Statnote 16: fitting a regression line to data

Fitting a linear regression to data provides much more information about the relationship between two variables than a simple correlation test. A goodness of fit test of the line should always be carried out. Hence, ‘r squared’ estimates the strength of the relationship between Y and X, ANOVA whether a statistically significant line is present, and the ‘t’ test whether the slope of the line is significantly different from zero. In addition, it is important to check whether the data fit the assumptions for regression analysis and, if not, whether a transformation of the Y and/or X variables is necessary.

Statnote 19: non-linear regression: fitting an exponential curve to data

Non-linear relationships are common in microbiological research and often necessitate the use of the statistical techniques of non-linear regression or curve fitting. In some circumstances, the investigator may wish to fit an exponential model to the data, i.e., to test the hypothesis that a quantity Y either increases or decays exponentially with increasing X. This type of model is straight forward to fit as taking logarithms of the Y variable linearises the relationship which can then be treated by the methods of linear regression.

Statnote 20: non-linear regression: fitting a general polynomial curve

In some circumstances, there may be no scientific model of the relationship between X and Y that can be specified in advance and indeed the objective of the investigation may be to provide a ‘curve of best fit’ for predictive purposes. In such an example, the fitting of successive polynomials may be the best approach. There are various strategies to decide on the polynomial of best fit depending on the objectives of the investigation.

Data methods in optometry. Part 6: fitting a regression line to data

1. Fitting a linear regression to data provides much more information about the relationship between two variables than a simple correlation test. A goodness of fit test of the line should always be carried out. Hence, r squared estimates the strength of the relationship between Y and X, ANOVA whether a statistically significant line is present, and the ‘t’ test whether the slope of the line is significantly different from zero. 2. Always check whether the data collected fit the assumptions for regression analysis and, if not, whether a transformation of the Y and/or X variables is necessary. 3. If the regression line is to be used for prediction, it is important to determine whether the prediction involves an individual y value or a mean. Care should be taken if predictions are made close to the extremities of the data and are subject to considerable error if x falls beyond the range of the data. Multiple predictions require correction of the P values. 3. If several individual regression lines have been calculated from a number of similar sets of data, consider whether they should be combined to form a single regression line. 4. If the data exhibit a degree of curvature, then fitting a higher-order polynomial curve may provide a better fit than a straight line. In this case, a test of whether the data depart significantly from a linear regression should be carried out.

Mediators of gram-positive septic shock

Septic shock can occur as a result of Gram-negative or Gram-positive infection and involves a complex interaction between bacterial factors and the host immune system producing a systemic inflammatory state that may progress to multiple organ failure and death. Gram-positive bacteria are increasingly becoming more prevalent especially Staphylococcus epidermidis in association with indwelling devices. Lipopolysaccaride (LPS) is the key Gram-negative component involved in this process, but it is not clear which components of Gram-positive bacteria are responsible for progression of this often fatal disease. The aim of this thesis was to investigate the effect of bacterial components on the immune systems. Lipid S, a short chain form of lipoteichoic acid (LTA) found to be excreted from bacteria during growth in culture medium was examined along with other Gram-positive cell wall components: LTA, peptidoglycan (PG) and wall teichoic acids (WTA) and LPS from Gram-negative bacteria. Lipid S, LTA, PG and LPS but not WTA all stimulated murine macrophages and cell lines to produce significant amounts of NO, TNF-a, IL-6 and IL-1 and would induce fever and tissue damage seen in inflammatory diseases. Lipid S proved to be the most potent out of the Gram-positive samples tested. IgG antibodies in patients serum were found to bind to and cross react with lipid S and LTA. Anti-inflammatory antibiotics, platelet activating factor (PAF), PAF receptor antagonists and monoclonal antibodies (mAbs) directed to LTA, CD14 and toll-like receptors were utilised to modulate cytokine and NO production. In cell culture the anti-LTA and the anti-CD14 mAbs failed to markedly attenuate the production of NO, TNF-a, IL-6 or IL-1, the anti-TLR4 antibody did greatly inhibit the ability of LPS to stimulate cytokine production but not lipid S. The tetracyclines proved to be the most effective compounds, many were active at low concentrations and showed efficacy to inhibit both lipid S and LPS stimulated macrophages to produce NO.

Heat shock proteins in leukaemia cell differentiation and cell death

When HL60 cells were induced to differentiate to granulocyte-like cells with the agents N-methylformamide and tunicamycin an concentrations marginally below those which were cytotoxic, there was a decrease in the synthesis of the glucose- regulated proteins which preceded the expression of markers of a differentiated phenotype. There was a transient increase in the amount of hsp70 after 36 hours in NMF treated cells but in differentiated cells negligible amounts were detected. Inducers which were known to modulate hsp70 such as azetadine carboxylic acid did not induce differentiation suggesting early changes in the endoplasmic reticulum may be involved in the commitment to terminal differentiation of HL60 cells. These changes in group synthesis were not observed when K562 human chronic myelogenous leukemia cells were induced to differentiate to erythroid-like cells but there was a comparable increase in amounts of hsp70. When cells were treated with concentrations of drugs which brought about a loss in cell viability there was an early increase in the amount of hsp70 protein in the absence of any increase in synthesis. HL60 cells were treated with NMF (225mM), Adriamycin (1μM), or CB3717 (5μM) and there was an increase in the amounts of hsp70, in the absence of any new synthesis, which preceded any loss of membrane integrity and any significant changes in cell cycle but was concomitant with a later loss in viability of > 50% and a loss in proliferative potential. The amounts of hsp70 in the cell after treatment with any of the drugs was comparable to that obtained after a heat shock. Following a heat shock hsp70 was translocated from the cytoplasm to the nucleus, but treatment with toxic concentrations of drug caused hsp70 to remain localised in the cytoplasm. Changes in hsp70 turn-over was observed after a heat shock compared to NMF-treated cells. Morphological studies suggested that cells that had been treated with NMF and CB3717 were undergoing necrosis whereas the Adriamycin cells showed characteristics that were indicative of apoptosis. The data supports the hypothesis that an increase in amounts of hsp70 is an early marker of cell death.

A sequential mechanism for clathrin cage disassembly by 70-kDa heat-shock cognate protein (Hsc70) and auxilin

An essential stage in endocytic coated vesicle recycling is the dissociation of clathrin from the vesicle coat by the molecular chaperone, 70-kDa heat-shock cognate protein (Hsc70), and the J-domain-containing protein, auxilin, in an ATP-dependent process. We present a detailed mechanistic analysis of clathrin disassembly catalyzed by Hsc70 and auxilin, using loss of perpendicular light scattering to monitor the process. We report that a single auxilin per clathrin triskelion is required for maximal rate of disassembly, that ATP is hydrolyzed at the same rate that disassembly occurs, and that three ATP molecules are hydrolyzed per clathrin triskelion released. Stopped-flow measurements revealed a lag phase in which the scattering intensity increased owing to association of Hsc70 with clathrin cages followed by serial rounds of ATP hydrolysis prior to triskelion removal. Global fit of stopped-flow data to several physically plausible mechanisms showed the best fit to a model in which sequential hydrolysis of three separate ATP molecules is required for the eventual release of a triskelion from the clathrin-auxilin cage.

Sustainable development, shock and awe? London 2012 and Civil Society

There is a disconnection between the top-down, elite, nature of sports mega-events and the ostensible redistributive and participatory sustainable development agendas staked out by BINGOs (Business-based International Non-Governmental Organizations) such as the contemporary International Olympic Committee (IOC). Focusing specifically on the London 2012 Summer Olympic and Paralympic Games, we argue that, for all the environmental technology advances offered by sports mega-events, their dominant model remains one of a hollowed-out form of sustainable development. Despite significant technical and methodological innovations in environmental stewardship, the development model of the London Olympics remains predicated on the satisfaction of transnational investment flows. We discuss what this means for claims about the staging of a ‘green’ Olympic Games.

Laminar distribution of the pathological changes in sporadic frontotemporal lobar degeneration with transactive response (TAR) DNA-binding protein of 43kDa (TDP-43) proteinopathy:a quantitative study using polynomial curve fitting

Aims: Previous data suggest heterogeneity in laminar distribution of the pathology in the molecular disorder frontotemporal lobar degeneration (FTLD) with transactive response (TAR) DNA-binding protein of 43kDa (TDP-43) proteinopathy (FTLD-TDP). To study this heterogeneity, we quantified the changes in density across the cortical laminae of neuronal cytoplasmic inclusions, glial inclusions, neuronal intranuclear inclusions, dystrophic neurites, surviving neurones, abnormally enlarged neurones, and vacuoles in regions of the frontal and temporal lobe. Methods: Changes in density of histological features across cortical gyri were studied in 10 sporadic cases of FTLD-TDP using quantitative methods and polynomial curve fitting. Results: Our data suggest that laminar neuropathology in sporadic FTLD-TDP is highly variable. Most commonly, neuronal cytoplasmic inclusions, dystrophic neurites and vacuolation were abundant in the upper laminae and glial inclusions, neuronal intranuclear inclusions, abnormally enlarged neurones, and glial cell nuclei in the lower laminae. TDP-43-immunoreactive inclusions affected more of the cortical profile in longer duration cases; their distribution varied with disease subtype, but was unrelated to Braak tangle score. Different TDP-43-immunoreactive inclusions were not spatially correlated. Conclusions: Laminar distribution of pathological features in 10 sporadic cases of FTLD-TDP is heterogeneous and may be accounted for, in part, by disease subtype and disease duration. In addition, the feedforward and feedback cortico-cortical connections may be compromised in FTLD-TDP. © 2012 The Authors. Neuropathology and Applied Neurobiology © 2012 British Neuropathological Society.

Specialist contact lens fitting

What is meant by the term ‘specialist contact lens fitting’? Or put another way, what would be considered non-specialist contact lens fitting? Is there such a thing as routine contact lens fitting? Soft or silicone hydrogel fitting for daily wear would probably be considered as routine contact lens fitting, but would extended or flexible wear remain in the same category or would they be considered a specialist fit? Different eras will classify different products as being ‘specialist’. Certainly twenty years ago soft toric contact lenses were considered as being speciality lenses but today would be thought of as routine lenses. Conversely, gas permeable lenses were thought of as mainstream twenty years ago but now are considered as speciality lenses. Although this would not be the same globally, as in some countries (such as Netherlands, France and Japan) gas permeable lens fitting remains popular and is not on the decline as in other countries (Canada, Australia and Sweden) [1]. Bandage soft lenses applied after surface laser refractive procedures would be considered as therapeutic lenses but in reality they are just plano thin hydrogel lenses worn constantly for 3–4 days to allow the underlying epithelium to convalesce and are then removed [2]. Some patients find that wearing hydrogel lenses during periods when they suffer from seasonal allergies actually improves their ocular comfort as the contact lens acts as a barrier to the allergen [3] and [4]. Scleral lenses have long been considered speciality lenses, apart from a time when they were the only lenses available but at that time all contact lens work would have been considered speciality practice! Nowadays we see the advent of mini-scleral designs and we see large diameter gas permeable lenses too. It is possible that these lenses increase the popularity of gas permeable lenses again and they become more main stream. So it would seem that the lines between routine and speciality contact lens fitting are not clear. Whether a lens is classed a specialist fit or not would depend on the lens type, why it was fitted, where in the world the fitting was being done and even the era in which it was fitted. This begs the question as to what would be considered entry level knowledge in contact lens fitting. This may not be an issue for most BCLA members or CLAE readers but certainly would be for bodies such as the College of Optometrists (UK) or the Association of British Dispensing Opticians when they are planning the final registration examinations for budding practitioners or when planning the level of higher level qualifications such as College Certificates or Diplomas. Similarly for training institutions when they are planning their course content. This becomes even trickier when trying to devise a qualification that spans across many countries, like the European Diploma in Optometry and Optics. How do we know if the training and examination level is correct? One way would be to analyse things when they go wrong and if patterns of malpractice are seen then maybe that could be used as an indicator to more training being needed. There were 162 Fitness to Practice Hearing at the General Optical Council between 2001 and 2010. Forty-seven of these were clinically related case, 39 fraud related, and 76 others. Of the clinical ones only 3 were contact lens related. So it would appear that as whole, in the profession, contact lens clinical skills are not being questioned too often (although it seems a few of us can’t keep our hands out the cookie jar!).

Transglutaminase 2 interaction with small heat shock proteins mediate cell survival upon excitotoxic stress

Transglutaminase 2 has been postulated to be involved in the pathogenesis of central nervous system neurodegenerative disorders. However, its role in neuronal cell death remains to be elucidated. Excitotoxicity is a common event underlying neurodegeneration. We aimed to evaluate the protein targets for transglutaminase 2 in cell response to NMDA-induced excitotoxic stress, using SH-SY5Y neuroblastoma cells which express high tranglutaminase 2 levels upon retinoic acid-driven differentiation toward neurons. NMDA-evoked calcium increase led to transglutaminase 2 activation that mediated cell survival, as at first suggested by the exacerbation of NMDA toxicity in the presence of R283, a synthetic competitive inhibitor of transglutaminase active site. Assays of R283-mediated transglutaminase inhibition showed the involvement of enzyme activity in NMDA-induced reduction in protein basal levels of pro-apoptotic caspase-3 and the stress protein Hsp20. However, this occurred in a way different from protein cross-linking, given that macromolecular assemblies were not observed in our experimental conditions for both proteins. Co-immunoprecipitation experiments provided evidence for the interaction, in basal conditions, between transglutaminase 2 and Hsp20, as well as between Hsp20 and Hsp27, a major anti-apoptotic protein promoting caspase-3 inactivation and degradation. NMDA treatment disrupted both these interactions that were restored upon transglutaminase 2 inhibition with R283. These results suggest that transglutaminase 2 might be protective against NMDA-evoked excitotoxic insult in neuronal-like SH-SY5Y cells in a way, independent from transamidation that likely involves its interaction with the complex Hsp20/Hsp27 playing a pro-survival role. © 2011 Springer-Verlag.

Spin transition of 1D, 2D and 3D iron(II) complex polymers - the tug-of-war between elastic interaction and a shock-absorber effect

The structures of linear chain Fe(II) spin-crossover compounds of α,β- and α,ω-bis (tetrazol-1-yl)alkane type ligands are described in relation to their magnetic properties. The first threefold interlocked 3-D catenane Fe(II) spin-transition system, [μ-tris(1,4-bis(tetrazol-1-yl)butane-N1,N1′) iron(II)] bis(perchlorate), will be discussed. An analysis is made among the structures and the cooperativity of the spin-crossover behaviour of polynuclear Fe(II) spin-transition materials.