251 research outputs found
Dimer-dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba
No full textArchaea use a variety of small basic proteins to package their DNA. One of the most widespread and highly conserved is the Alba (Sso10b) protein. Alba interacts with both DNA and RNA in vitro, and we show in the present study that it binds more tightly to dsDNA (double-stranded DNA) than to either ssDNA (single-stranded DNA) or RNA. The Alba protein is dimeric in solution, and forms distinct ordered complexes with DNA that have been visualized by electron microscopy studies; these studies suggest that, on binding dsDNA, the protein forms extended helical protein fibres. An end-to-end association of consecutive Alba dimers is suggested by the presence of a dimer-dimer interface in crystal structures of Alba from several species, and by the strong conservation of the interface residues, centred on Are and Phe(60). In the present study we map perturbation of the polypeptide backbone of Alba upon binding to DNA and RNA by NMR, and demonstrate the central role of Phe(60) in forming the dimer dimer interface. Site-directed spin labelling and pulsed ESR are used to confirm that an end-to-end, dimer dimer interaction forms in the presence of dsDNA.Peer reviewe
Participants’ perspectives of being recruited into a randomised trial of a weight loss intervention before colorectal cancer surgery: a qualitative interview study
No full textBackground: the period between cancer diagnosis and surgery presents an opportunity for trials to assess the feasibility of behaviour change interventions. However, this can be a worrying time for patients and may hinder recruitment. We describe the perspectives of patients with excess weight awaiting colorectal cancer surgery about their recruitment into a randomised trial of a prehabilitation weight loss intervention.Methods: we interviewed the first 26 participants from the 8 recruitment sites across England in the ‘CARE’ feasibility trial. Participants were randomised into either usual care (n=13) or a low-energy nutritionally-replete total diet replacement programme with weekly remote behavioural support by a dietitian (n=13). The semi-structured interviews occurred shortly after recruitment and the questions focused on participants’ recollections of being recruited into the trial. We analysed data rapidly and then used a mind-mapping technique to develop descriptive themes. Themes were agreed by all co-authors, including a person with lived-experience of colorectal surgery.Results: participants had a mean body mass index (± SD) of 38 kg/m2 (± 6), age of 50 years (± 12), and 42% were female. People who participated in the trial were motivated by the offer of structured weight loss support that could potentially help them improve their surgical outcomes. However, participants also had concerns around the potential unpalatability of the intervention diet and side effects. Positive attitudes of clinicians towards the trial facilitated recruitment but participants were disappointed when they were randomised to usual care due to clinical teams’ overemphasis on the benefits of losing weight.Conclusions: patients were motivated to take part by the prospect of improved surgical outcomes. However, the strong preference to be allocated to the intervention suggests that balanced communication of equipoise is crucial to minimise disappointment from randomisation to usual care and differential dropout from the trial.<br/
A ALBA e a luta pela hegemonia no continente americano: uma topologia do discurso bolivariano
No full textDissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Filosofia e Ciências Humanas. Programa de Pós-graduação em Sociologia PolíticaO objetivo da dissertação é analisar o movimento bolivariano, liderado pela Venezuela, enquanto projeto de construção de uma nova hegemonia na América Latina e o Caribe. Tal projeto se constrói discursivamente em oposição à histórica hegemonia pan-americana liderada pelos Estados Unidos (EUA). Para isso é estudada a ALBA (Aliança Bolivariana para os Povos de nossa América) como organização internacional que facilita a alineação de países e sociedades latino-americanos em relação ao movimento bolivariano, gerando novas modalidades de construção de sentido, assim como novas vias e regras de relacionamento internacional. A pesquisa analisa os discursos de mandatários nas reuniões de Cúpula da ALBA, e, apelando à teoria do discurso de Ernesto Laclau, identifica nesse conjunto os três passos previstos pelo autor na configuração de um desafio hegemônico: (1) o estabelecimento de um antagonismo face ao imperialismo dos EUA que é identificado como o poder hegemônico institucionalizado, e a dicotomização do espaço social americano através da construção de uma fronteira entre esse poder e o resto da comunidade (América Latina e o Caribe); (2) a articulação contingente entre diversas demandas sociais, características da América Latina e do Caribe, cuja insatisfação é atribuída ao imperialismo dos EUA; e (3) a formação de um campo popular, através da expressão positiva dessas demandas numa nova identidade, no caso a identidade bolivariana. A pesquisa conclui que o movimento bolivariano consegue gerar elementos para permitir uma nova lógica de construção de sentido, configurando assim estruturalmente um campo de luta pela hegemonia. Porém, também são destacados vários problemas nessa tarefa, especialmente ligados à identificação de diversas unidades com o bolivarianismo.The dissertation research the Bolivarian Movement, headed by Venezuela, as a new hegemonic project, still under construction, at Latin America and the Caribbean. This hegemonic project is discursively constructed in opposition to the historic Pan American hegemony, led by the U.S. In this way, the Bolivarian Alliance for the Peoples of Our America (ALBA) is approached as an international organization that seeks to align the Latin American countries and societies behind the Bolivarian Movment. The ALBA generates new ways of sense-making, as well as new norms of international relations. The research analyzes the speeches at the ALBA's presidential summits, using the Ernesto Laclau's Discourse Theory, and identifying the three steps proposed by this author to the hegemonic construction: Firstly, the establishment of an antagonism against U.S. imperialism and the dicotomization of the hemispheric social space, through the definition of a boundary between the powerful country and the rest of continental community (Latina America and the Caribe). Secondly, the contingent articulation of a variety of social demands, which dissatisfaction are ascribed to the U.S. imperialism. Thirdly, the formation of a new popular field, through the positive expression on a new identity of this unified set of demands, in this case the Bolivarian identity. The dissertation concludes that the Bolivarian movement manages a new logic of sense-making, and therefore places the hegemonic struggle in a new structural field. However, it also identified some problems on this task, particularly in the difficulty to construct a Bolivarian identity shared by various social unities (countries, societies and social sectors)
Genome Assembly and Annotation of <i>Populus alba</i> '<i>Berolinensis</i>' L.
No full textPopulus alba 'Berolinensis', a superior hybrid triploid material for studying the genomic mechanisms in heterosis of polyploid. In this project, we established a high-quality assembly of Populus alba 'Berolinensis', and found the stress-related gene sequence differences between its three haploid genomes, which provided a foundation for molecular breeding and deeper insights into polyploidy species.
This dataset has also been deposited in CNCB Genome Warehouse (BioProject: PRJCA009923), and NCBI GenBank (BioProject: PRJNA845083, PRJNA845082, and PRJNA845081). Raw sequencing data are available in the NCBI Sequence Read Archive (SRA) database (BioProject: PRJNA635615 and PRJNA721517). The gene expression information has been deposited into our polyploid genome online analysis website TreeGenomes (https://www.treegenomes.com).
Citation:
Chen, S., Yu, Y., Wang, X., Wang, S., Zhang, T., Zhou, Y., He, R., Meng, N., Wang, Y., Liu, W., Liu, Z., Liu, J., Guo, Q., Huang, H., Sederoff, R.R., Wang, G., Qu, G. and Chen, S. (2023), Chromosome-level genome assembly of a triploid poplar Populus alba 'Berolinensis'. Mol Ecol Resour. Accepted Author Manuscript. </p
Informed consent in randomised controlled trials:further development and evaluation of the participatory and informed consent (PIC) measure
No full textBackgroundInformed consent is an accepted ethical and legal prerequisite for trial participation, yet there is no standardised method of assessing patient understanding for informed consent. The participatory and informed consent (PIC) measure was developed for application to recruitment discussions to evaluate recruiter information provision and evidence of patient understanding. Preliminary evaluation of the PIC indicated the need to improve inter-rater and intra-rater reliability ratings and conduct further psychometric evaluation. This paper describes the assessment, revision and evaluation of the PIC within the context of OPTiMISE, a pragmatic primary care-based trial.MethodsThis study used multiple methods across two phases. In phase one, one researcher applied the existing PIC measure to 18 audio-recorded recruitment discussions from the OPTiMISE study and made detailed observational notes about any uncertainties in application. Appointments were sampled to be maximally diverse for patient gender, study centre, recruiter and before and after an intervention to optimise information provision. Application uncertainties were reviewed by the study team, revisions made and a coding manual developed and agreed. In phase two, the coding manual was used to develop tailored guidelines for applying the PIC to appointments within the OPTiMISE trial. Two researchers then assessed 27 further appointments, purposively sampled as above, to evaluate inter-rater and intra-rater reliability, content validity and feasibility.ResultsApplication of the PIC to 18 audio-recorded OPTiMISE recruitment discussions resulted in harmonisation of the scales rating recruiter information provision and evidence of patient understanding, minor amendments to clarify wording and the development of detailed generic coding guidelines for applying the measure within any trial. Application of the revised measure using these guidelines to 27 further recruitment discussions showed good feasibility (time to complete), content validity (completion rate) and reliability (inter- and intra-rater) of the measure.ConclusionThe PIC provides a means to evaluate the content of information provided by recruiters, patient participation in recruitment discussions and, to some extent, evidence of patient understanding. Future work will use the measure to evaluate recruiter information provision and evidence of patient understanding both across and within trials
Estudo da variação da densidade básica da madeira de Eucalyptus alba Reinw e Eucalyptus saligna Smith
No full textI) No presente trabalho o autor estudou a variabilidade da densidade básica da madeira de 128 árvores de Eucalyptus alba Reinw. e de 112 de Eucalyptus saligna Smith, nas idades de 5 e 7 anos, com o objetivo de estabelecer a possibilidade do uso de amostras da madeira retiradas ao nível do D.L.P., como representativas da densidade básica média da arvore; II) O trabalho foi desenvolvi.do em três etapas diferentes: 1) Estudo da variação da densidade básica média em função da altura da árvore; 2) Estudo da variação da densidade básica média da árvore em função do D.A.P. da árvore; 3) Estudo da variação da densidade básica média da árvore em função da densidade média ao nível do D.A.P.; III) Dois métodos de determinação da densidade foram usados: a) Método destrutivo (usando como amostras secções transversais do caule, tomadas de 2 em 2 m, em tôda extensão deste, e ao nível do D.A.P.); b) Método não destrutivo (usando duas amostras da madeira retiradas de 2 em 2 metros ao longo do caule e ao nível do D.A.P., nas direções Norte-Sul, Leste-Oeste, e no sentido casca à casca, utilizando-se para tal as difundidas sondas de Pressler). Com base nos resultados obtidos o autor chegou às seguintes conclusões: 1) A densidade básica média (d) da madeira das árvores de da Eucalyptus alba Reinw. e Eucalyptus saligna Smith, aos 5 e 7 anos, variou linearmente em função da altura (h). As equações que expressam essa variação são: Eucalyptus alba Reinw. Y = 0,554198 + 0,002261 X (Método destrutivo). Y = 0,542260 + 0,003590 X (Método não destrutivo). Eucalyptus saligna Smith Y = 0,528583 + 0,001804 X (Método destrutivo). Y = 0,530640 + 0,002751 X (Método não destrutivo) sendo X= altura (m) Y = densidade básica média das árvores(g/cm3); 2) A densidade básica média das árvores de Eucalyptus alba Reinw. nas idades de 5 e 7 anos não é função direta ou inversa do vigor das mesmas. As variações entre árvores nos povoamentos estudados, foram bem pronunciadas podendo-se encontrar árvores com densidades básicas médias de 0,443 g/cm3 a 0,667 g/cm3. Para o Eucalyptus saligna Smith aos 5 e 7 anos, utilizando tanto o método destrutivo como o não destrutivo, as árvores mais vigorosas possuem em média maior densidade básica média, do que as menos vigorosas. Essa variação pode ser expressa pela equação de regressão (significativa ao nível de 5% de probabilidade): onde Y = 0,434796 + 0,008168 X, Y = densidade básica média da árvore (g/cm3), X = D.A.P. (cm). Embora tenha havido acréscimo na densidade básica média em função do diâmetro, as variações individuais persistiram, podendo ser encontradas árvores vigorosas com baixa densidade básica média e árvores não vigorosas com densidade alta; 4) Na determinação da densidade básica média de árvores de Eucalyptus alba Reinw. e Eucalyptus saligna Smith, nas idades de 5 e 7 anos, tanto para o método destrutivo como para o não destrutivo, amostras tomadas ao nível do D.A.P. podem estimar a densidade média da árvore. As equações que possibilitam essas estimativas são: Eucalyptus alba Reinw. (I) Y = 0,057106 + 0,908740 X (Método destrutivo) (II) Y = 0,123903 + 0,799198 X (Método não destrutivo); Eucalyptus saligna Smith (III) Y = 0,119291 + 0,788530 X (Método destrutivo) (IV) Y = 0,094370 + 0,832950 (Método não destrutivo sendo Y = densidade básica média da árvore (g/cm3, X = densidade básica média ao nível do D.A.P. (g/cm3); 5) Embora as equações I, II, III e IV tenham coeficientes lineares diferentes, considerando porém a importância prática do uso de uma única equação para as duas espécies, elas foram reunidas e a equação geral obtida foi: Y = 0,90759 + 0,847806 X (as discrepâncias existentes entre os coeficientes lineares das equações I, II, III e IV, são atribuídas pelo autor, ao fato de serem utilizadas árvores diferentes nas determinações pelos dois métodos).I) In this paper the author presents the results of an investigation made on 128 trees of Eucalyptus alba Reinw. and 112 trees of Eucalyptus saligna Smith at the ages of 5 and 7 years, with the objective of establising a possible relationship between the basic density of wood samples taken at D.B.H. (Diameter at Breast Height) level, and tree basic density (average for merchantable volume); II) The work was carried out in three different phases: a) Determination of the relationship between average basic density and tree height; b) Determination of the relationship between average basic density of the tree and tree D.B.H.; c) Determination of the relationship between average basic density of the tree and the average basic density at D.B.H. level; III) Two methods were used in the determination of the basic density of wood: a) Destructive method (samples consisted of transversal sections of the bole taken at each two meters along the bole and at D.B.H.); b) Non destructive method (two samples were taken in the directions North-South and East-West from bark, to bark, at each two meters along the bole and at D.B.H., using a Pressler increment borer). On the basis of the variation found in the study of the 240 trees, the following conclusions were reached: 1) The average basic density (d) of the trees is a linear function of the height (h), and is expressed by the following equations: Eucalyptus alba Reinw. d= 0,554198 + 0,002261h (Destructive method); d= 0,542260 + 0,003590h (Non destructive method) Eucalyptus salygna Smith d= 0,528583 + 0,001804h (Destructive method); d= 0,530640 + 0,002751h (Non destructive method); 2) The tree average basic density of E. alba Reinw, at the ages of 5 and 7 years does not bear any relationship to its rate of growth. The variation of the basic density values between trees is very high (from 0,443 gram/cubic centimeter to 0,667 gram/cubic centimeter); 3) The tree average basic density (d) of E. saligna Smith at the ages of 5 and 7 years, is a liner function of D.B.H. (at level 5% of probability). The relationship between tree average basic density and D.B.H. (centimeter) is expressed by the following equation for both methods of determination: d = 0,434796 + 0,008168 D.B.H. The variation between trees, was also very high for this species (from 0,433 gram/cubic centimeter to 0,634 gram/cubic centimeter); 4) There is a definite relationship between average basic density at D.B.H. level (X), and the tree basic density (Y) (average for merchantable volume), which is expressed by the following equations: Eucalyptus alba Reinw. Y = 0,057106 + 0,908740 X (Destructive method) Y = 0,123903 + 0,799198 X (Non destructive method). Eucalyptus saligna Smith Y = 0,119291 + 0,788530 X (Destructive method), Y = 0,094370 + 0,832950 X (Non destructive method). For practical purposes the following equation can be used for both species, both methods and both ages: Y = 0,090759 + 0,847806 X
The effect of wind speed and wetting on thermal resistance of the barn owl (Tyto alba). I: Total heat loss, boundary layer and total resistance
No full text1. 1. The sensible heat loss and thermal resistance of a barn owl (Tyto alba) were determined using a heat transfer model in a wind tunnel.
2. 2. Heat loss was a linear function of wind speed and increased by 60% between 0 and 7 m s−1. Wetting the model increased heat loss by 30%.
3. 3. Boundary layer resistance of the model decreased from 223 s m−1 in still air to 56 s m−1 at a wind speed of 1.3 m s−1 and remained constant at wind speeds up to 7 m s−1.
4. 4. The relationship between Nusselt and Reynolds numbers for the model was linear, as was the relationship for cylinders over the range in Reynolds numbers. Nusselt numbers for the plumage-covered model were, however, 30% lower than those derived for the uncovered model.
5. 5. Total thermal resistance of the model was 508 s m−1 (dry) and 486 s m−1 (wet), decreasing by almost 60% from 0 to 7 m s−1. There was a nonlinear decrease in total resistance with increasing wind speed, mainly due to the change in boundary resistance between 0 and 1.3 m s−1.
Author Keywords: Thermal resistance; heat loss; wind speed; wetting; barn owl; Tyto alb
Optimization of the Track Reconstruction Algorithm in a Pixel Based Range Telescope for Proton Computed Tomography
No full textThe use of protons to treat cancer has expanded rapidly in the past two decades. For safe and effective proton therapy, the proton range in a patient’s body must be accurately determined. Current treatment planning is based on X-ray computed tomography images, which might cause uncertainty because of the different behaviour between protons and X-rays. As an alternative, proton Computed Tomography (pCT) has been proposed to directly measure the Relative Stopping Power (RSP) map in the patient and reduce this uncertainty. During a proton CT scan, a high-energy proton beam is directed at the patient. Then, the proton’s residual energy and position are measured with a detector placed behind the patient. This information is used to calculate the volumetric RSP. In the case of using a pixel based detector, a tracking algorithm is required in order to increase the proton intensity capacity of the detector. A proton track reconstruction system has been already developed by Pettersen [1], however, it has some limitations on the track density that can be reconstructed correctly. The algorithm is based on the track-following scheme, in which a growing track searches for deeper- laying activated pixels. This thesis introduces proton therapy and the advantages of pCT and proton radiography for treatment planning. Then, the main track reconstruction techniques found in the literature are reviewed. Improvements in the reconstruction process are proposed and their efficiencies are discussed. While current algorithm begins from the layer closest to the patient, in the present study a new reconstruction algorithm is developed. It differs by starting the reconstruction process from the distal end of the detector. Based on this new algorithm, studies related to its optimization are conducted. Lastly, an algorithm based on the identification of the most probable scenario is developed. The potential algorithms are evaluated on data simulated with GATE (based on Monte Carlo interactions) and PROCASIM (design to simplify the physical interactions between protons and the detector). The fraction of correctly reconstructed tracks and the computational eciency of the algorithms are analyzed to determine the most viable one. [1] H. E. S. Pettersen. A Digital Tracking Calorimeter for Proton Computed Tomography. PhD thesis, University of Bergen, Norway, February 2018.Biomedical Engineerin
Additional file 2: of How outcome prediction could affect patient decision making in knee replacements: a qualitative study
No full textFocus group guide. (DOCX 25 kb
The development of a prototype measure of the co-production of health in routine consultations for people with long-term conditions
No full textObjectives
(i) To develop a prototype measure of co-production of health (CPH) in consultations for people with long-term conditions (LTCs); and (ii) to undertake initial validation of it, using a measure of patient-centred care, as defined by the Roter interaction analysis system (RIAS).
Methods
Mixed methods were applied. A qualitative study gathered 11 experts’ views on what comprised CPH behaviours. These were operationalised and a prototype measure applied to a convenience sample of 50 video-recorded consultations involving clinicians trained in self-management support and patients with LTCs at health services in six UK locations.
Results
Twenty-two CPH behaviours were identified. High frequencies of CPH behaviours in consultations were associated with greater patient-centeredness, less clinician verbal dominance, and more patient communication control in comparison to consultations where CPH behaviours were less frequent.
Conclusion
Although the CPH tool is promising, further testing is required in order to improve reliability and validity.
Practical implications
In the future, the measure could be used to test interventions to promote patient participation in decision making about self-management
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