Information management for high content live cell imaging.

BACKGROUND: High content live cell imaging experiments are able to track the cellular localisation of labelled proteins in multiple live cells over a time course. Experiments using high content live cell imaging will generate multiple large datasets that are often stored in an ad-hoc manner. This hinders identification of previously gathered data that may be relevant to current analyses. Whilst solutions exist for managing image data, they are primarily concerned with storage and retrieval of the images themselves and not the data derived from the images. There is therefore a requirement for an information management solution that facilitates the indexing of experimental metadata and results of high content live cell imaging experiments. RESULTS: We have designed and implemented a data model and information management solution for the data gathered through high content live cell imaging experiments. Many of the experiments to be stored measure the translocation of fluorescently labelled proteins from cytoplasm to nucleus in individual cells. The functionality of this database has been enhanced by the addition of an algorithm that automatically annotates results of these experiments with the timings of translocations and periods of any oscillatory translocations as they are uploaded to the repository. Testing has shown the algorithm to perform well with a variety of previously unseen data. CONCLUSION: Our repository is a fully functional example of how high throughput imaging data may be effectively indexed and managed to address the requirements of end users. By implementing the automated analysis of experimental results, we have provided a clear impetus for individuals to ensure that their data forms part of that which is stored in the repository. Although focused on imaging, the solution provided is sufficiently generic to be applied to other functional proteomics and genomics experiments. The software is available from: fhttp://code.google.com/p/livecellim/RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Effectiveness of a national quality improvement programme to improve survival after emergency abdominal surgery (EPOCH): a stepped-wedge cluster-randomised trial

BACKGROUND: Emergency abdominal surgery is associated with poor patient outcomes. We studied the effectiveness of a national quality improvement (QI) programme to implement a care pathway to improve survival for these patients. METHODS: We did a stepped-wedge cluster-randomised trial of patients aged 40 years or older undergoing emergency open major abdominal surgery. Eligible UK National Health Service (NHS) hospitals (those that had an emergency general surgical service, a substantial volume of emergency abdominal surgery cases, and contributed data to the National Emergency Laparotomy Audit) were organised into 15 geographical clusters and commenced the QI programme in a random order, based on a computer-generated random sequence, over an 85-week period with one geographical cluster commencing the intervention every 5 weeks from the second to the 16th time period. Patients were masked to the study group, but it was not possible to mask hospital staff or investigators. The primary outcome measure was mortality within 90 days of surgery. Analyses were done on an intention-to-treat basis. This study is registered with the ISRCTN registry, number ISRCTN80682973. FINDINGS: Treatment took place between March 3, 2014, and Oct 19, 2015. 22 754 patients were assessed for elegibility. Of 15 873 eligible patients from 93 NHS hospitals, primary outcome data were analysed for 8482 patients in the usual care group and 7374 in the QI group. Eight patients in the usual care group and nine patients in the QI group were not included in the analysis because of missing primary outcome data. The primary outcome of 90-day mortality occurred in 1210 (16%) patients in the QI group compared with 1393 (16%) patients in the usual care group (HR 1·11, 0·96-1·28). INTERPRETATION: No survival benefit was observed from this QI programme to implement a care pathway for patients undergoing emergency abdominal surgery. Future QI programmes should ensure that teams have both the time and resources needed to improve patient care. FUNDING: National Institute for Health Research Health Services and Delivery Research Programme

Effectiveness of a national quality improvement programme to improve survival after emergency abdominal surgery (EPOCH): a stepped-wedge cluster-randomised trial

Background: Emergency abdominal surgery is associated with poor patient outcomes. We studied the effectiveness of a national quality improvement (QI) programme to implement a care pathway to improve survival for these patients. Methods: We did a stepped-wedge cluster-randomised trial of patients aged 40 years or older undergoing emergency open major abdominal surgery. Eligible UK National Health Service (NHS) hospitals (those that had an emergency general surgical service, a substantial volume of emergency abdominal surgery cases, and contributed data to the National Emergency Laparotomy Audit) were organised into 15 geographical clusters and commenced the QI programme in a random order, based on a computer-generated random sequence, over an 85-week period with one geographical cluster commencing the intervention every 5 weeks from the second to the 16th time period. Patients were masked to the study group, but it was not possible to mask hospital staff or investigators. The primary outcome measure was mortality within 90 days of surgery. Analyses were done on an intention-to-treat basis. This study is registered with the ISRCTN registry, number ISRCTN80682973. Findings: Treatment took place between March 3, 2014, and Oct 19, 2015. 22 754 patients were assessed for elegibility. Of 15 873 eligible patients from 93 NHS hospitals, primary outcome data were analysed for 8482 patients in the usual care group and 7374 in the QI group. Eight patients in the usual care group and nine patients in the QI group were not included in the analysis because of missing primary outcome data. The primary outcome of 90-day mortality occurred in 1210 (16%) patients in the QI group compared with 1393 (16%) patients in the usual care group (HR 1·11, 0·96–1·28). Interpretation: No survival benefit was observed from this QI programme to implement a care pathway for patients undergoing emergency abdominal surgery. Future QI programmes should ensure that teams have both the time and resources needed to improve patient care. Funding: National Institute for Health Research Health Services and Delivery Research Programme

Transient ureteric obstruction following pelvic floor reconstruction

We describe the first reported case of transient distal ureteric obstruction attributed to post-surgical oedema in a patient with a solitary kidney. This occurred following combined pelvic floor repair and sacrospinous fixation for recurrent pelvic organ prolapse and manifested clinically as anuria, radiological hydroureter and acute kidney injury in the postoperative period. The transient nature of this obstruction, which was managed by a temporary percutaneous nephrostomy, indicates that it was caused by ureteric compression secondary to soft tissue oedema following surgery. We highlight the importance of this potential complication in females with a history of nephrectomy, unilateral renal tract anomalies or severely diminished renal reserve.</jats:p

Antenatal Dads and First Year Families program: a qualitative study of fathers’ and program facilitators’ experiences of a community-based program in Australia

Abstract Aim: Currently, there is limited knowledge on the impact of father-only sessions or parenting programs supporting impending fatherhood. This research explored an antenatal dads program aimed at fathers to assess the benefits of such interventions. Background: Literature regarding parenting programs and early childhood education initiatives, especially those aimed at children and families in disadvantaged circumstance, have been demonstrated to act as a buffer to poorer health and lifestyle outcomes in later life. Methods: A qualitative research approach was used to explore the experiences of 16 fathers and 6 staff of a community-based parenting program with sessions focusing on fatherhood. Findings: Four main themes were identified from the data regarding the experiences of groups engaged with the Antenatal Dads and First Year Families program. The first theme ‘Knowledge and Capacity Building’ stated that the information provided in the program helped fathers to be better informed and prepared for their impending fatherhood. The second theme was ‘Mental Health Awareness’ and identified the importance of raising awareness of depression and suicide in fathers, including where and how to get help. The third theme was ‘Soft-Entry’ and highlighted how the attendance at one service helped participants to learn about additional services through word of mouth and targeted promotion. The final theme was ‘Feeling Connected’, which helped fathers to feel more connected with the process of childbirth and development including playing and engaging with their children. Overall, the fathers found that the male-only sessions assisted them by supporting frank discussions on fatherhood. Additionally, the study helped identify the advantages of fathers meeting other fathers through attendance in the program, or even other couples in similar situations that helped fathers to feel less lonely regarding their situation. </jats:sec

Data from: Dynamic NF-κB and E2F interactions control the priority and timing of inflammatory signalling and cell proliferation

Dynamic cellular systems reprogram gene expression to ensure appropriate cellular fate responses to specific extracellular cues. Here we demonstrate that the dynamics of Nuclear Factor kappa B (NF-κB) signalling and the cell cycle are prioritised differently depending on the timing of an inflammatory signal. Using iterative experimental and computational analyses, we show physical and functional interactions between NF-κB and the E2 Factor 1 (E2F-1) and E2 Factor 4 (E2F-4) cell cycle regulators. These interactions modulate the NF-κB response. In S-phase, the NF-κB response was delayed or repressed, while cell cycle progression was unimpeded. By contrast, activation of NF-κB at the G1/S boundary resulted in a longer cell cycle and more synchronous initial NF-κB responses between cells. These data identify new mechanisms by which the cellular response to stress is differentially controlled at different stages of the cell cycle.Peak RelA Nuclear Amplitude for HeLa CellsPeak RelA Nuclear Amplitude for HeLa Cells following TNF stimulation arranged by virtual synchronization of cell cycle. Single cell traces upon which the peak amplitude data is based are also included021009 061109 061109e combined.xls020611 ALL CELLS_SK-N-ASPeak RelA Nuclear Amplitude for SK-N_AS Cells following TNF stimulation arranged by virtual synchronization of cell cycle. Single cell traces upon which the peak amplitude data is based are also includedHeLa FUCCI ANALYSISAnalysis of cell cycle transition from G1 to S using Fucci vectors in HeLa cells as well as analysis of mean Mitosis length in the cell type090909 HeLa FUCCI r2 ANALYSIS.xls120210 AS FUCCI O+G CTRL ANALYSISAnalysis of cell cycle transition from G1 to S using Fucci vectors in SK-N-AS cells as well as analysis of mean Mitosis length in the cell typeEffect of TNFalpha on HeLa and SK-N-AS cell cycle lengthCell cycle lengths for SK-N-AS and HeLa cells without and with TNFalpha stimulation. Effect extension on cell cycle following stimulation is also shown at G1 and S phases.Origin cc.opjRelA-DsRedxp E2F1-Venus BAC stables Representitive cell tracesRelA-DsRedexpress and E2F1-Venus BAC stables Representative cell traces separated into cell cycle phases by virtual synchronization.Representitive cell traces.xlsxRelA-DsRedxp E2F1-Venus BAC stables FCS molecular fluoresence DataMolecular fluorescence counts in single cells of RelA-DsRedxp E2F1-Venus BAC stables and correlation data.C11_nuc_table.xlsxRelA-DsRedxp E2F1-Venus BAC stables FCS Autocorrolation and cross-corrolation dataRelA-DsRedxp E2F1-Venus BAC stables FCS autocorrolation and cross-corrolation dataC11_TNF.xlsxBAC BAC Stable cell phase Meta data_DryadTraces of BAC-BAC E2F-1-Venus and Rel-A-dsRedexpress sorted into different cell cycle phases