Extracting fluorescent reporter time courses of cell lineages from high-throughput microscopy at low temporal resolution

Live Cell Imaging and High Throughput Screening are rapidly evolving techniques and have found many applications in recent years. Modern microscopy enables the visualisation of internal changes in the cell through the use of fluorescently tagged proteins which can be targeted to specific cellular components. A system is presented here which is designed to track cells at low temporal resolution within large populations, and to extract fluorescence data which allows relative expression rates of tagged proteins to be monitored. Cell detection and tracking are performed as separate steps, and several methods are evaluated for suitability using timeseries images of Hoechst-stained C2C12 mouse mesenchymal stem cells. The use of Hoechst staining ensures cell nuclei are visible throughout a time-series. Dynamic features, including a characteristic change in Hoechst fluorescence intensity during chromosome condensation, are used to identify cell divisions and resulting daughter cells. The ability to detect cell division is integrated into the tracking, aiding lineage construction. To establish the efficiency of the method, synthetic cell images have been produced and used to evaluate cell detection accuracy. A validation framework is created which allows the accuracy of the automatic segmentation and tracking systems to be measured and compared against existing state of the art software, such as CellProfiler. Basic tracking methods, including nearest-neighbour and cell-overlap, are provided as a baseline to evaluate the performance of more sophisticated methods. The software is demonstrated on a number of biological systems, starting with a study of different control elements of the Msx1 gene, which regulates differentiation of mesenchymal stem cells. Expression is followed through multiple lineages to identify asymmetric divisions which may be due to cell differentiation. The lineage construction methods are applied to Schizosaccharomyces pombe time-series image data, allowing the extraction of generation lengths for individual cells. Finally a study is presented which examines correlations between the circadian and cell cycles. This makes use of the recently developed FUCCI cell cycle markers which, when used in conjunction with a circadian indicator such as Rev-erbα-Venus, allow simultaneous measurements of both cycles

Understanding Task-Performance Chain Feed-Forward and Feedback Relationships in E-health

The associations between the use of effective technology and user performance, and the effect of user performance on technology use and task-technology fit (TTF), requires further research (Furneauz, 2012). To address this call for future research, we examined the feed-forward from use and TTF to performance and the feedback from performance to use and TTF by using longitudinal data (n = 156) collected from participants using two custom-built e-health systems that we designed to provide education to develop self-management practices for study participants with newly diagnosed type 2 diabetes. We captured participants’ use of the two systems, their perceptions of TTF, and their health performance through biomedical outcomes every three months over a 12month period. Our findings show significant and different feed-forward and feedback relationships. In general, our results also show that system use and a negative TTF-use interaction significantly affected performance through feed-forward, while participant performance significantly affected use and negatively affects TTF through feedback. We discuss the implications for task-performance chain (TPC) research and developing and using e-health systems in chronic care

Extracting fluorescent reporter time courses of cell lineages from high-throughput microscopy at low temporal resolution

Live Cell Imaging and High Throughput Screening are rapidly evolving techniques and have found many applications in recent years. Modern microscopy enables the visualisation of internal changes in the cell through the use of fluorescently tagged proteins which can be targeted to specific cellular components. A system is presented here which is designed to track cells at low temporal resolution within large populations, and to extract fluorescence data which allows relative expression rates of tagged proteins to be monitored. Cell detection and tracking are performed as separate steps, and several methods are evaluated for suitability using timeseries images of Hoechst-stained C2C12 mouse mesenchymal stem cells. The use of Hoechst staining ensures cell nuclei are visible throughout a time-series. Dynamic features, including a characteristic change in Hoechst fluorescence intensity during chromosome condensation, are used to identify cell divisions and resulting daughter cells. The ability to detect cell division is integrated into the tracking, aiding lineage construction. To establish the efficiency of the method, synthetic cell images have been produced and used to evaluate cell detection accuracy. A validation framework is created which allows the accuracy of the automatic segmentation and tracking systems to be measured and compared against existing state of the art software, such as CellProfiler. Basic tracking methods, including nearest-neighbour and cell-overlap, are provided as a baseline to evaluate the performance of more sophisticated methods. The software is demonstrated on a number of biological systems, starting with a study of different control elements of the Msx1 gene, which regulates differentiation of mesenchymal stem cells. Expression is followed through multiple lineages to identify asymmetric divisions which may be due to cell differentiation. The lineage construction methods are applied to Schizosaccharomyces pombe time-series image data, allowing the extraction of generation lengths for individual cells. Finally a study is presented which examines correlations between the circadian and cell cycles. This makes use of the recently developed FUCCI cell cycle markers which, when used in conjunction with a circadian indicator such as Rev-erbα-Venus, allow simultaneous measurements of both cycles.EThOS - Electronic Theses Online ServiceEngineering and Physical Sciences Research Council (EPSRC)GBUnited Kingdo

The Clinical Impact of eHealth on the Self-Management of Diabetes: A Double Adoption Perspective

The development, adoption, and acceptance of eHealth systems that change and improve patient self-care have been promising, but the results have been mixed and the work mostly atheoretical. In this paper, we respond to this opportunity by developing and assessing an eHealth system for newly diagnosed type 2 diabetes patients. Study participants used the eHealth system for a 12-month period after diagnosis in an attempt to acquire an understanding about their diabetes, develop self-care activities (e.g., blood glucose testing), and improve their biomedical outcomes. Drawing upon theories and methods from information systems and upon the Precede-Proceed model of health promotion planning, we explored the double adoption of eHealth technology and its antecedents, self-care practices and their antecedents, and improvements in biomedical outcomes important to long-term diabetes health. Path model results indicate important implications for information systems, eHealth, and health promotion practice and research, which are discussed

The 'sluice-gate' public sphere and the national DNA database in the UK

Habermas’s amendments to his original public sphere thesis have been recognized by a number of media scholars in recent years. His original thesis of a decline or refeudalization of the public sphere where politics is played out in front of the public has been modified, under the influence of Bernhard Peters’ work, to incorporate the possibility of action from the periphery of the public sphere influencing, if not exclusively determining, decisions made at the administrative core via sluice-gates. There has been limited work, however, on exploring the operation of the sluices in greater detail, and particularly on the role of the mass media in acting as a communication channel between peripheral publics and core elites. The purpose of this article is to do so via a case study of the mass media public debate in the UK about the existence and extent of the national DNA database as it is a prima facie candidate for observing the operation of the sluice-gates

SciRepEval: A Multi-Format Benchmark for Scientific Document Representations

Learned representations of scientific documents can serve as valuable input features for downstream tasks, without the need for further fine-tuning. However, existing benchmarks for evaluating these representations fail to capture the diversity of relevant tasks. In response, we introduce SciRepEval, the first comprehensive benchmark for training and evaluating scientific document representations. It includes 25 challenging and realistic tasks, 11 of which are new, across four formats: classification, regression, ranking and search. We then use the benchmark to study and improve the generalization ability of scientific document representation models. We show how state-of-the-art models struggle to generalize across task formats, and that simple multi-task training fails to improve them. However, a new approach that learns multiple embeddings per document, each tailored to a different format, can improve performance. We experiment with task-format-specific control codes and adapters in a multi-task setting and find that they outperform the existing single-embedding state-of-the-art by up to 1.5 points absolute.Comment: 21 pages, 2 figures, 9 tables. For associated code, see https://github.com/allenai/scirepeva

ARIES: A Corpus of Scientific Paper Edits Made in Response to Peer Reviews

Revising scientific papers based on peer feedback is a challenging task that requires not only deep scientific knowledge and reasoning, but also the ability to recognize the implicit requests in high-level feedback and to choose the best of many possible ways to update the manuscript in response. We introduce this task for large language models and release ARIES, a dataset of review comments and their corresponding paper edits, to enable training and evaluating models. We study two versions of the task: comment-edit alignment and edit generation, and evaluate several baselines, including GPT-4. We find that models struggle even to identify the edits that correspond to a comment, especially in cases where the comment is phrased in an indirect way or where the edit addresses the spirit of a comment but not the precise request. When tasked with generating edits, GPT-4 often succeeds in addressing comments on a surface level, but it rigidly follows the wording of the feedback rather than the underlying intent, and includes fewer technical details than human-written edits. We hope that our formalization, dataset, and analysis will form a foundation for future work in this area.Comment: 11 pages, 2 figure

Prospectus, October 31, 1979

FROM POLIDENT TO EFFERVESCENT: DOWNTOWN TO BE VINTAGE; Week in Review: Across the globe, In the nation, Throughout the state, Around the town; Poltergeists bump at night; Elam wins state CC; Correction…; Wilson thanks Ziggy fans; Briefs: Forum discusses survey, Brazilian pianist at Monticello Nov. 4, Debate: has America failed?, Art field trip features Toulouse-Lautrec, NHB sponsors student awards, One woman is \u27nine Women\u27, EMT workshop at PC Nov. 17, Parkland presents Survival Program; Weekly Calendar; Preppy yet potent: Heads progress the hard way; Letters to the Editor: Rep. Johnson opposes veto; When weather break thieves break in; Foreigners complain again; Treaters shouldn\u27t \u27trick\u27; Amittyville: fact or fiction?; Survey handed out next week; Classifieds; Checks cashable in Nov.; College Day at PC Nov. 7; Model govt. needs plans; Earn less than $6,000? Elgible for higher grant; Parkland offers Folkore; Harmful materials to be discusses; Knee surgery ousts Short; Home no help for golfers; You\u27ve waited long enough: shape up; Soccer club wins; Freddy heading toward poverty; Fast Freddy Contesthttps://spark.parkland.edu/prospectus_1979/1006/thumbnail.jp

Prospectus, October 24, 1979

SURVEY MAKES WAVES; The Week in Review: Across the globe, In the nation, Throughout the state, Around the town, Etc….; Briefs: College to host math contest, Parkland Players present \u27Dracula\u27, Summary of board listed, Champaign council approves bonds, Women\u27s program seeks young blood, Monticello council to discuss tax rate, Program on strokes to be presented, Arthritis program to be presented, Future educators program tomorrow, Nutritionm health, disease are topics, Store celebrates 1st; Letter to editor: Dean congratulates foreigners; Weekly Calendar; Area high schools to visit campus; S.T.O. raffle winners are announced; Give a little blood, then see blood; Women at Home on Tuesday; Editorial: Censorship at WPCD?; PATH raises grievances; Pumpkins and costumes in contest next week; Lincoln Square has art show; Oktoberfest today: a taste of German; Reviews: Ending to the beat has better taste, B-52s: a glimpse of future and past; Classifieds; Music club has enthusiasm; Athletic and rec fields near completion; V-ball gains momentum; Golf team advances to state; Elam blows off competition: harriers 3rd; PC hosts golf, gets 2nd; Fast Freddy loses again; Fast Freddy Contesthttps://spark.parkland.edu/prospectus_1979/1007/thumbnail.jp