KnotProt: a database of proteins with knots and slipknots.

The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints.

Taking care of the most vulnerable : a descriptive study of patients with 12 attendances or more at a Swiss university hospital emergency department in 2009

Introduction: Patients who repeatedly attend the Emergency Department (ED) often have a distinct and complex vulnerability profile that includes poor somatic, psychological, and social indicators. This profile has an impact on the patients' well-being as well as on hospital costs. The objective of the study was to specify the characteristics of hyper users (HU) and explore the connection with ED care and hospital costs. Methods: The study sample comprised all adult patients with 12 or more attendances at the ED of the Lausanne University Hospital in 2009. The data were collected by retrospectively searching internal databases to identify the patients concerned and then analysing the profiles of these patients. Information gathered included demographic, somatic, psychological, at-risk behaviour, and social indicators, and health system consumption including costs. Results: In 2009, 23 patients (0.1%) attended 12 times or more (425 attendances, 0.8%). The average age was about 43 years, 60.9% were female, and 47.8% single. Of these 95.7% had basic insurance, 87.0% had a general practitioner, and 30.4% were under legal guardianship. The majority attended in the evening or at night (67.1%), and almost one quarter of these attendances resulted in inpatient treatment (24.0%). Most HU had attended the ED in previous years too (95.7% in 2008). The most prevalent diagnoses concerned 'mental disorders' (87.0%). About 30.4% of patients had attempted suicide (all were female patients). Other frequent diagnoses concerned 'trauma' (65.2%), and the 'digestive' and the 'nervous system' (each 56.5%). At-risk behaviour such as severe alcohol consumption (34.8%), or excessive use of medicines (26.1%) was very frequent, and some patients used illicit drugs (21.7%). There was only a weak association between the number of ED attendances and the resulting costs. However, a reduction of one outpatient visit per patient would have decreased ED outpatient costs by 8.5%. Conclusions: HU often have a particularly vulnerable profile. Mental problems are prevalent among them, as are at-risk behaviour and severe somatic conditions. The complexity of the patients' profiles demands specific care that cannot be guaranteed within an everyday ED routine. The use of an interdisciplinary case management team might be a promising approach in diminishing the number of attendances and the associated costs, although the profiles of HU are such that they probably cannot completely give up ED attendance.

Jambes lourdes, insuffisance veineuse des membres inférieurs et hormonothérapie substitutive [Heavy legs, venous insufficiency of the legs and hormone substitution therapy]

The effects of estrogens and gestagens on veins and circulation have been studied since prescription of these hormones as oral contraception and description of related thromboembolic events. The identification of different receptors and the description of these receptors in venous walls have helped to understand some hormonal effects. However, the actual knowledge remains insufficient to explain the complexity of the actions of hormones on venous function. The distribution, the density and the receptor types vary with age, gender, hormonal status and vascular bed. Gestagens mainly reduce the tone of venous walls, whereas estrogens have various effects. Between 25% and 50% of European adults and even 80% or more in some risk groups complain about heavy legs, with or without chronic venous insufficiency. The number of women to whom hormonal substitution is or could be prescribed increases along with aging of populations and the better understanding of potential benefits. The need for a better understanding of vascular effects of sexual hormones is growing, since the incidence of chronic venous insufficiency of the legs increases with age. The life prognosis will not be affected by a deterioration of a chronic venous insufficiency. In contrast, the quality of life, morbidity and the cost of treatment will be expected to change. In addition, thromboembolic events have to be considered, as has been shown in recent studies. These findings outline the need for further studies on the relation between hormones and venous function and for some caution when prescribing hormonal substitution.

@neurIST infrastructure for advanced disease management through integration of heterogeneous data, computing, and complex processing services

The increasing volume of data describing humandisease processes and the growing complexity of understanding, managing, and sharing such data presents a huge challenge for clinicians and medical researchers. This paper presents the@neurIST system, which provides an infrastructure for biomedical research while aiding clinical care, by bringing together heterogeneous data and complex processing and computing services. Although @neurIST targets the investigation and treatment of cerebral aneurysms, the system’s architecture is generic enough that it could be adapted to the treatment of other diseases.Innovations in @neurIST include confining the patient data pertaining to aneurysms inside a single environment that offers cliniciansthe tools to analyze and interpret patient data and make use of knowledge-based guidance in planning their treatment. Medicalresearchers gain access to a critical mass of aneurysm related data due to the system’s ability to federate distributed informationsources. A semantically mediated grid infrastructure ensures that both clinicians and researchers are able to seamlessly access andwork on data that is distributed across multiple sites in a secure way in addition to providing computing resources on demand forperforming computationally intensive simulations for treatment planning and research.

Bureaucracy and the flypaper effect : Evidence from intercommunal fiscal equalisation in the canton of Vaud

Unlike classical theoretical expectations, our empirical study shows that financial transfers to decentralised governments increase local public expenditures much more than would be triggered by an equivalent rise in local income. This empirical evidence of the presence of a flypaper effect is achieved using panel data from 375 municipalities located in the Swiss canton of Vaud covering the period 1994 to 2005. During that time there was a major change in the financial equalisation scheme. Furthermore, our study confirms the analysis of the public choice theory: the effect depends partly on the degree of complexity of the municipal bureaucracy. These results show that local bureaucratic behaviour may impede the effectiveness of a financial equalisation scheme that aims to reduce disparities in local tax.

Automatic Lexical Semantic Classification of Nouns

The work we present here addresses cue-based noun classification in English and Spanish. Its main objective is to automatically acquire lexical semantic information by classifying nouns into previously known noun lexical classes. This is achieved by using particular aspects of linguistic contexts as cues that identify a specific lexical class. Here we concentrate on the task of identifying such cues and the theoretical background that allows for an assessment of the complexity of the task. The results show that, despite of the a-priori complexity of the task, cue-based classification is a useful tool in the automatic acquisition of lexical semantic classes.

Delay of extubation in neonates and children after cardiac surgery: impact of ventilator-associated pneumonia.

OBJECTIVE: This study was undertaken to determine the delay of extubation attributable to ventilator-associated pneumonia (VAP) in comparison to other complications and complexity of surgery after repair of congenital heart lesions in neonates and children. METHODS: Cohort study in a pediatric intensive care unit of a tertiary referral center. All patients who had cardiac operations during a 22-month period and who survived surgery were eligible (n = 272, median age 1.3 years). Primary outcome was time to successful extubation. Primary variable of interest was VAP Surgical procedures were classified according to complexity. Cox proportional hazards models were calculated to adjust for confounding. Potential confounders comprised other known risk factors for delayed extubation. RESULTS: Median time to extubation was 3 days. VAP occurred in 26 patients (9.6%). The rate of VAP was not associated with complexity of surgery (P = 0.22), or cardiopulmonary bypass (P = 0.23). The adjusted analysis revealed as further factors associated with delayed extubation: other respiratory complications (n = 28, chylothorax, airway stenosis, diaphragm paresis), prolonged inotropic support (n = 48, 17.6%), and the need for secondary surgery (n = 51, 18.8%; e.g., re-operation, secondary closure of thorax). Older age promoted early extubation. The median delay of extubation attributable to VAP was 3.7 days (hazards ratio HR = 0.29, 95% CI 0.18-0.49), exceeding the effect size of secondary surgery (HR = 0.48) and other respiratory complications (HR = 0.50). CONCLUSION: VAP accounts for a major delay of extubation in pediatric cardiac surgery.

Assessment of transcript reconstruction methods for RNA-seq.

We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data.

Measurement of nurses' workload in an oncology outpatient clinic

The growing demand and the degree of patient care in oncological outpatient services, as well as the complexity of treatment have had an impact on the workload of nurses. This study aimed at measuring the workload and productivity of nurses in an oncological outpatient service. An observational study using a work sampling technique was conducted and included seven nurses working in an oncological outpatient service in the south-eastern region of Brazil. A total of 1,487 intervention or activity samples were obtained. Nurses used 43.2% of their time on indirect care, 33.2% on direct care, 11.6% on associated activities, and 12% on personal activities. Their mean productivity was 88.0%. The findings showed that nurses in this service spend most of their time in indirect care activities. Moreover, the productivity index in this study was above that recommended in the literature.

Social support from the perspective of adolescent victims of domestic violence

Objective: Assess the understanding of adolescents regarding the social support received in situations of domestic violence. Method: A qualitative study with data collection carried out through focus groups with 17 adolescent victims of domestic violence, institutionally welcomed in Campinas-SP, and through semi-structured interviews with seven of these adolescents. Information was analyzed by content analysis, thematic modality. Results: Observing the thematic categories it was found that social support for the subjects came from the extended family, the community, the Guardianship Council, the interpersonal relationships established at the user embracement institution and from the religiosity/spirituality. Conclusion: The mentioned sources of support deserve to be enhanced and expanded. With the current complexity of the morbidity and mortality profiles, especially in children and adolescents, the (re)signification and the (re)construction of health actions is imperative.



The decision of an obese woman to have bariatric surgery: the social phenomenology

Objective To understand the process by which an obese woman decides to have bariatric surgery. Method A qualitative survey with a social phenomenology approach, carried out in 2012, with 12 women, using the phenomenological interview. Results A woman bases the decision to have the surgery on: the inappropriateness of her eating habits; a physical appearance that is incompatible with an appearance that is standardized by society; the social prejudice that she has to live with; the limitations imposed by obesity; and her lack of success with previous attempts to lose weight. Outcomes that she hopes for from the decision to have the surgery include: restoring her health; achieving social inclusion; and entering the labor market. Conclusion This study allows one to reflect that prescriptive actions do not give a satisfactory response to a complexity of the subjective questions involved in the decision to have surgery for obesity. For this, what is called for is a program of work based on an interdisciplinary approach, and training that gives value to the bio-psycho-social aspects involved in a decision in favor of surgical treatment.

Systematic review of meaning in life assessment instruments.

BACKGROUND: The construct of "meaning in life" (MiL) has raised the interest of clinicians working in psycho-oncology and end-of-life care. It has become a topic of scientific investigation where diverse assessment approaches have been applied. Aims: We present a comprehensive systematic review of existing MiL assessment instruments. METHODS: Electronic searches of articles published in English peer-reviewed journals were performed in Psycinfo, Medline, Embase and Cinahl. Instruments are appraised with regard to ten measurement properties. RESULTS: In total, 59 nomothetic and idiographic MiL instruments were identified. Most instruments were developed in North America and meet basic psychometric criteria. They assess presence of and search for MiL, crisis and sources of MiL, meaning making, meaningful activity, MiL in the context of illness, breadth, depth, and other structural indicators. These aspects are largely consistent with existing MiL definitions. Nine out of 59 instruments included cancer populations in test development. CONCLUSIONS: This overview of available instruments underscores the complexity of the construct and might assist researchers to select an appropriate instrument for their research needs. Finally, it points to the need for more integrative theorizing and research on MiL. Copyright © 2012 John Wiley & Sons, Ltd.

Mapping Nursing language terms of Parkinson's disease

OBJECTIVE Implementing cross-mapping of Nursing language terms with the terminology of NANDA International, contained in records of patients with Parkinson's disease in rehabilitation. METHOD Descriptive study of cross mapping, carried out in three steps. A simple random sample of 67 files of patients who participated in the rehabilitation in the period between March 2009 and April 2013. RESULTS We identified 454 terms of Nursing language that resulted in 54 diagnoses after cross-mapping, present in 11 of the 13 taxonomy domains. The most mapped diagnosis was "Impaired urinary elimination" (59.7%), followed by "Urgent urinary incontinence" (55.2%), "Willingness to self-control improved health" (50.7%), "Constipation" (47.8%) and "Compromised physical mobility" (29.9%). Seven described terms were not mapped due to a corresponding defining characteristic being absent. CONCLUSION It was possible to determine the profile of patients, as well as the complexity of nursing care in the rehabilitation of patients with Parkinson's disease.

Multi-faceted functions of secretory IgA at mucosal surfaces.

Secretory IgA (SIgA) plays an important role in the protection and homeostatic regulation of intestinal, respiratory, and urogenital mucosal epithelia separating the outside environment from the inside of the body. This primary function of SIgA is referred to as immune exclusion, a process that limits the access of numerous microorganisms and mucosal antigens to these thin and vulnerable mucosal barriers. SIgA has been shown to be involved in avoiding opportunistic pathogens to enter and disseminate in the systemic compartment, as well as tightly controlling the necessary symbiotic relationship existing between commensals and the host. Clearance by peristalsis appears thus as one of the numerous mechanisms whereby SIgA fulfills its function at mucosal surfaces. Sampling of antigen-SIgA complexes by microfold (M) cells, intimate contact occurring with Peyer's patch dendritic cells (DC), down-regulation of inflammatory processes, modulation of epithelial, and DC responsiveness are some of the recently identified processes to which the contribution of SIgA has been underscored. This review aims at presenting, with emphasis at the biochemical level, how the molecular complexity of SIgA can serve these multiple and non-redundant modes of action.

English as a world language: its role as a lingua francaa sociolinguistic profile of students of secondary schools in Santiago Island, in the Archipelago of Cape Verde

Esta tese centra-se em aspectos relevantes do inglês como uma língua universal, no actual contexto globalizado e examina possíveis mudanças relacionadas com o seu uso, em especial no continente africano, particularmente no caso de Cabo Verde, no sentido de ponderar eventuais alternativas nas pedagogias linguísticas no ensino desta língua que impliquem uma adaptação à realidade contemporânea. Uma vez que, nos nossos tempos, o inglês é a língua de eleição para a comunicação intercultural entre povos com várias experiências culturais e linguísticas, o conhecimento deste idioma torna-se, a cada dia que passa, impreterível e indispensável, na interacção intercultural. Em África, as funções desempenhadas pelo inglês são complexas; além da língua inglesa ser usada para comunicação entre etnias, com o estatuto de língua franca, também tem o papel de preservar a identidade nacional e de estabelecer a unidade entre os povos da mesma nação. Por conseguinte, é de considerar talvez ainda com mais pertinência, a adopção de uma nova filosofia de pedagogia de ensino que permita dotar os seus cidadãos de capacidades que lhes possibilitem comunicar de forma inteligível com povos de outras culturas e línguas. O primeiro capítulo aborda aspectos teóricos relacionados com a expansão, comunicação e mudança associadas à língua inglesa e suas implicações no ensino em países onde esta não é língua nativa (L1). O segundo capítulo reflecte, em primeiro lugar, sobre a situação linguística em África e as línguas francas predominantes no continente, incluindo a língua inglesa. Considera também questões relacionadas com o multilinguismo e a identidade, bem como assuntos relacionados com as implicações da diversidade linguística para a educação dos povos africanos.