Open Data for Global Science

The global science system stands at a critical juncture. On the one hand, it is overwhelmed by a hidden avalanche of ephemeral bits that are central components of modern research and of the emerging ‘cyberinfrastructure’4 for e-Science.5 The rational management and exploitation of this cascade of digital assets offers boundless opportunities for research and applications. On the other hand, the ability to access and use this rising flood of data seems to lag behind, despite the rapidly growing capabilities of information and communication technologies (ICTs) to make much more effective use of those data. As long as the attention for data policies and data management by researchers, their organisations and their funders does not catch up with the rapidly changing research environment, the research policy and funding entities in many cases will perpetuate the systemic inefficiencies, and the resulting loss or underutilisation of valuable data resources derived from public investments. There is thus an urgent need for rationalised national strategies and more coherent international arrangements for sustainable access to public research data, both to data produced directly by government entities and to data generated in academic and not-for-profit institutions with public funding. In this chapter, we examine some of the implications of the ‘data driven’ research and possible ways to overcome existing barriers to accessibility of public research data. Our perspective is framed in the context of the predominantly publicly funded global science system. We begin by reviewing the growing role of digital data in research and outlining the roles of stakeholders in the research community in developing data access regimes. We then discuss the hidden costs of closed data systems, the benefits and limitations of openness as the default principle for data access, and the emerging open access models that are beginning to form digitally networked commons. We conclude by examining the rationale and requirements for developing overarching international principles from the top down, as well as flexible, common-use contractual templates from the bottom up, to establish data access regimes founded on a presumption of openness, with the goal of better capturing the benefits from the existing and future scientific data assets. The ‘Principles and Guidelines for Access to Research Data from Public Funding’ from the Organisation for Economic Cooperation and Development (OECD), reported on in another article by Pilat and Fukasaku,6 are the most important recent example of the high-level (inter)governmental approach. The common-use licenses promoted by the Science Commons are a leading example of flexible arrangements originating within the community. Finally, we should emphasise that we focus almost exclusively on the policy—the institutional, socioeconomic, and legal aspects of data access—rather than on the technical and management practicalities that are also important, but beyond the scope of this article

Patient-derived xenograft (PDX) models in basic and translational breast cancer research

Patient-derived xenograft (PDX) models of a growing spectrum of cancers are rapidly supplanting long-established traditional cell lines as preferred models for conducting basic and translational preclinical research. In breast cancer, to complement the now curated collection of approximately 45 long-established human breast cancer cell lines, a newly formed consortium of academic laboratories, currently from Europe, Australia, and North America, herein summarizes data on over 500 stably transplantable PDX models representing all three clinical subtypes of breast cancer (ER+, HER2+, and "Triple-negative" (TNBC)). Many of these models are well-characterized with respect to genomic, transcriptomic, and proteomic features, metastatic behavior, and treatment response to a variety of standard-of-care and experimental therapeutics. These stably transplantable PDX lines are generally available for dissemination to laboratories conducting translational research, and contact information for each collection is provided. This review summarizes current experiences related to PDX generation across participating groups, efforts to develop data standards for annotation and dissemination of patient clinical information that does not compromise patient privacy, efforts to develop complementary data standards for annotation of PDX characteristics and biology, and progress toward "credentialing" of PDX models as surrogates to represent individual patients for use in preclinical and co-clinical translational research. In addition, this review highlights important unresolved questions, as well as current limitations, that have hampered more efficient generation of PDX lines and more rapid adoption of PDX use in translational breast cancer research

Clinical, physiologic, and radiographic factors contributing to development of hypoxemia in moderate to severe COPD:a cohort study

Background: Hypoxemia is a major complication of COPD and is a strong predictor of mortality. We previously identified independent risk factors for the presence of resting hypoxemia in the COPDGene cohort. However, little is known about characteristics that predict onset of resting hypoxemia in patients who are normoxic at baseline. We hypothesized that a combination of clinical, physiologic, and radiographic characteristics would predict development of resting hypoxemia after 5-years of follow-up in participants with moderate to severe COPD Methods: We analyzed 678 participants with moderate-to-severe COPD recruited into the COPDGene cohort who completed baseline and 5-year follow-up visits and who were normoxic by pulse oximetry at baseline. Development of resting hypoxemia was defined as an oxygen saturation ≤88% on ambient air at rest during follow-up. Demographic and clinical characteristics, lung function, and radiographic indices were analyzed with logistic regression models to identify predictors of the development of hypoxemia. Results: Forty-six participants (7%) developed resting hypoxemia at follow-up. Enrollment at Denver (OR 8.30, 95%CI 3.05–22.6), lower baseline oxygen saturation (OR 0.70, 95%CI 0.58–0.85), self-reported heart failure (OR 6.92, 95%CI 1.56–30.6), pulmonary artery (PA) enlargement on computed tomography (OR 2.81, 95%CI 1.17–6.74), and prior severe COPD exacerbation (OR 3.31, 95%CI 1.38–7.90) were independently associated with development of resting hypoxemia. Participants who developed hypoxemia had greater decline in 6-min walk distance and greater 5-year decline in quality of life compared to those who remained normoxic at follow-up. Conclusions: Development of clinically significant hypoxemia over a 5-year span is associated with comorbid heart failure, PA enlargement and severe COPD exacerbation. Further studies are needed to determine if treatments targeting these factors can prevent new onset hypoxemia. Trial registration COPDGene is registered at ClinicalTrials.gov: NCT00608764 (Registration Date: January 28, 2008) Electronic supplementary material The online version of this article (doi:10.1186/s12890-016-0331-0) contains supplementary material, which is available to authorized users

Ambulatory oxygen: why do COPD patients not use their portable systems as prescribed? A qualitative study

Background: patients with COPD on long term oxygen therapy frequently do not adhere to their prescription, and they frequently do not use their ambulatory oxygen systems as intended. Reasons for this lack of adherence are not known. The aim of this study was to obtain in-depth information about perceptions and use of prescribed ambulatory oxygen systems from patients with COPD to inform ambulatory oxygen design, prescription and management.Methods: a qualitative design was used, involving semi-structured face-to-face interviews informed by a grounded theory approach. Twenty-seven UK community-dwelling COPD patients using NHS prescribed ambulatory systems were recruited. Ambulatory oxygen systems comprised cylinders weighing 3.4 kg, a shoulder bag and nasal cannulae.Results: participants reported that they: received no instruction on how to use ambulatory oxygen; were uncertain of the benefits; were afraid the system would run out while they were using it (due to lack of confidence in the cylinder gauge); were embarrassed at being seen with the system in public; and were unable to carry the system because of the cylinder weight. The essential role of carers was also highlighted, as participants with no immediate carers did not use ambulatory oxygen outside the house.Conclusions: these participants highlighted previously unreported problems that prevented them from using ambulatory oxygen as prescribed. Our novel findings point to: concerns with the lack of specific information provision; the perceived unreliability of the oxygen system; important carer issues surrounding managing and using ambulatory oxygen equipment. All of these issues, as well as previously reported problems with system weight and patient embarrassment, should be addressed to improve adherence to ambulatory oxygen prescription and enhance the physical and social benefits of maintaining mobility in this patient group. Increased user involvement in both system development and service provision planning, could have avoided many of the difficulties highlighted by this stud

An integrative review of systematic reviews related to the management of breathlessness in respiratory illnesses

Background: breathlessness is a debilitating and distressing symptom in a wide variety of diseases and still a difficult symptom to manage. An integrative review of systematic reviews of non-pharmacological and pharmacological interventions for breathlessness in non-malignant disease was undertaken to identify the current state of clinical understanding of the management of breathlessness and highlight promising interventions that merit further investigation.Methods: systematic reviews were identified via electronic databases between July 2007 and September 2009. Reviews were included within the study if they reported research on adult participants using either a measure of breathlessness or some other measure of respiratory symptoms.Results: in total 219 systematic reviews were identified and 153 included within the final review, of these 59 addressed non-pharmacological interventions and 94 addressed pharmacological interventions. The reviews covered in excess of 2000 trials. The majority of systematic reviews were conducted on interventions for asthma and COPD, and mainly focussed upon a small number of pharmacological interventions such as corticosteroids and bronchodilators, including beta-agonists. In contrast, other conditions involving breathlessness have received little or no attention and studies continue to focus upon pharmacological approaches. Moreover, although there are a number of non-pharmacological studies that have shown some promise, particularly for COPD, their conclusions are limited by a lack of good quality evidence from RCTs, small sample sizes and limited replication.Conclusions: more research should focus in the future on the management of breathlessness in respiratory diseases other than asthma and COPD. In addition, pharmacological treatments do not completely manage breathlessness and have an added burden of side effects. It is therefore important to focus more research on promising non-pharmacological intervention

A Delphi Survey of Canadian Respiratory Therapists' Practice Statements on Pediatric Mechanical Ventilation.

BACKGROUND: Pediatric mechanical ventilation practice guidelines are not well established; therefore, the European Society for Paediatric and Neonatal Intensive Care (ESPNIC) developed consensus recommendations on pediatric mechanical ventilation management in 2017. However, the guideline's applicability in different health care settings is unknown. This study aimed to determine the consensus on pediatric mechanical ventilation practices from Canadian respiratory therapists' (RTs) perspectives and consensually validate aspects of the ESPNIC guideline. METHODS: A 3-round modified electronic Delphi survey was conducted; contents were guided by ESPNIC. Participants were RTs with at least 5 years of experience working in standalone pediatric ICUs or units with dedicated pediatric intensive care beds across Canada. Round 1 collected open-text feedback, and subsequent rounds gathered feedback using a 6-point Likert scale. Consensus was defined as ≥ 75% agreement; if consensus was unmet, statements were revised for re-ranking in the subsequent round. RESULTS: Fifty-two RTs from 14 different pediatric facilities participated in at least one of the 3 rounds. Rounds 1, 2, and 3 had a response rate of 80%, 93%, and 96%, respectively. A total of 59 practice statements achieved consensus by the end of round 3, categorized into 10 sections: (1) noninvasive ventilation and high-flow oxygen therapy, (2) tidal volume and inspiratory pressures, (3) breathing frequency and inspiratory times, (4) PEEP and FIO2 , (5) advanced modes of ventilation, (6) weaning, (7) physiological targets, (8) monitoring, (9) general, and (10) equipment adjuncts. Cumulative text feedback guided the formation of the clinical remarks to supplement these practice statements. CONCLUSIONS: This was the first study to survey RTs for their perspectives on the general practice of pediatric mechanical ventilation management in Canada, generally aligning with the ESPNIC guideline. These practice statements considered information from health organizations and institutes, supplemented with clinical remarks. Future studies are necessary to verify and understand these practices' effectiveness

Implementation Strategies Used to Reduce Unplanned Extubations in the Neonatal ICU.

Background: Unplanned extubation (UE) is the premature or unintended removal of an artificial airway and can cause worse patient outcomes. Study objectives were to describe implementation strategies used to reduce UE in the Hospital for Sick Children neonatal ICU (NICU) and their influence on UE rates, and contributing factors and patient characteristics of infants who had an UE, and compare them between the biological sexes. We hypothesized that the boys would experience more UEs and worse outcomes compared to the girls. Methods: The single-center retrospective cohort study included all infants who experienced UE (2007-2019). Outcomes consisted of implementation reduction strategies developed by using the plan-do-study-act quality-improvement methodology and UE characteristics, including patient (eg, sex, length of stay) and unplanned extubation situation characteristics (eg, events and/or procedures, repeats). Five plan-do-study-act cycles were implemented. Analyses included text summaries of all strategies, and quantitative descriptive and comparative statistics. Results: UE per 100 ventilator days decreased from 3.46 to 0.14. Key success factors included setting achievable goals; ensuring that strategies were evaluated and amended; maintaining consistency over the long-term; incorporating strategies in the NICU; having institutional support and validation; and having good communication. There were 302 UE in 257 infants, 141 boys (55%), average ± SD gestational age of 31 ± 6 weeks, and 31 (12%) had 45 repeated UEs. The only significant difference between the biological sexes was that more boys (129 [92%]) versus girls (94 [83%]) received the Hospital for Sick Children NICU endotracheal tube taping protocol (P = .030). The incidence of UE occurred in a 2-peaked pattern, highest for those  32 weeks gestational age, the median (interquartile range) duration of mechanical ventilation was 38 (16-77) d versus 6 (3-13) d and hospital length of stay 61 (30-100) d versus 16 (10-41) d. For infants with repeated versus no repeated unplanned extubations, duration of mechanical ventilation was 69 (26-125) d versus 13 (4-52) d and hospital length of stay 90 (39-137) d versus 32 (12-75) d. Conclusions: Detailed well-planned UE reduction strategies significantly reduced the rate of UEs with key factors of success identified. UE characteristics and infant morbidity did not differ between the biological sexes. Infants < 32 weeks of gestational age and with repeated UE had a longer duration of mechanical ventilation and length of stay