GRIPP2 reporting checklists: tools to improve reporting of patient and public involvement in research.

BACKGROUND: While the patient and public involvement (PPI) evidence base has expanded over the past decade, the quality of reporting within papers is often inconsistent, limiting our understanding of how it works, in what context, for whom, and why. OBJECTIVE: To develop international consensus on the key items to report to enhance the quality, transparency, and consistency of the PPI evidence base. To collaboratively involve patients as research partners at all stages in the development of GRIPP2. METHODS: The EQUATOR method for developing reporting guidelines was used. The original GRIPP (Guidance for Reporting Involvement of Patients and the Public) checklist was revised, based on updated systematic review evidence. A three round Delphi survey was used to develop consensus on items to be included in the guideline. A subsequent face-to-face meeting produced agreement on items not reaching consensus during the Delphi process. RESULTS: One hundred forty-three participants agreed to participate in round one, with an 86% (123/143) response for round two and a 78% (112/143) response for round three. The Delphi survey identified the need for long form (LF) and short form (SF) versions. GRIPP2-LF includes 34 items on aims, definitions, concepts and theory, methods, stages and nature of involvement, context, capture or measurement of impact, outcomes, economic assessment, and reflections and is suitable for studies where the main focus is PPI. GRIPP2-SF includes five items on aims, methods, results, outcomes, and critical perspective and is suitable for studies where PPI is a secondary focus. CONCLUSIONS: GRIPP2-LF and GRIPP2-SF represent the first international evidence based, consensus informed guidance for reporting patient and public involvement in research. Both versions of GRIPP2 aim to improve the quality, transparency, and consistency of the international PPI evidence base, to ensure PPI practice is based on the best evidence. In order to encourage its wide dissemination this article is freely accessible on The BMJ and Research Involvement and Engagement journal websites.

GRIPP2 reporting checklists: tools to improve reporting of patient and public involvement in research.

Background While the patient and public involvement (PPI) evidence base has expanded over the past decade, the quality of reporting within papers is often inconsistent, limiting our understanding of how it works, in what context, for whom, and why.Objective To develop international consensus on the key items to report to enhance the quality, transparency, and consistency of the PPI evidence base. To collaboratively involve patients as research partners at all stages in the development of GRIPP2.Methods The EQUATOR method for developing reporting guidelines was used. The original GRIPP (Guidance for Reporting Involvement of Patients and the Public) checklist was revised, based on updated systematic review evidence. A three round Delphi survey was used to develop consensus on items to be included in the guideline. A subsequent face-to-face meeting produced agreement on items not reaching consensus during the Delphi process.Results 143 participants agreed to participate in round one, with an 86% (123/143) response for round two and a 78% (112/143) response for round three. The Delphi survey identified the need for long form (LF) and short form (SF) versions. GRIPP2-LF includes 34 items on aims, definitions, concepts and theory, methods, stages and nature of involvement, context, capture or measurement of impact, outcomes, economic assessment, and reflections and is suitable for studies where the main focus is PPI. GRIPP2-SF includes five items on aims, methods, results, outcomes, and critical perspective and is suitable for studies where PPI is a secondary focus.Conclusions GRIPP2-LF and GRIPP2-SF represent the first international evidence based, consensus informed guidance for reporting patient and public involvement in research. Both versions of GRIPP2 aim to improve the quality, transparency, and consistency of the international PPI evidence base, to ensure PPI practice is based on the best evidence. In order to encourage its wide dissemination this article is freely accessible on The BMJ and Research Involvement and Engagement journal websites.

A method for the blind correction of the effects of attenuation and shading in light micrographs based upon moderated histogram equalization.

A means of correcting for the effects of attenuation and shading in multi-dimensional, digital, light micrographs, blindly, i.e. without the need for additional control sets of image data that record these effects, is described. The method, termed trans-elemental moderated histogram equalization (TEMHE), works with all three types of image that are collected in light microscopy: bright objects viewed against a dark background, bright and dark objects set against a grey background and darker objects set against a light background. In its most simple form TEMHE requires that the features of interest are distributed widely and evenly throughout the image data. If, however, the pattern of attenuation or shading is extracted, smoothed and the result used to correct the original set of image data, then the only restriction is that when different classes of feature are present the boundaries between them are not approximately parallel to the axes of one, or more, of the dimensions to be corrected. Moreover, when it is possible to formulate a simple model of the pattern of attenuation or shading this is no longer a constraint. The method does need to analyse a large number of elements of image data (pixels, voxels, etc.) to function correctly but it will correct shading in single frames of image data providing that they are quite large and the overall signal-to-noise ratio is relatively high.

Sharing digital micrographs and other data files between computers.

It ought to be easy to exchange digital micrographs and other computer data files with a colleague even on another continent. In practice, this often is not the case. The advantages and disadvantages of various methods that are available for exchanging data files between computers are discussed. When possible, data should be transferred through computer networking. When data are to be exchanged locally between computers with similar operating systems, the use of a local area network is recommended. For computers in commercial or academic environments that have dissimilar operating systems or are more widely spaced, the use of FTPs is recommended. Failing this, posting the data on a website and transferring by hypertext transfer protocol is suggested. If peer to peer exchange between computers in domestic environments is needed, the use of Messenger services such as Microsoft Messenger or Yahoo Messenger is the method of choice. When it is not possible to transfer the data files over the internet, single use, writable CD ROMs are the best media for transferring data. If for some reason this is not possible, DVD-R/RW, DVD+R/RW, 100 MB ZIP disks and USB flash media are potentially useful media for exchanging data files.

Moderated histogram equalization, an automatic means of enhancing the contrast in digital light micrographs reversibly.

A means for improving the contrast in the images produced from digital light micrographs is described that requires no intervention by the experimenter: zero-order, scaling, tonally independent, moderated histogram equalization. It is based upon histogram equalization, which often results in digital light micrographs that contain regions that appear to be saturated, negatively biased or very grainy. Here a non-decreasing monotonic function is introduced into the process, which moderates the changes in contrast that are generated. This method is highly effective for all three of the main types of contrast found in digital light micrography: bright objects viewed against a dark background, e.g. fluorescence and dark-ground or dark-field image data sets; bright and dark objects sets against a grey background, e.g. image data sets collected with phase or Nomarski differential interference contrast optics; and darker objects set against a light background, e.g. views of absorbing specimens. Moreover, it is demonstrated that there is a single fixed moderating function, whose actions are independent of the number of elements of image data, which works well with all types of digital light micrographs, including multimodal or multidimensional image data sets. The use of this fixed function is very robust as the appearance of the final image is not altered discernibly when it is applied repeatedly to an image data set. Consequently, moderated histogram equalization can be applied to digital light micrographs as a push-button solution, thereby eliminating biases that those undertaking the processing might have introduced during manual processing. Finally, moderated histogram equalization yields a mapping function and so, through the use of look-up tables, indexes or palettes, the information present in the original data file can be preserved while an image with the improved contrast is displayed on the monitor screen.

Formats of image data files that can be used for routine digital light micrography. Part one.

Failing to open computer files that describe image data is not the most frustrating experience that the user of a computer can suffer, but it is high on list of possible aggravations. To ameliorate this, the structure of uncompressed image data files is described here. The various ways in which information that describes a picture can be recorded are related, and a primary distinction between raster or bitmap based and vector or object based image data files is drawn. Bitmap based image data files are the more useful of the two formats for recording complicated images such as digital light micrographs, whereas object based files are better for recording illustrations and cartoons. Computer software for opening a very large variety of different formats of digital image data is recommended, and if these fail, ways are described for opening bitmap based digital image data files whose format is unknown.

Formats of image data files that can be used in routine digital light micrography. Part two.

This is part two of an article that describes the properties of the image data files that are encountered routinely in digital light micrography. In the current part of the article, the differences between saving image data as large intact files and smaller files that have had some information removed, i.e., using lossy compression, are related first. Subsequently, appropriate ways of configuring computers to deal with the large intact image data files are suggested. The structures of the image data files used for recording dynamic sequences and kinematic animations of series of digital light micrographs, i.e., movie formats, are then described. Finally, some information is supplied about choosing file formats for compressing both static and dynamic image data sets.

Application of a laser scalpel to sectioning fragile tissues prior to optical sectioning microscopy and 3D reconstruction.

A method is described for the cutting of fragile material with a laser scalpel which minimizes damage to friable materials, making the interior of structures accessible for optical sectioning microscopy or for high resolution X-ray microtomography followed by 3D reconstruction.

Proliferation and differentiation in the human breast during pregnancy.

Using multiple immunofluorescence labelling on human breast tissues obtained and freshly frozen at the 12th, 15th, and 18th weeks of pregnancy, we have shown that markers of mammary functional differentiation, milk proteins (beta-casein and kappa-casein), are synthesised by actively cycling (Ki67 positive) as well as non-cycling (Ki67 negative) cells. These results demonstrate that functional differentiation/maturation does not coincide with loss of proliferative potential in human mammary luminal epithelial cells. In addition, we have examined expression patterns of integrin subunits (alpha1, alpha2, alpha3, alpha6, beta1, and beta4) and extracellular matrix components (laminin, fibronectin, collagen I, and collagen IV), since they have been shown to exert influences on mammary differentiation and morphogenesis in vitro. Compared to human breast tissues obtained from non-pregnant women, a decrease in alpha2 labelling on luminal epithelial cells was observed, particularly in expanding acini that showed abundant Ki67 positivity. The expression patterns of other integrin subunits, however, did not change, indicating that the expression patterns of most integrins existing prior to pregnancy are sufficient to support the morphological and functional development associated with milk protein synthesis.

A comparison between the use of a high-resolution CCD camera and 35 mm film for obtaining coloured micrographs.

In light microscopy, colour CCD cameras are now capable of generating image data sets that contain more information than can be captured with slow 35 mm colour reversal film. The resolution of colour CCD cameras with a high density of sensor elements (> or = 3300 x 2200 per channel of colour) is equivalent to that of slow 35 mm colour film over typical fields of view for objectives with a wide range of magnifications and numerical apertures. The contrast that can be achieved in images derived from the data sets obtained with colour CCD cameras far exceeds that found with film and can exceed that of human vision. Finally, the data sets collected with high-resolution colour CCD cameras are capable of being displayed at a wide range (four-fold) of different magnifications easily and interchangeably. Consequently, the combination of a data set that describes a relatively large field of view with one or two data sets that describe specific details taken with an eight-fold increase in magnification are all that is necessary to describe the salient features of the vast majority of stained specimens examined with transmitted light microscopy.

Regulation of TNF-alpha-induced reorganization of the actin cytoskeleton and cell-cell junctions by Rho, Rac, and Cdc42 in human endothelial cells.

We have investigated the role of the small guanosine-trisphosphate (GTP)-binding proteins, Rho, Rac, and Cdc42, in the early responses of human umbilical vein endothelial cells (HUVECs) to TNF-alpha (tumor necrosis factor-alpha). Quiescent confluent HUVECs incubated with TNF-alpha for 5-30 min showed an increased formation of membrane ruffles, filopodia, and actin stress fibres followed by cell retraction and formation of intercellular gaps. This process was accompanied by the dispersion of cadherin-5 from intercellular junctions. TNF-alpha also induced a transient increase in polymerized F-actin, as determined both by measuring G-actin content and by quantifying fluorescent emission from fluorescein isothiocyanate (FITC)-phalloidin-labelled F-actin. Microinjection of cells with activated RhoA protein led to an increase in polymerized actin, formation of stress fibres, cell retraction as well as dispersion of cadherin-5. The proteins Cdc42 and Rac induced qualitatively similar effects to Rho, although not as dramatic and in addition induced formation of filopodia and lamellipodia. Microinjection of cells with a Rho inhibitor, C3 transferase, prevented gap formation caused by TNF-alpha. Similar effects were observed in cells microinjected with the dominant inhibitory proteins N17Cdc42 and N17Rac1. Cell retraction and gap formation were also prevented by inhibitors of myosin light chain kinase (MLCK). Our data suggest that Cdc42, Rac, and Rho are activated in a hierarchical cascade following stimulation with TNF-alpha leading to actomyosin-mediated cell retraction and formation of intercellular gaps.

Myogenic cells express multiple myosin isoforms.

In vivo and in vitro, proliferating motile myoblasts form aligned groups of cells, with a characteristic bipolar morphology, subsequently become post-mitotic, begin to express skeletal myosin and fuse. We were interested in whether members of the myosin superfamily were involved in myogenesis. We found that the myoblasts expressed multiple myosin isoforms, from at least five different classes of the myosin superfamily (classes I, II, V, VII and IX), using RT-PCR and degenerate primers to conserved regions of myosin. All of these myosin isoforms were expressed most highly in myoblasts and their expression decreased as they differentiated into mature myotubes, by RNAse protection assays, and Western analysis. However, only myosin I alpha, non-muscle myosin IIA and IIB together with actin relocalize in response to the differentiative state of the cell. In single cells, myosin I alpha was found at the leading edge, in rear microspikes and had a punctate cytoplasmic staining, and non-muscle myosin was associated with actin bundles as previously described for fibroblasts. In aligned groups of cells, all these proteins were found at the plasma membrane. Co-staining for skeletal myosin II, and myosin I alpha showed that myosin I alpha also appeared to be expressed at higher levels in post-mitotic myoblasts that had begun to express skeletal myosin prior to fusion. In early myotubes, actin and non-muscle myosin IIA and IIB remained localized at the membrane. All of the other myosin isoforms we looked at, myosin V, myosin IX and a second isoform of myosin I (mouse homologue to myr2) showed a punctate cytoplasmic staining which did not change as the myoblasts differentiated. In conclusion, although we found that myoblasts express many different isoforms of the myosin superfamily, only myosin I alpha, non-muscle myosin IIA and IIB appear to play any direct role in myogenesis.

Semi-automated positional analysis using laser scanning microscopy of cells transfected in a regenerating newt limb.

Limb regeneration in urodele amphibians such as the newt is a key system for investigating the positional identity of cells. The regenerate arises locally from blastemal cells, mesenchymal progenitors that normally give rise to structures distal to the amputation plane but which can be respecified (proximalized) by treatment with retinoic acid (RA) such that proximal structures are formed. To establish an assay for positional identity, cells of distal and RA-treated distal blastemas are labeled by transfection with an alkaline phosphatase marker gene using particle bombardment (biolistics). After grafting the distal blastema to a proximal stump, a context known as intercalary regeneration, the proximodistal distribution of labeled cells in the resulting regenerate is an index of positional identity. We use enzyme-labeled fluorescence (ELF) in conjunction with laser scanning microscopy to detect transfected cells within a section of the entire regenerate. A semi-automated analysis of the positional distribution of marked cells along the proximal-distal axis demonstrates that cells from both distal and RA-treated blastemas contribute to the regenerate. This procedure provides an efficient and accurate tool for positional analysis of transfected cells, and should be applicable for studying genes that play a role in specifying cell position during morphogenesis.

Activation of a single retinoic acid receptor isoform mediates proximodistal respecification.

BACKGROUND: The regenerating limb of urodele amphibians is an important system for evaluating the effects of retinoic acid (RA) on pattern formation. Regeneration proceeds by local formation of the blastema, a mesenchymal growth zone which normally only gives rise to structures distal to its level of origin. RA can respecify proximodistal identity in amphibian limb regeneration, and this activity of RA on the blastema is observed in two contexts. First, exposure to RA proximalizes a distal blastema resulting in duplication of structures proximal to the level of amputation. Second, after transplantation of a distal blastema to a proximal stump, the transplanted cells normally make only a minor contribution to the intercalary regenerate, but if transplanted cells are exposed to RA they occupy positions proximal to their level of origin and contribute to the regeneration of the intermediate tissue. Multiple isoforms of RA receptors (RARs) are expressed in the newt limb and are thought to mediate the respecification of positional identity. RESULTS: To identify which receptor(s) mediates proximodistal respecification, we have used the biolistics (particle bombardment) technique to transfect the blastemal mesenchyme with plasmids encoding chimeric proteins containing partial amino-acid sequences of the various newt RAR isoforms fused to a partial sequence of the thyroid hormone (3,5, 3'-triiodothyronine; T3) receptor. We then used T3 treatment to selectively activate individual RAR isoforms in vivo. By analyzing the distributions of transfected cells in regenerates derived from distal-to-proximal transplantation we find that activation of a single RAR isoform, delta 2, specifically mediates proximalization. CONCLUSIONS: These results demonstrate that the ability of RA to respecify proximodistal identity is mediated by a specific RAR isoform, delta 2. Activation of the RA pathway in individual cells indicates that positional respecification can be cell-autonomous. RA can respecify axial identity in several contexts in vertebrate development, but this is the first case where the RAR mediating respecification has been identified.

The effects of the neuN and neuT genes on differentiation and transformation of mammary epithelial cells.

Overexpression of the proto-oncogene product, p185neuN, in a non-tumorigenic mammary epithelial line (31E) facilitates aspects of lactogenic differentiation. Formation of branching cords and induction of beta-casein synthesis by 31E cells normally require co-culture of these cells with fibroblasts, or the presence of collagen or fibronectin. In contrast, 31E cells expressing p185neuN spontaneously form branching cords when grown on tissue culture plastic and can synthesize beta-casein in the absence of exogenous substrates or feeder layers. Under these conditions, the cells deposit laminin and fibronectin, indicating a possible role for p185neuN in the deposition of extracellular matrix proteins. Overexpression of the corresponding oncogene product, p185neuT, has markedly different effects. Expression of p185neuT does not facilitate the formation of branching cords or the synthesis of beta-casein when grown on tissue culture plastic, although these cells do deposit laminin and fibronectin. Confocal microscopy indicates a significant difference in the distribution of laminin and fibronectin in 31E cells expressing p185neuT compared to those expressing p185neuN. The effects of p185neuN and p185neuT expression on cell transformation depend on cell type. Expression of both p185neuN and p185neuT increases anchorage-independent growth of 31E cells, but only p185neuT induces anchorage-independent growth of NIH 3T3 fibroblasts. This lineage specificity in the action of p185neuN may be related to observations that overexpression of p185c-erbB-2 (the human homologue of p185neuN) is only associated with the development of human epithelial cancers. The effects of p185neuN on laminin deposition by 31E cells may be relevant to the transforming ability of p185neuN, since laminin can induce anchorage-independent growth of mouse mammary cells. These results suggest that p185neuN and p185neuT could exert their effects on differentiation and transformation of mammary epithelial cells in part by promoting the deposition of extracellular matrix proteins.

The Eck receptor tyrosine kinase is implicated in pattern formation during gastrulation, hindbrain segmentation and limb development.

Members of the protein superfamily of transmembrane receptor tyrosine kinases are key components of intercellular signal transduction pathways that elicit appropriate cellular responses to environmental cues during development of multicellular organisms. In a search for additional receptor tyrosine kinases expressed during mouse embryogenesis we cloned the murine homolog of Eck, a member of the Eph subfamily, that maps to the distal region of mouse chromosome 4. Specific antisera defined Eck in murine embryonic cells as a glycoprotein of 130 kDa with an intrinsic autophosphorylation activity. Immunohistochemical staining and laser scanning microscopy revealed a dynamic and tightly regulated distribution of Eck receptor protein in the developing mouse embryo. During gastrulation, a high transient distribution of Eck was seen in mesodermal cells aggregating in the midline as notochordal plate. A similar restriction of Eck receptor protein was apparent along the rostrocaudal axis of the developing neural tube. In hindbrain neuroepithelia, Eck protein localised specifically to cells of rhombomere 4 and was also seen transiently in cells populating second and third branchial arches and neurogenic facial crest VII-VIII and IX-X. Receptor distribution also implicated Eck in development of the proximodistal axis of the limb, expression being restricted to distal regions of limb bud mesenchyme. At later stages, additional sites of Eck protein expression were seen in the cartilaginous model of the skeleton, tooth primordia, infundibular component of the pituitary and various fetal tissue epithelia. Taken together, our data suggest pleiotropic functions for the Eck receptor, initially in distinctive aspects of pattern formation and subsequently in development of several fetal tissues, and reveal possible allelism with known mouse developmental mutant loci.

Single cell analysis of the expression of a nuclear protein, SCIP, by fluorescent immunohistochemistry visualized with confocal microscopy.

A widely applicable method for the accurate quantification or semiquantification of macromolecules at the level of individual cells is described and validated; this is a method which may considerably facilitate the study of many biological processes. This method relies on measuring fluorescent emission in immunocytochemically labelled cells with a confocal microscope. Emission is related quantitatively to the level of the fluorophore by the combination of an analysis of the polarization of the fluorescent emission and fluorophore rationing methods. The method was applied to the study of the expression of the suppressed cyclic AMP-induced POU protein (SCIP) transcription factor in glial cells of the central nervous system. In particular, the method allowed the study of transcription factor expression in defined cells present in heterogeneous cultures and in cell types which cannot be isolated in sufficient numbers for biochemical analysis using conventional techniques.

The characterization of astrocyte cell lines that display properties of glial scar tissue.

The glial scar has been proposed to be a major impediment to regeneration in the adult CNS. Analysis of glial scars in vivo is complicated, however, by the large number of cell types present in such lesions. We have attempted to simplify analysis of the glial scar environment by deriving a series of conditionally immortal astrocyte cell lines that display several properties expressed by glial scar tissue in vitro. The astrocyte lines, which were derived from H-2KbtsA58 transgenic mice, expressed macromolecules associated with glial scars in vivo and were significantly less effective than neonatal astrocytes at promoting neurite outgrowth from postnatal central and peripheral neurons. The astrocyte lines also inhibited migration of oligodendrocyte type-2 astrocyte progenitor cells in vitro. We propose that certain properties shown previously to be expressed by glial scars may be reconstituted in vitro by astrocytes alone.

The microanatomy of the alveolar duct of the human lung imaged by confocal microscopy and visualised with computer-based 3D reconstruction.

The most widely accepted model of human lung alveolar duct systems is that they are constructed from central helical fibres between the turns of which lie alveolar opening. Experimental difficulties of handling and sectioning lung tissue have made it difficult to confirm this. Confocal laser scanning microscopy (CLSM) was therefore used to generate optical serial sections of the lung that were reconstructed in three dimensions and displayed using volume rendering techniques. From images of the reconstructions, a new structure is proposed in which alveolar ducts consist of collections of connected oval, twisted loop structures with eccentric openings.

The immune response to and expression of cross-reactive retroviral gag sequences in autoimmune disease.

To examine the immune response to retroviral gag sequences in autoimmune disease, we measured antibody levels to synthetic peptides representing the major epitopes on HTLV-1 p19 gag and a homologous sequence on the endogenous retrovirus, HRES-1, in sera from 121 patients with autoimmune disease and 52 healthy controls. In the absence of HTLV-1 antibodies, using a conventional diagnostic assay, significantly elevated levels of antibodies to the HTLV-1 peptide were found in 23% of multiple sclerosis and 20% of anti-Sm antibody positive systemic lupus erythematosus patients. Elevated antibody levels to HRES-1 were found in 32% of Sjögren's syndrome and 19% of multiple sclerosis patients. Evidence of reactivity with both HTLV-1 and HRES-1 was found in human sera and cross-reactivity demonstrated with affinity purified rabbit anti-peptide antibodies. Expression of HRES-1, detected by antibodies and Northern blots, was found in lymphoblastoid cells, salivary gland biopsy sections and salivary gland epithelial cells in culture. This study confirms previous reports of low levels of anti-retroviral gag antibodies in autoimmune disease. The cross-reactions support the concept that reports of elevated HTLV-1 antibodies may be due to an endogenous agent such as HRES-1. The expression of HRES-1 salivary gland may explain its antigenicity in a small proportion of Sjögren's syndrome patients as well as suggesting mechanisms whereby it may contribute to the chronic inflammation of autoimmune disease.