Portfolio Vol. I N 2

Wiley, Thomas R. In the Cathedral, Mexico City . Picture. 2. Whitehead, Richard Jr. Izzy was a Lady, After All . Prose. 3. Beckham, Adela. Rain on a March morning . Poem. 6. Beckham, Adela. Heaven . Poem. 6. Deane, Dorothy. Temptation . Poem. 6. Kellogg, Elizabeth. Gruess Dich Gott . Prose. 7. Nadel, Norman. The Duchess . Poem. 8. Dick, Pewilla. The Sligo Fisherman . Prose. 9. Deane, Dorothy. Against the Winter . Poem 12. Flory, Doris Jean. A problem . Poem 12. Travis, Paul Bough. My First View of the Congo Forest . Picture. 13. Bellows, George. Stag at Sharkey\u27s . Picture. 13. B.C.W. Aspiration . Poem. 14. Stewart, John. On Record . Prose 14. Sweitzer, Harry J. Playing Around . Prose. 15. Ellsberg, Edward. Book Parade: Hell on Ice . Prose. 15. B.C.W. End of Winter . Poem. 16. Wiley, Thomas R. End of Winter . Picture. 16. Deeter, Robert. Television, How, Where, and When . Prose. 17. Brush, Jane. Love A La Mode . Poem. 20. Brush, Jane. Radio! . Poem. 20. Brush, Jane. Backward Glance . Poem. 20. Brush, Jane. Homo Paradoxus . Poem. 20. Brush, Jane. The Sardonic Slant . Poem. 20. Brush, Jane. Baths . Prose. 20. Wilson, Gordon. Brushword . Cartoon. 20

Annotating digital documents for asynchronous collaboration

Thesis (Ph. D.)--University of Washington, 2002Annotations are a natural way to record comments and ideas in specific contexts within a document. When people read, they often underline important parts of a document or write notes in the margin. While we typically think of annotating paper documents, systems that support annotating digital documents are becoming increasingly common. Annotations on digital documents are easily shared among groups of people, making them valuable for a wide variety of tasks, including online discussion and providing feedback.This research explores three issues that arise when using annotations for asynchronous collaboration. First, I present the results of using a prototype annotation system, WebAnn, to support online discussions in an educational setting. In a field study in a graduate class, students contributed twice as much content to the discussion using annotations compared to a traditional bulletin board. Annotations also encouraged a different discussion style that focused on specific points in the paper being discussed. The study results suggest valuable improvements to the annotation system and factors to consider when incorporating online discussion into a class.Second, I examine providing appropriate notification mechanisms to support online discussion using annotations. After studying notifications in a large-scale commercial system and finding them lacking, I designed and deployed enhancements to the system. A field study of the new notifications found that overall awareness of annotation activity on software specifications increased with my enhancements. The study also found that providing more information in notification messages, supporting multiple communication channels through which notifications can be received, and allowing customization of notification messages were particularly important.Third, I explore how to anchor annotations robustly to documents to meet user expectations on documents that evolve over time. I describe two studies designed to explore what users expect to happen to their annotations. The studies suggest that users focused on how well unique words in the text that they annotated were tracked among successive versions of the document. Based on this observation, I designed the Keyword Anchoring algorithm, which locates an appropriate new position for an annotation using unique words in the text annotated by the user

obophenotype/cell-ontology: 2017-04-14 release

New releases, fixes #462 Fixed axiom annotation APs. Fixes #465 Fixed xref for FMA supressor T lymphocyte, fixes #463 Fixed malformed orcid IDs for neural crest cell definition references Added group 3 innate lymphoid cell and additional minor fixes to these cell types, Partial work on innate lymphoid cell request, including group 1 and group 2 ILCs #456 #449 #404 added synonym to cell of skeletal muscle. closes #436 made 'external supporting cell of Claudius' a related sun for 'claudius cell' addresses #458 made 'sebocyte' a broad sun of 'acing cell of sebaceous gland' addresses #458 made 'non-striated muscle cell' a narrow synonym of 'smooth muscle cell' addresses #458 relabeled GAG secreting cell, made hyaluronic acid secreting cell a narrow synonym. Made hyaluronic acid secreting cell a narrow synonym for 'synovial cell' Addresses #458 relabeled zygote to animal zygote. closes #454 removed all animal cells have microvilli. Fixes #455 New classes: [Term] id: CL:0001061 name: abnormal cell namespace: cell def: "A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models." [GOC:add, GOC:cg, GOC:wdd] comment: https://github.com/obophenotype/cell-ontology/issues/448 xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 is_a: CL:0000000 ! cell is_a: GO:0005623 ! cell intersection_of: GO:0005623 ! cell intersection_of: bearer_of PATO:0000460 ! abnormal relationship: bearer_of PATO:0000460 ! abnormal property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331 property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T18:53:32Z xsd:dateTime [Term] id: CL:0001062 name: effector memory CD8-positive, alpha-beta T cell, terminally differentiated namespace: cell @@ -13860,6 +13880,55 @@ relationship: lacks_plasma_membrane_part PR:000001017 ! receptor-type tyrosine-p relationship: lacks_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 [Term] id: CL:0001063 name: neoplastic cell namespace: cell def: "An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism." [GOC:add, GOC:cg, GOC:wdd] comment: https://github.com/obophenotype/cell-ontology/issues/448 synonym: "tumor cell" RELATED [] synonym: "tumour cell" RELATED [] xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12922 is_a: CL:0001061 ! abnormal cell intersection_of: CL:0001061 ! abnormal cell intersection_of: bearer_of PATO:0002011 ! neoplastic relationship: bearer_of PATO:0002011 ! neoplastic property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331 property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T19:16:26Z xsd:dateTime [Term] id: CL:0001064 name: malignant cell namespace: cell def: "A neoplastic cell that is capable of entering a surrounding tissue" [GOC:add, GOC:cg, GOC:wdd] comment: https://github.com/obophenotype/cell-ontology/issues/448 synonym: "cancer cell" RELATED [] xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12917 is_a: CL:0001063 ! neoplastic cell intersection_of: CL:0001063 ! neoplastic cell intersection_of: bearer_of PATO:0002097 ! neoplastic, malignant relationship: bearer_of PATO:0002097 ! neoplastic, malignant property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331 property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T19:39:12Z xsd:dateTime [Term] id: CL:0001065 name: innate lymphoid cell namespace: cell def: "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417] is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: capable_of GO:0045087 ! innate immune response intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0045087 ! innate immune response relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331 property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T20:20:48Z xsd:dateTime [Term] id: CL:0001066 name: erythroid progenitor cell, mammalian namespace: cell @@ -13901,10 +13970,45 @@ relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G [Term] id: CL:0001067 name: group 1 innate lymphoid cell namespace: cell def: "An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines." [GOC:add, GOC:dsd, PMID:23348417] is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032609 ! interferon-gamma production relationship: capable_of GO:0032609 ! interferon-gamma production property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331 property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T20:42:44Z xsd:dateTime [Term] id: CL:0001068 name: ILC1 namespace: cell def: "A group 1 innate lymphoid cell that is non-cytotoxic." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417] is_a: CL:0001067 ! group 1 innate lymphoid cell property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331 property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T20:54:12Z xsd:dateTime [Term] id: CL:0001069 name: group 2 innate lymphoid cell namespace: cell def: "An innate lymphoid cell that is capable of producing T-helper 2-cell associated cytokines upon stimulation." [GOC:add, GOC:dsd, PMID:23292121, PMID:23562755] synonym: "ILC2" EXACT [] synonym: "nuocyte" EXACT [] is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032634 ! interleukin-5 production relationship: capable_of GO:0032634 ! interleukin-5 production property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331 property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T21:20:08Z xsd:dateTime [Term] id: CL:0001070 name: beige adipocyte namespace: cell -def: "A fat cell that is beige in color, thermogenic, and which differentiates in white fat tissue from a Myf5-negative progenitor." [] {comment="PMID:22796012", comment="GOC:ymb", comment="GOC:add", comment="GOC:cvs", comment="PMID:25851693"} def: "A fat cell that is beige in color, thermogenic, and which differentiates in white fat tissue from a Myf5-negative progenitor." [GOC:add, GOC:cvs, GOC:ymb, PMID:22796012, PMID:25851693] synonym: "beige brown adipocyte" EXACT [] synonym: "beige fat cell" EXACT [] synonym: "beige/brite adipocyte" EXACT [] @@ -13915,6 +14019,19 @@ is_a: CL:0000136 ! fat cell relationship: part_of UBERON:0001347 ! white adipose tissue [Term] id: CL:0001071 name: group 3 innate lymphoid cell namespace: An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22. {xref="GOC:add", xref="GOC:dsd", xref="PMID:23348417", xref="PMID:23292121"} namespace: cell synonym: "ILC3" EXACT [] is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 relationship: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331 property_value: http://purl.org/dc/elements/1.1/date 2017-01-31T20:21:26Z xsd:dateTim

Impact of video-assisted thoracoscopic lobectomy versus open lobectomy for lung cancer on recovery assessed using self-reported physical function: VIOLET RCT

Background: Lung cancer is the leading cause of cancer death. Surgery remains the main method of managing early-stage disease. Minimal-access video-assisted thoracoscopic surgery results in less tissue trauma than open surgery; however, it is not known if it improves patient outcomes. Objective: To compare the clinical effectiveness and cost-effectiveness of video-assisted thoracoscopic surgery lobectomy with open surgery for the treatment of lung cancer. Design, setting and participants: A multicentre, superiority, parallel-group, randomised controlled trial with blinding of participants (until hospital discharge) and outcome assessors conducted in nine NHS hospitals. Adults referred for lung resection for known or suspected lung cancer, with disease suitable for both surgeries, were eligible. Participants were followed up for 1 year. Interventions: Participants were randomised 1 : 1 to video-assisted thoracoscopic surgery lobectomy or open surgery. Video-assisted thoracoscopic surgery used one to four keyhole incisions without rib spreading. Open surgery used a single incision with rib spreading, with or without rib resection. Main outcome measures: The primary outcome was self-reported physical function (using the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire Core 30) at 5 weeks. Secondary outcomes included upstaging to pathologic node stage 2 disease, time from surgery to hospital discharge, pain in the first 2 days, prolonged pain requiring analgesia at > 5 weeks, adverse health events, uptake of adjuvant treatment, overall and disease-free survival, quality of life (Quality of Life Questionnaire Core 30, Quality of Life Questionnaire Lung Cancer 13 and EQ-5D) at 2 and 5 weeks and 3, 6 and 12 months, and cost-effectiveness. Results: A total of 503 patients were randomised between July 2015 and February 2019 (video-assisted thoracoscopic surgery, n = 247; open surgery, n = 256). One participant withdrew before surgery. The mean age of patients was 69 years; 249 (49.5%) patients were men and 242 (48.1%) did not have a confirmed diagnosis. Lobectomy was performed in 453 of 502 (90.2%) participants and complete resection was achieved in 429 of 439 (97.7%) participants. Quality of Life Questionnaire Core 30 physical function was better in the video-assisted thoracoscopic surgery group than in the open-surgery group at 5 weeks (video-assisted thoracoscopic surgery, n = 247; open surgery, n = 255; mean difference 4.65, 95% confidence interval 1.69 to 7.61; p = 0.0089). Upstaging from clinical node stage 0 to pathologic node stage 1 and from clinical node stage 0 or 1 to pathologic node stage 2 was similar (p ≥ 0.50). Pain scores were similar on day 1, but lower in the video-assisted thoracoscopic surgery group on day 2 (mean difference –0.54, 95% confidence interval –0.99 to –0.09; p = 0.018). Analgesic consumption was 10% lower (95% CI –20% to 1%) and the median hospital stay was less (4 vs. 5 days, hazard ratio 1.34, 95% confidence interval 1.09, 1.65; p = 0.006) in the video-assisted thoracoscopic surgery group than in the open-surgery group. Prolonged pain was also less (relative risk 0.82, 95% confidence interval 0.72 to 0.94; p = 0.003). Time to uptake of adjuvant treatment, overall survival and progression-free survival were similar (p ≥ 0.28). Fewer participants in the video-assisted thoracoscopic surgery group than in the open-surgery group experienced complications before and after discharge from hospital (relative risk 0.74, 95% confidence interval 0.66 to 0.84; p < 0.001 and relative risk 0.81, 95% confidence interval 0.66 to 1.00; p = 0.053, respectively). Quality of life to 1 year was better across several domains in the video-assisted thoracoscopic surgery group than in the open-surgery group. The probability that video-assisted thoracoscopic surgery is cost-effective at a willingness-to-pay threshold of £20,000 per quality-adjusted life-year is 1. Limitations: Ethnic minorities were under-represented compared with the UK population (< 5%), but the cohort reflected the lung cancer population. Conclusions: Video-assisted thoracoscopic surgery lobectomy was associated with less pain, fewer complications and better quality of life without any compromise to oncologic outcome. Use of video-assisted thoracoscopic surgery is highly likely to be cost-effective for the NHS. Future work: Evaluation of the efficacy of video-assisted thoracoscopic surgery with robotic assistance, which is being offered in many hospitals. Trial registration: This trial is registered as ISRCTN13472721. Funding: This project was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 26, No. 48. See the NIHR Journals Library website for further project information

Impact of video-assisted thoracoscopic lobectomy versus open lobectomy for lung cancer on recovery assessed using self-reported physical function: VIOLET RCT

BackgroundLung cancer is the leading cause of cancer death. Surgery remains the main method of managing early-stage disease. Minimal-access video-assisted thoracoscopic surgery results in less tissue trauma than open surgery; however, it is not known if it improves patient outcomes.ObjectiveTo compare the clinical effectiveness and cost-effectiveness of video-assisted thoracoscopic surgery lobectomy with open surgery for the treatment of lung cancer.Design, setting and participantsA multicentre, superiority, parallel-group, randomised controlled trial with blinding of participants (until hospital discharge) and outcome assessors conducted in nine NHS hospitals. Adults referred for lung resection for known or suspected lung cancer, with disease suitable for both surgeries, were eligible. Participants were followed up for 1 year.InterventionsParticipants were randomised 1 : 1 to video-assisted thoracoscopic surgery lobectomy or open surgery. Video-assisted thoracoscopic surgery used one to four keyhole incisions without rib spreading. Open surgery used a single incision with rib spreading, with or without rib resection.Main outcome measuresThe primary outcome was self-reported physical function (using the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire Core 30) at 5 weeks. Secondary outcomes included upstaging to pathologic node stage 2 disease, time from surgery to hospital discharge, pain in the first 2 days, prolonged pain requiring analgesia at &gt; 5 weeks, adverse health events, uptake of adjuvant treatment, overall and disease-free survival, quality of life (Quality of Life Questionnaire Core 30, Quality of Life Questionnaire Lung Cancer 13 and EQ-5D) at 2 and 5 weeks and 3, 6 and 12 months, and cost-effectiveness.ResultsA total of 503 patients were randomised between July 2015 and February 2019 (video-assisted thoracoscopic surgery, n = 247; open surgery, n = 256). One participant withdrew before surgery. The mean age of patients was 69 years; 249 (49.5%) patients were men and 242 (48.1%) did not have a confirmed diagnosis. Lobectomy was performed in 453 of 502 (90.2%) participants and complete resection was achieved in 429 of 439 (97.7%) participants. Quality of Life Questionnaire Core 30 physical function was better in the video-assisted thoracoscopic surgery group than in the open-surgery group at 5 weeks (video-assisted thoracoscopic surgery, n = 247; open surgery, n = 255; mean difference 4.65, 95% confidence interval 1.69 to 7.61; p = 0.0089). Upstaging from clinical node stage 0 to pathologic node stage 1 and from clinical node stage 0 or 1 to pathologic node stage 2 was similar (p ≥ 0.50). Pain scores were similar on day 1, but lower in the video-assisted thoracoscopic surgery group on day 2 (mean difference –0.54, 95% confidence interval –0.99 to –0.09; p = 0.018). Analgesic consumption was 10% lower (95% CI –20% to 1%) and the median hospital stay was less (4 vs. 5 days, hazard ratio 1.34, 95% confidence interval 1.09, 1.65; p = 0.006) in the video-assisted thoracoscopic surgery group than in the open-surgery group. Prolonged pain was also less (relative risk 0.82, 95% confidence interval 0.72 to 0.94; p = 0.003). Time to uptake of adjuvant treatment, overall survival and progression-free survival were similar (p ≥ 0.28). Fewer participants in the video-assisted thoracoscopic surgery group than in the open-surgery group experienced complications before and after discharge from hospital (relative risk 0.74, 95% confidence interval 0.66 to 0.84; p &lt; 0.001 and relative risk 0.81, 95% confidence interval 0.66 to 1.00; p = 0.053, respectively). Quality of life to 1 year was better across several domains in the video-assisted thoracoscopic surgery group than in the open-surgery group. The probability that video-assisted thoracoscopic surgery is cost-effective at a willingness-to-pay threshold of £20,000 per quality-adjusted life-year is 1.LimitationsEthnic minorities were under-represented compared with the UK population (&lt; 5%), but the cohort reflected the lung cancer population.ConclusionsVideo-assisted thoracoscopic surgery lobectomy was associated with less pain, fewer complications and better quality of life without any compromise to oncologic outcome. Use of video-assisted thoracoscopic surgery is highly likely to be cost-effective for the NHS.Future workEvaluation of the efficacy of video-assisted thoracoscopic surgery with robotic assistance, which is being offered in many hospitals.Trial registrationThis trial is registered as ISRCTN13472721