Reflexões multidisciplinares da Ciência Aberta em vivências de Discente e Docentes

O movimento em prol da Ciência Aberta (CA) abarca diferentes escolas de pensamento e diferentes iniciativas, defendendo não somente o acesso aberto às publicações e aos dados, mas também uma maior transparência no processo de pesquisa. Entretanto percebe-se uma resistência do pesquisador à adesão às práticas de CA. Este artigo sintetiza argumentos pró e contra ao movimento da CA percebidos a partir de reflexões desenvolvidas no âmbito de disciplina eletiva de curso de pós-graduação stricto sensu interdisciplinar. Os resultados da discussão realizada por discentes e docentes são apresentadas em oito categorias: reprodutibilidade, acesso aberto, dados abertos, transparência, assimetria entre setor público e privado, integridade, avaliação por pares aberta e preprints, sistema de avaliação da produção científica e políticas de Ciência Aberta. Em síntese, por um lado o uso das práticas de CA parece ter potência para revelar dilemas sobre integridade e promover a abertura de dados de pesquisa, o que pode "assombrar" pesquisadores. Por outro lado, a possibilidade de mitigar riscos à qualidade das evidências científicas, fortalecer a reprodutibilidade e a credibilidade na ciência favorece a disseminação destas práticas e de seu debate nos ambientes formativos do pesquisador contribuindo para o distensionamento ao uso de práticas de CA.

A pattern language of compassion in intensive care and palliative care contexts.

BACKGROUND: Compassion has been identified as important for therapeutic relationships in clinical medicine however there have been few empirical studies looking at how compassion is expressed different contexts. The purpose of this study was to explore how context impacts perceptions and expressions of compassion in the intensive care unit and in palliative care. METHODS: This was an inductive qualitative study that employed sensitizing concepts from activity theory, realist inquiry, phenomenology and autoethnography. Clinicians working in intensive care units and palliative care services wrote guided field notes on their observations and experiences of how suffering and compassion were expressed in these settings. Data were analyzed using constructivist grounded theory. RESULTS: Fifty-eight field notes were generated, along with transcripts from three focus groups. Clinicians conceptualized, observed, and expressed compassion in different ways within different contexts. Patterns of compassion identified were relational, dispositional, activity-focused, and situational. A pattern language of compassion in healthcare was developed based on these findings. CONCLUSIONS: Recognizing compassion as shifting patterns of diverse attitudes, behaviours, and relationships raises numerous questions as to how compassion can be developed, supported and recognized in different clinical settings.

The 2009/2010 Caribbean drought: a case study.

The impacts of drought in the Caribbean have not been as dramatic as in some other parts of world, but it is not exempt from the experiences of drought. As a result of the effects of a prolonged drought in 2009/2010, the agenda for the 21st Inter-Sessional Meeting of the Caribbean Community (CARICOM) paid particular attention to the issue of drought. This paper reviews the management framework for responding to drought disasters in five CARICOM countries. The paper also reports on some of the effects of the 2009/2010 drought with particular reference to Grenada and the Grenadines. During the drought in these islands there were numerous bush fires with devastating effects on agriculture, severe water shortages that impacted on the tourism industry and other social effects. It is evident that there was inadequate preparation for the event. Greater planning and investment are therefore required to reduce future impacts.

The plasmids of Chlamydia trachomatis and Chlamydophila pneumoniae (N16): accurate determination of copy number and the paradoxical effect of plasmid-curing agents.

A 7.5 kbp cryptic plasmid is found in almost all isolates of Chlamydia trachomatis. Real-time PCR assays, using TaqMan chemistry, were set up to quantify accurately both the chlamydial plasmid and the single copy, chromosomal omcB gene in the infectious, elementary bodies (EBs) of C. trachomatis L1 440. Plasmid copy number was also determined in the EBs of six other lymphogranuloma venereum (LGV) isolates (serovars L1-L3), ten trachoma isolates (serovars A-C) and nine urogenital isolates (serovars D-J). The results indicated an average plasmid copy number of 4.0+/-0.8 (mean+/-95 % confidence interval) plasmids per chromosome. During the chlamydial developmental cycle, up to 7.6 plasmids per chromosome were detected, indicating an increased plasmid copy number in the actively replicating reticulate bodies. Attempts to eliminate the plasmid from strain L1 440 using the plasmid-curing agents ethidium bromide, acridine orange or imipramine/novobiocin led to a paradoxical increase in plasmid copy number. It is speculated that the stress induced by chemical curing agents may stimulate the activity of plasmid-encoded replication (Rep) proteins. In contrast to C. trachomatis, only a single isolate of Chlamydophila pneumoniae bears a plasmid. C. pneumoniae strain N16 supports a 7.4 kbp plasmid in which ORF1, encoding one of the putative Rep proteins, is disrupted by a deletion and split into two smaller ORFs. Similar assay techniques revealed 1.3+/-0.2 plasmids per chromosome (mean+/-95 % confidence interval) in EBs of this strain. These findings are in agreement with the hypothesis that the ORF1-encoded protein is involved in, but not essential for, plasmid replication and control of copy number.

Chlamydiaphage Chp2, a skeleton in the phiX174 closet: scaffolding protein and procapsid identification.

Chlamydiaphage Chp2 is a member of the family Microviridae, of which bacteriophage phiX174 is the type species. Although grouped in the same family, the relationship between the Microviridae coliphages and the Chp2-like viruses, which infect obligate intracellular parasitic bacteria, is quite distant, with major differences in structural protein content and scaffolding protein dependence. To investigate the morphogenesis of Chp2, large particles were isolated from infected Chlamydophila abortus by equilibrium and rate zonal sedimentation. A monoclonal antibody that recognizes only assembled viral coat proteins was used in these detection assays. Thus, the detected particles represent virions and/or postcapsid formation assembly intermediates. Two distinct particle types were detected, differing in both protein and DNA content. Filled particles lacked VP3, the putative internal scaffolding protein, whereas empty particles contained this protein. These results indicate that VP3 is a scaffolding protein and that the isolated VP3-containing particles most likely represent Chp2 procapsids.

Isolation, molecular characterisation and genome sequence of a bacteriophage (Chp3) from Chlamydophila pecorum.

Chlamydiae are obligate intracellular pathogens that have a unique developmental cycle. Thirty nine viable isolates representing all nine currently recognised chlamydial species were screened by immunofluorescence with a cross-reacting chlamydiaphage monoclonal antibody. A novel chlamydiaphage (Chp3) was detected in C. pecorum, a chlamydial species not previously known to carry bacteriophages. Chp3 belongs to the Microviridae, members of this virus family are characterised by circular, single-stranded DNA genomes and small T = 1 icosahedral capsids. Double-stranded replicative form Chp3 DNA was purified from elementary bodies and used as a template to determine the complete genome sequence. The genome of Chp3 is 4,554 base pairs and encodes eight open reading frames organised in the same genome structure as other chlamydiaphages. An unrooted phylogenetic tree was constructed based on the major coat proteins of 11 members of the Microviridae and Chp3. This showed that the Microviridae are clearly divided into two discrete sub-families; those that infect the Enterobacteriaceae e.g. ØX174 and the bacteriophages that infect obligate intracellular bacteria or mollicutes including SpV4 (Spiroplasma melliferum), ØMH2K (Bdellovibrio bacteriovorus) and the chlamydiaphages. Comparative analyses demonstrate that the chlamydiaphages can be further subdivided into two groupings, one represented by Chp2/Chp3 and the other by ØCPG1/ØCPAR39.

Host range of chlamydiaphages phiCPAR39 and Chp3.

The host range of phiCPAR39 is limited to four Chlamydophila species: C. abortus, C. caviae, C. pecorum, and C. pneumoniae. Chp3 (a newly discovered bacteriophage isolated from C. pecorum) shares three of these hosts (C. abortus, C. caviae, and C. pecorum) but can additionally infect Chlamydophila felis. The ability to support replication was directly correlated with the binding properties of the respective bacteriophages with their host species. Binding studies also show that phiCPAR39 and Chp3 use different host receptors to infect the same host cells: cell binding is sensitive to proteinase K treatment, confirming that the chlamydiaphage receptors are proteinaceous in nature.

Biological properties and cell tropism of Chp2, a bacteriophage of the obligate intracellular bacterium Chlamydophila abortus.

A number of bacteriophages belonging to the Microviridae have been described infecting chlamydiae. Phylogenetic studies divide the Chlamydiaceae into two distinct genera, Chlamydia and Chlamydophila, containing three and six different species, respectively. In this work we investigated the biological properties and host range of the recently described bacteriophage Chp2 that was originally discovered in Chlamydophila abortus. The obligate intracellular development cycle of chlamydiae has precluded the development of quantitative approaches to assay bacteriophage infectivity. Thus, we prepared hybridomas secreting monoclonal antibodies (monoclonal antibodies 40 and 55) that were specific for Chp2. We demonstrated that Chp2 binds both C. abortus elementary bodies and reticulate bodies in an enzyme-linked immunosorbent assay. Monoclonal antibodies 40 and 55 also detected bacteriophage Chp2 antigens in chlamydia-infected eukaryotic cells. We used these monoclonal antibodies to monitor the ability of Chp2 to infect all nine species of chlamydiae. Chp2 does not infect members of the genus Chlamydia (C. trachomatis, C. suis, or C. muridarum). Chp2 can infect C. abortus, C. felis, and C. pecorum but is unable to infect other members of this genus, including C. caviae and C. pneumoniae, despite the fact that these chlamydial species support the replication of very closely related bacteriophages.

Molecular characterization of a bacteriophage (Chp2) from Chlamydia psittaci.

Comparisons of the proteome of abortifacient Chlamydia psittaci isolates from sheep by two-dimensional gel electrophoresis identified a novel abundant protein with a molecular mass of 61.4 kDa and an isoelectric point of 6.41. C-terminal sequence analysis of this protein yielded a short peptide sequence that had an identical match to the viral coat protein (VP1) of the avian chlamydiaphage Chp1. Electron microscope studies revealed the presence of a 25-nm-diameter bacteriophage (Chp2) with no apparent spike structures. Thin sections of chlamydia-infected cells showed that Chp2 particles were located to membranous structures surrounding reticulate bodies (RBs), suggesting that Chp2 is cytopathic for ovine C. psittaci RBs. Chp2 double-stranded circular replicative-form DNA was purified and used as a template for DNA sequence analysis. The Chp2 genome is 4,567 bp and encodes up to eight open reading frames (ORFs); it is similar in overall organization to the Chp1 genome. Seven of the ORFs (1 to 5, 7, and 8) have sequence homologies with Chp1. However, ORF 6 has a different spatial location and no cognate partner within the Chp1 genome. Chlamydiaphages have three viral structural proteins, VP1, VP2, and VP3, encoded by ORFs 1 to 3, respectively. Amino acid residues in the phiX174 procapsid known to mediate interactions between the viral coat protein and internal scaffolding proteins are conserved in the Chp2 VP1 and VP3 proteins. We suggest that VP3 performs a scaffolding-like function but has evolved into a structural protein.

Interaction of primary human endometrial cells with Neisseria gonorrhoeae expressing green fluorescent protein.

Infection of the endometrium by Neisseria gonorrhoeae is a pivotal stage in the development of pelvic inflammatory disease in women. An ex vivo model of cultures of primary human endometrial cells was developed to study gonococcal-host cell interactions. To facilitate these studies, gonococci were transformed with a hybrid shuttle vector containing the gfp gene from Aequoria victoria, encoding the green fluorescent protein (GFP), to produce intrinsically fluorescent bacteria. The model demonstrated that both pili and Opa proteins were important for both mediating gonococcal interactions with endometrial cells and inducing the secretion of pro-inflammatory cytokines and chemokines. Pil+ gonococci showed high levels of adherence and invasion, regardless of Opa expression, which was associated with increased secretion of IL-8 chemokine and reduced secretion of IL-6 cytokine. Gonococcal challenge also caused increased secretion of TNF-alpha cytokine, but this did not correlate with expression of pili or Opa, suggesting that release of components from non-adherent bacteria may be involved in TNF-alpha induction. Thus, the use of cultured primary endometrial cells, together with gonococci expressing green fluorescent protein, has the potential to extend significantly our knowledge, at the molecular level, of the role of this important human pathogen in the immunobiology of pelvic inflammatory disease.

A systematic evaluation of preferences identified through person-centered planning for people with profound multiple disabilities.

Person-centered planning is becoming a popular means of designing supports for people with disabilities. However, very little research evaluating person-centered planning exists. We evaluated the degree to which items and activities reported to be preferred in person-centered plans represented accurate preferences based on how individuals responded when presented with the items and activities. Person-centered planning meetings were conducted with 4 individuals with profound multiple disabilities to develop preference maps and to identify leisure-related preferences. A sample of the reported preferences in the plans was then systematically assessed by observing each participant's approach and avoidance responses to the items and activities. Of the sampled items and activities reported to be preferred in the plans, 42% represented moderate preferences based on the latter assessment process and 33% represented strong preferences. With 2 participants, several preferences identified in the plans were nonpreferred items and activities based on the preference assessments, and some were frequently avoided. These results suggested that although person-centered plans may identify some accurate preferences for people with profound multiple disabilities, this approach should be used cautiously. Results also suggested that such plans should be supplemented with systematic preference assessments to ensure the accuracy of identified preferences. Future research areas focus on evaluating other aspects of person-centered planning.

A Canadian hospital-based HIV/hepatitis C look-back notification program.

OBJECTIVE: To describe the process used to notify pediatric patients who received transfusions of blood or blood products at our institution before donor blood was routinely screened for antibodies to HIV (1985) and hepatitis C virus (1990), and to evaluate the effectiveness of the notification program. DESIGN: Patients who had received transfusions were identified through the hospital's medical records and the records from the Transfusion Medicine Laboratory. Patients were contacted by registered mail to provide notification of transfusion. A questionnaire was included with the notification to obtain information about the patient's awareness of the transfusion and whether he or she had undergone or planned to undergo testing for HIV and hepatitis C virus. SETTING: Tertiary care university-affiliated teaching hospital in Hamilton, Ont. PATIENTS: Patients 16 years of age or younger who had received blood products between February 1978 and November 1985. Patients who had received only albumin or immune serum globulin were not included as these products were not associated with viral transmission in Canada. RESULTS: Notification letters were sent to 1546 patients. Of these letters 522 (33.8%) were returned undelivered. Of the 1024 patients contacted 493 (48.1%) responded to the questionnaire, of whom 157 (31.8%) were not aware of their transfusion. A total of 130 (26.4%) of the respondents had already undergone testing for HIV, and 342 (69.4%) indicated that they would undergo such testing as a result of the notification. In contrast, only 30 (6.3%) of 474 respondents had undergone testing for hepatitis C virus, but 425 (89.7%) indicated that they would undergo such testing. Overall, the patients' response to the notification was neutral or positive; however, a number of patients expressed dissatisfaction and anxiety. CONCLUSIONS: The high proportion of patients who were unaware that they had undergone transfusion and who decided to undergo testing for HIV and hepatitis C virus as a result of notification supports the use of notification programs such as this one.

The CrP operon of Chlamydia psittaci and Chlamydia pneumoniae.

One of the critical developmental events during the unique intracellular life cycle of Chlamydiae is their differentiation from a metabolically active, replicative form or reticulate body (RB) to an infectious extracellular form of the organism (elementary body or EB). This process is characterized by the expression of two extraordinarily cysteine-rich envelope proteins of molecular masses 9 kDa and 60 kDa. We describe the molecular cloning and sequence determination of the 9 kDa cysteine-rich proteins (CrPs) of C. pneumoniae and C. psittaci. Comparison of these 9 kDa CrP amino acid sequences with those of C. trachomatis showed regions of structural variation and conservation. Transcription of the 9 kDa CrP genes occurred as both a monocistronic message and as a bicistronic message which included the 60 kDa CrP gene. Transcription of the 9 kDa and 60 kDa CrP genes was tightly linked to the chlamydial growth cycle with synthesis of their mRNAs and consequent translation of the 60 kDa CrPs occurring as RBs differentiated to form EBs. The maximal rate of transcription occurred late in the growth cycle from a single but highly conserved promoter which had close similarity with the Escherichia coli consensus promoter sequences. A stem and loop structure which could be involved in regulating translation of mRNA occurred in all three species between the transcriptional start point and the ribosome binding site. Although transcription is initiated from a single promoter in all three chlamydial species, transcriptional termination points for the monocistronic and bicistronic mRNAs differ in both number and position.

Indicator-based audit of cataract surgery in four neighbouring hospitals in East Anglia.

To review and compare management and outcomes of patients undergoing cataract surgery in order to improve practice by identifying weaknesses and standardising best practice where appropriate, a concurrent and prospective audit from June to October 1993 was carried out in four neighbouring ophthalmic units in East Anglia. Six hundred and twenty-seven consecutive patients were undergoing cataract surgery in the audit period. The main measures and results were as follows: (1) Patients with visual acuity reduced to 6/60 or less should not wait longer than 3 months from consultation to surgery; 69.5% met standard. (2) Patients with visual acuity reduced to 6/18 or less should not wait longer than 12 months from consultation to surgery; 85.8% met standard. (3) Patients who have had cataract surgery should achieve 6/12 or better corrected visual acuity by 3 months post-operatively; 88.6% met standard. (4) There should be less than 2% sight-threatening complications of surgery; 4.2% suffered sight-threatening complications. (5) There should be no life-threatening complications of surgery; 100% met standard. The audit identified key areas of variation in practice, and analysis of reasons for differences in outcome has led to some changes in the management of patients with cataracts in the four units.

Immunoreactivity of the 60 kDa cysteine-rich proteins of Chlamydia trachomatis, Chlamydia psittaci and Chlamydia pneumoniae expressed in Escherichia coli.

The 60 kDa cysteine-rich proteins (CrPs) of Chlamydia are developmentally regulated outer envelope proteins synthesized late in the chlamydial growth cycle. These proteins, found only on the extracellular infectious elementary bodies, elicit major antibody responses in chlamydial infection. We have cloned and expressed in Escherichia coli the complete 60 kDa CrP genes from Chlamydia trachomatis, C. psittaci and C. pneumoniae. The recombinant products were expressed as either 'native' proteins or as fusions with the bacteriophage T7 gene 10 protein. Electron microscopy showed that recombinant proteins were produced as insoluble inclusions within the E. coli host cells. The recombinant 60 kDa CrPs were purified and used to raise high titre polyclonal antisera. In immunoblot analysis these antisera reacted with the 60 kDa CrPs from purified elementary bodies of all three chlamydial species in a genus-specific manner. Further molecular analysis allowed the genus-specific cross-reacting epitopes to be localized by using overlapping synthetic peptides covering the C. trachomatis 60 kDa CrP. Immunogold labelling experiments, using purified infectious elementary bodies from the three chlamydial species indicated that the 60 kDa CrPs are not surface accessible to antibody binding.

Epitope specificities of human serum antibodies reactive with respiratory syncytial virus fusion protein.

Respiratory syncytial (RS) virus continues to cause serious human respiratory disease and no prophylactic vaccine is yet available. Serum antibodies to RS virus fusion protein (F) that have the appropriate specificities and activities could confer protection against severe RS virus infections. To explore human serum antibody responses to RS virus F we first characterised four epitopes on F and then measured the concentrations of human serum antibodies to these sites for 389 sera. Individuals varied in serum antibody concentration to the epitopes. The distribution patterns of the concentrations of antibodies reactive to each epitope were different. Antigenic variation of F at these epitopes in Southampton RS virus isolates was examined by immunofluorescence. The F proteins from different isolates varied within and between RS virus subtypes which co-circulated in the outbreak of winter 1985-1986. Variations in F detected by immunofluorescence were consistent with differences between the strains' susceptibilities to monoclonal antibody antiviral action.

School-to-work transition for youth who are both deaf and blind.

Transition, collaborative planning for desired adult opportunities, and implementation of objectives and activities can increase the postsecondary employment opportunities open to youth who are deaf and blind. Collaborative transition planning is characterized by family-professional partnerships in developing visionary personal profiles, systematic and transdisciplinary vocational preparation in community-based settings, and infusion of related services within educational programs.

Chlamydia trachomatis major outer membrane protein epitopes expressed as fusions with LamB in an attenuated aro A strain of Salmonella typhimurium; their application as potential immunogens.

The major outer-membrane protein (MOMP) of Chlamydia trachomatis is the focus of attention for chlamydial vaccine design, particularly those serovar- and subspecies-specific epitopes which provoke neutralizing immune responses. Selected surface-exposed B-cell epitopes of MOMP, incorporating B-subspecies specificities, were expressed as fusions with LamB, an inducible outer-membrane transport protein of Escherichia coli. These recombinant chlamydial-LamB proteins were correctly transported to the outer membrane of both E. coli and an aro A mutant of Salmonella typhimurium. The immunogenicity of the constructs was investigated in a mouse model of chlamydial salpingitis. After oral immunization, recombinant S. typhimurium were recovered from the livers of mice for up to two weeks, and a serum IgG response was induced both to the Salmonella and to the inserted chlamydial epitopes. By contrast, intravenous inoculation was ineffective. Although these LamB fusions proved only weakly immunogenic, this approach should be useful for investigating the ability of attenuated S. typhimurium vaccines incorporating chlamydial epitopes to stimulate protective mucosal immunity in the mouse model of chlamydial salpingitis.

The major outer-membrane proteins of Chlamydia trachomatis serovars A and B: intra-serovar amino acid changes do not alter specificities of serovar- and C subspecies-reactive antibody-binding domains.

The major outer-membrane protein (MOMP) of Chlamydia trachomatis is a promising candidate antigen for chlamydial vaccine development. We have sequenced the MOMP genes for a serovar A and a serovar B isolate and have compared these new sequences with those already reported. Intra-serovar changes in the inferred amino acid sequences of the surface-exposed variable segments known to be responsible for binding of neutralizing antibody were observed. Nevertheless, epitope mapping with solid-phase peptides showed that these intra-serovar changes did not affect the binding of serovar- and subspecies-specific, potentially protective antibodies. Variable segment 1 of C. trachomatis serovar A contained two adjacent antibody-binding sites, one of which was C-subspecies specific while the other was serovar A specific. Therefore the subspecies binding site for C-complex organisms is in variable segment 1, whilst that for B-complex organisms is in variable segment 4. This work shows that MOMP sequences are relatively stable within the serovar categorization for isolates taken decades apart from different continents. Within a given serovar, however, limited interchange of functionally related amino acids may occur without impairing the binding of serovar-specific antibody.