Maintenance (CBM) should be implemented to reduce the costs. For this purpose, an experimental full-scale test rig for the CBM of VHST traction equipment has been designed to investigate in detail failures in the main mechanical components of system, i.e. motor, bearings and gearbox. The paper describes the main characteristics of this unique test rig, able to reproduce accurately the train operating conditions, including the relative movements of the motor, the gearbox and the wheel axle. Gearbox, bearing seats and motor are equipped by accelerometers, thermocouples, torque meter and other sensors in different positions. The testing results give important information about the most suitable sensor position and type to be installed for each component and show the effectiveness of the techniques used for the signal analysis in order to identify faults of the gearbox and motor bearings.

Maintaining a focus on opportunities at work: The interplay between age, job complexity, and the use of selection, optimization, and compensation strategies

The concept of focus on opportunities describes how many new goals, options, and possibilities employees believe to have in their personal future at work. This study investigated the specific and shared effects of age, job complexity, and the use of successful aging strategies called selection, optimization, and compensation (SOC) in predicting focus on opportunities. Results of data collected from 133 employees of one company (mean age = 38 years, SD = 13, range 16–65 years) showed that age was negatively, and job complexity and use of SOC strategies were positively related to focus on opportunities. In addition, older employees in high-complexity jobs and older employees in low-complexity jobs with high use of SOC strategies were better able to maintain a focus on opportunities than older employees in low-complexity jobs with low use of SOC strategies.

Complexity, age and motor competence effects on fine motor kinematics

Prehension is a fundamental skill usually performed as part of a complex action sequence in everyday tasks. Using an information processing framework, these studies examined the effects of task complexity, defined by the number of component movement elements (MEs), on performance of prehension tasks. Of interest was how motor control and organisation might be influenced by age and/or motor competence. Three studies and two longitudinal case studies examined kinematic characteristics of prehension tasks involving one-, two- and three-MEs: reach and grasp (low-complexity); reach, grasp and object placement (moderate-complexity); and reach, grasp and double placement of object (high-complexity). A pilot study established the suitability of tasks and procedures for children aged 5-, 8- and 11-years and showed that responses to task complexity and object size manipulations were sensitive to developmental changes, with increasing age associated with faster movements. Study 2 explored complexity and age effects further for children aged 6- and 11-years and adults. Increasing age was associated with shorter and less variable movement times (MTs) and proportional deceleration phases (%DTs) across all MEs. Task complexity had no effect on simple reaction time (SRT), suggesting that there may be little preprogramming of movements beyond the first ME. In addition, MT was longer and more on-line corrections were evident for the high- compared to the moderate-complexity task for ME1. Task complexity had a greater influence on movements in ME2 and ME3 than ME1. Adults, but not children, showed task specific adaptations in ME2. Study 3 examined performance of children with different levels of motor competence aged between 5- and 10-years. Increasing age was associated with shorter SRTs, and MTs for ME1 only. A decrease in motor competence was associated with greater difficulty in planning and controlling movements as indicated by longer SRTs, higher %DTs and more on-line corrections, especially in ME2. Task complexity affected movements in all MEs, with a greater influence on ME1 compared to Study 2. Findings also indicated that performance in MEs following prehension may be especially sensitive to motor competence effects on movement characteristics. Case studies for two children at risk of Developmental Coordination Disorder (DCD) revealed two different patterns of performance change over a 16-17 month period, highlighting the heterogeneous nature of DCD. Overall, findings highlighted age-related differences, and the role of motor competence, in the ability to adapt movements to task specific requirements. Results are useful in guiding movement education programmes for children with both age-appropriate and lower levels of motor competence.

Complexity of management and health outcomes in a prospective cohort study of 573 heart failure patients in Australia : does more equal less?

Aims and objectives : To compare the efficacy of chronic heart failure management programmes (CHF-MPs) according to a scoring algorithm used to quantify the level of applied interventions–the Heart Failure Intervention Score (HF-IS).

Background : The overall efficacy of heart failure programmes has been proven in several meta-analyses. However, the debate continues as to which components are essential in a heart failure programme to improve patient outcomes.

Design : Prospective cohort study of patients participating in heart failure programmes.

Method : Forty-eight of 62 (77%) programmes in Australia participating in a national register of CHF-MPs were evaluated using the HF-IS: derived from a summed and weighted score of each intervention applied by the CHF-MP (27 interventions overall). The CHF-MPs were prospectively categorised as relatively low (HF-IS < 190 – n = 39 programmes & 407 patients) or high (HF-IS ≥ 190 – n = 9 programmes & 166 patients) in complexity. Six-month morbidity and mortality rates in 573 consecutively recruited patients with systolic dysfunction and in New York Heart Association Class II–IV were prospectively examined.

Results : Patients exposed to CHF-MPs with a high HF-IS had a lower rate of unplanned, all-cause hospitalisation (n = 24, 14% vs. n = 102, 25%) compared with CHF-MPs with a low HF-IS within six months. On an adjusted basis, CHF-MPs with a high HF-IS were associated with a reduced risk of unplanned hospitalisation and/or death within six months and remained event-free longer.

Conclusion : High complexity CHF-MPs applying more evidence-based interventions are associated with a higher event-free survival over six months.

Relevance to clinical practice : The HF-IS is an easy-to-use evidence-based tool to assist programme coordinators to improve the quality of their heart failure programme which may also improve patient outcomes.

Cogeneration design problem Computational complexity analysis and solution through an expert system

Purpose - The purpose of this paper is twofold: to analyze the computational complexity of the cogeneration design problem; to present an expert system to solve the proposed problem, comparing such an approach with the traditional searching methods available.Design/methodology/approach - The complexity of the cogeneration problem is analyzed through the transformation of the well-known knapsack problem. Both problems are formulated as decision problems and it is proven that the cogeneration problem is np-complete. Thus, several searching approaches, such as population heuristics and dynamic programming, could be used to solve the problem. Alternatively, a knowledge-based approach is proposed by presenting an expert system and its knowledge representation scheme.Findings - The expert system is executed considering two case-studies. First, a cogeneration plant should meet power, steam, chilled water and hot water demands. The expert system presented two different solutions based on high complexity thermodynamic cycles. In the second case-study the plant should meet just power and steam demands. The system presents three different solutions, and one of them was never considered before by our consultant expert.Originality/value - The expert system approach is not a "blind" method, i.e. it generates solutions based on actual engineering knowledge instead of the searching strategies from traditional methods. It means that the system is able to explain its choices, making available the design rationale for each solution. This is the main advantage of the expert system approach over the traditional search methods. On the other hand, the expert system quite likely does not provide an actual optimal solution. All it can provide is one or more acceptable solutions.

Modeling soil system: complexity under your feet

A clear statement in these lines textually cited (Byers et al., 1938) defines the framework of this special issue: “True soil is the product of the action of climate and living organism upon the parent material, as conditioned by the local relief. The length of time during which these forces are operative is of great importance in determining the character of the ultimate product. Drainage conditions are also important and are controlled by local relief, by the nature of the parent material or underlying rock strata, or by the amount of precipitation in relation to rate of percolation and runoff water. There are, therefore, five principal factors of soil formation: Parent material, climate, biological activity, relief and time. These soil forming factors are interdependent, each modifying the effectiveness of the others.” Due to these various processes associated to its formation and genesis soil dynamics reveals high complexity that creates several levels of structure using this term in a broad sense

High volume fabrication of laser targets using MEMS techniques

The latest techniques for the fabrication of high power laser targets, using processes developed for the manufacture of Micro-Electro-Mechanical System (MEMS) devices are discussed. These laser targets are designed to meet the needs of the increased shot numbers that are available in the latest design of laser facilities. Traditionally laser targets have been fabricated using conventional machining or coarse etching processes and have been produced in quantities of 10s to low 100s. Such targets can be used for high complexity experiments such as Inertial Fusion Energy (IFE) studies and can have many complex components that need assembling and characterisation with high precision. Using the techniques that are common to MEMS devices and integrating these with an existing target fabrication capability we are able to manufacture and deliver targets to these systems. It also enables us to manufacture novel targets that have not been possible using other techniques. In addition, developments in the positioning systems that are required to deliver these targets to the laser focus are also required and a system to deliver the target to a focus of an F2 beam at 0.1Hz is discussed.

Identifying the triggers for management services in business transformation management

Business transformations are complex organisational change endeavours that result in a business performing current work differently, or performing different work. Information Technology (IT) is a key enabler of such initiatives, but comes with its challenges, as revamping the IT infrastructure in large-scale organisations implies high complexity, high risk, and often high failure rates. We view business transformations as a collection of management services that are demanded and enacted at a program level, defined as abstract resources that provide the managerial capabilities necessary for business transformations. In this research-in-progress, we explore what triggers the need for management services in response to the challenges in business transformation management. We analyse data from two exploratory case studies using the critical incident technique as our qualitative analysis method. Early findings indicate that management service triggers reside on either the strategic level, which may be internally or externally driven, or at the program management level, which may be situational, influential or reactional. We detail implications for our on-going research.

Controlled automated discovery of collections of business process models

Automated process discovery techniques aim at extracting process models from information system logs. Existing techniques in this space are effective when applied to relatively small or regular logs, but generate spaghetti-like and sometimes inaccurate models when confronted to logs with high variability. In previous work, trace clustering has been applied in an attempt to reduce the size and complexity of automatically discovered process models. The idea is to split the log into clusters and to discover one model per cluster. This leads to a collection of process models – each one representing a variant of the business process – as opposed to an all-encompassing model. Still, models produced in this way may exhibit unacceptably high complexity and low fitness. In this setting, this paper presents a two-way divide-and-conquer process discovery technique, wherein the discovered process models are split on the one hand by variants and on the other hand hierarchically using subprocess extraction. Splitting is performed in a controlled manner in order to achieve user-defined complexity or fitness thresholds. Experiments on real-life logs show that the technique produces collections of models substantially smaller than those extracted by applying existing trace clustering techniques, while allowing the user to control the fitness of the resulting models.

Playing Games on Sets and Models

The most prominent objective of the thesis is the development of the generalized descriptive set theory, as we call it. There, we study the space of all functions from a fixed uncountable cardinal to itself, or to a finite set of size two. These correspond to generalized notions of the universal Baire space (functions from natural numbers to themselves with the product topology) and the Cantor space (functions from natural numbers to the {0,1}-set) respectively. We generalize the notion of Borel sets in three different ways and study the corresponding Borel structures with the aims of generalizing classical theorems of descriptive set theory or providing counter examples. In particular we are interested in equivalence relations on these spaces and their Borel reducibility to each other. The last chapter shows, using game-theoretic techniques, that the order of Borel equivalence relations under Borel reduciblity has very high complexity. The techniques in the above described set theoretical side of the thesis include forcing, general topological notions such as meager sets and combinatorial games of infinite length. By coding uncountable models to functions, we are able to apply the understanding of the generalized descriptive set theory to the model theory of uncountable models. The links between the theorems of model theory (including Shelah's classification theory) and the theorems in pure set theory are provided using game theoretic techniques from Ehrenfeucht-Fraïssé games in model theory to cub-games in set theory. The bottom line of the research declairs that the descriptive (set theoretic) complexity of an isomorphism relation of a first-order definable model class goes in synch with the stability theoretical complexity of the corresponding first-order theory. The first chapter of the thesis has slightly different focus and is purely concerned with a certain modification of the well known Ehrenfeucht-Fraïssé games. There we (me and my supervisor Tapani Hyttinen) answer some natural questions about that game mainly concerning determinacy and its relation to the standard EF-game