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In clinical and translational research, data science is often and fortuitously integrated with data collection. This contrasts to the typical position of data scientists in other settings, where they are isolated from data collectors. Because of this, effective use of data science techniques to resolve translational questions requires innovation in the organization and management of these data.
We propose an operational framework that respects this important difference in how research teams are organized. To maximize the accuracy and speed of the clinical and translational data science enterprise under this framework, we define a set of eight best practices for data management.
In our own work at the University of Rochester, we have strived to utilize these practices in a customized version of the open source LabKey platform for integrated data management and collaboration. We have applied this platform to cohorts that longitudinally track multidomain data from over 3000 subjects.
We argue that this has made analytical datasets more readily available and lowered the bar to interdisciplinary collaboration, enabling a team-based data science that is unique to the clinical and translational setting.
Important Bird and Biodiversity Areas (IBAs) are sites identified as being globally important for the conservation of bird populations on the basis of an internationally agreed set of criteria. We present the first review of the development and spread of the IBA concept since it was launched by BirdLife International (then ICBP) in 1979 and examine some of the characteristics of the resulting inventory. Over 13,000 global and regional IBAs have so far been identified and documented in terrestrial, freshwater and marine ecosystems in almost all of the world’s countries and territories, making this the largest global network of sites of significance for biodiversity. IBAs have been identified using standardised, data-driven criteria that have been developed and applied at global and regional levels. These criteria capture multiple dimensions of a site’s significance for avian biodiversity and relate to populations of globally threatened species (68.6% of the 10,746 IBAs that meet global criteria), restricted-range species (25.4%), biome-restricted species (27.5%) and congregatory species (50.3%); many global IBAs (52.7%) trigger two or more of these criteria. IBAs range in size from < 1 km2 to over 300,000 km2 and have an approximately log-normal size distribution (median = 125.0 km2, mean = 1,202.6 km2). They cover approximately 6.7% of the terrestrial, 1.6% of the marine and 3.1% of the total surface area of the Earth. The launch in 2016 of the KBA Global Standard, which aims to identify, document and conserve sites that contribute to the global persistence of wider biodiversity, and whose criteria for site identification build on those developed for IBAs, is a logical evolution of the IBA concept. The role of IBAs in conservation planning, policy and practice is reviewed elsewhere. Future technical priorities for the IBA initiative include completion of the global inventory, particularly in the marine environment, keeping the dataset up to date, and improving the systematic monitoring of these sites.
Families express a need for information to support people with severe anorexia nervosa.
To examine the impact of the addition of a skills training intervention for caregivers (Experienced Caregivers Helping Others, ECHO) to standard care.
Patients over the age of 12 (mean age 26 years, duration 72 months illness) with a primary diagnosis of anorexia nervosa and their caregivers were recruited from 15 in-patient services in the UK. Families were randomised to ECHO (a book, DVDs and five coaching sessions per caregiver) or treatment as usual. Patient (n=178) and caregiver (n=268) outcomes were measured at discharge and 6 and 12 months after discharge.
Patients with caregivers in the ECHO group had reduced eating disorder psychopathology (EDE-Q) and improved quality of life (WHO-Quol; both effects small) and reduced in-patient bed days (7–12 months post-discharge). Caregivers in the ECHO group had reduced burden (Eating Disorder Symptom Impact Scale, EDSIS), expressed emotion (Family Questionnaire, FQ) and time spent caregiving at 6 months but these effects were diminished at 12 months.
Small but sustained improvements in symptoms and bed use are seen in the intervention group. Moreover, caregivers were less burdened and spent less time providing care. Caregivers had most benefit at 6 months suggesting that booster sessions, perhaps jointly with the patients, may be needed to maintain the effect. Sharing skills and information with caregivers may be an effective way to improve outcomes. This randomised controlled trial (RCT) was registered with Current Controlled Trials ISRCTN06149665.
The Numeniini is a tribe of 13 wader species (Scolopacidae, Charadriiformes) of which seven are Near Threatened or globally threatened, including two Critically Endangered. To help inform conservation management and policy responses, we present the results of an expert assessment of the threats that members of this taxonomic group face across migratory flyways. Most threats are increasing in intensity, particularly in non-breeding areas, where habitat loss resulting from residential and commercial development, aquaculture, mining, transport, disturbance, problematic invasive species, pollution and climate change were regarded as having the greatest detrimental impact. Fewer threats (mining, disturbance, problematic native species and climate change) were identified as widely affecting breeding areas. Numeniini populations face the greatest number of non-breeding threats in the East Asian-Australasian Flyway, especially those associated with coastal reclamation; related threats were also identified across the Central and Atlantic Americas, and East Atlantic flyways. Threats on the breeding grounds were greatest in Central and Atlantic Americas, East Atlantic and West Asian flyways. Three priority actions were associated with monitoring and research: to monitor breeding population trends (which for species breeding in remote areas may best be achieved through surveys at key non-breeding sites), to deploy tracking technologies to identify migratory connectivity, and to monitor land-cover change across breeding and non-breeding areas. Two priority actions were focused on conservation and policy responses: to identify and effectively protect key non-breeding sites across all flyways (particularly in the East Asian- Australasian Flyway), and to implement successful conservation interventions at a sufficient scale across human-dominated landscapes for species’ recovery to be achieved. If implemented urgently, these measures in combination have the potential to alter the current population declines of many Numeniini species and provide a template for the conservation of other groups of threatened species.
The prevalence of the metabolic syndrome components including abdominal obesity, dyslipidaemia and insulin resistance is increasing in both developed and developing countries. It is generally accepted that the development of these features is preceded by, or accompanied with, impaired mitochondrial function. The present study was designed to analyse the effects of a mitochondrial-targeted lipophilic ubiquinone (MitoQ) on muscle lipid profile modulation and mitochondrial function in obesogenic diet-fed rats. For this purpose, twenty-four young male Sprague–Dawley rats were divided into three groups and fed one of the following diets: (1) control, (2) high fat (HF) and (3) HF+MitoQ. After 8 weeks, mitochondrial function markers and lipid metabolism/profile modifications in skeletal muscle were measured. The HF diet was effective at inducing the major features of the metabolic syndrome – namely, obesity, hepatic enlargement and glucose intolerance. MitoQ intake prevented the increase in rat body weight, attenuated the increase in adipose tissue and liver weights and partially reversed glucose intolerance. At the muscle level, the HF diet induced moderate TAG accumulation associated with important modifications in the muscle phospholipid classes and in the fatty acid composition of total muscle lipid. These lipid modifications were accompanied with decrease in mitochondrial respiration. MitoQ intake corrected the lipid alterations and restored mitochondrial respiration. These results indicate that MitoQ protected obesogenic diet-fed rats from some features of the metabolic syndrome through its effects on muscle lipid metabolism and mitochondrial activity. These findings suggest that MitoQ is a promising candidate for future human trials in the metabolic syndrome prevention.
Primary and secondary care services are charged with failing to adequately detect and treat mental disorder in older adults due to the ‘understandability phenomenon’; the belief that mental disorder in old age is inevitable and therefore not worthy of intervention. Quantitative data appear to support this hypothesis but lack the explanatory power of detailed accounts. Nine general practitioners (GPs) participated in group interviews about their assessment and treatment of older patients, and their expectations and experience of referral to secondary care. Resulting transcripts were subject to Thematic Analysis. Respondents recognised the unique features of these clients, and their impact on the detailed, recursive processes of assessment, clinical decision-making and intervention. GPs described confidence in managing most cases of mental disorder, describing the role of secondary care as one of consultancy in extreme or unusual cases. GPs did view mental disorder as commonly originating in adverse circumstances, and queried the validity of pharmacological or psychological interventions in these cases. They did not, however, equate understandability with acceptability, and called for social interventions to be integrated with health-care interventions to tackle the cause of mental disorder in older adults. At a wider level, findings highlight the discrepancy between assumptions about GP attitudes and actions, and their own accounts. At a local level, findings will assist in focusing secondary care service development where need is perceived, into consultancy and training.
Depression is a common and costly comorbidity in dementia. There are very few data on the cost-effectiveness of antidepressants for depression in dementia and their effects on carer outcomes.
To evaluate the cost-effectiveness of sertraline and mirtazapine compared with placebo for depression in dementia.
A pragmatic, multicentre, randomised placebo-controlled trial with a parallel cost-effectiveness analysis (trial registration: ISRCTN88882979 and EudraCT 2006-000105-38). The primary cost-effectiveness analysis compared differences in treatment costs for patients receiving sertraline, mirtazapine or placebo with differences in effectiveness measured by the primary outcome, total Cornell Scale for Depression in Dementia (CSDD) score, over two time periods: 0–13 weeks and 0–39 weeks. The secondary evaluation was a cost-utility analysis using quality-adjusted life years (QALYs) computed from the Euro-Qual (EQ-5D) and societal weights over those same periods.
There were 339 participants randomised and 326 with costs data (111 placebo, 107 sertraline, 108 mirtazapine). For the primary outcome, decrease in depression, mirtazapine and sertraline were not cost-effective compared with placebo. However, examining secondary outcomes, the time spent by unpaid carers caring for participants in the mirtazapine group was almost half that for patients receiving placebo (6.74 v. 12.27 hours per week) or sertraline (6.74 v. 12.32 hours per week). Informal care costs over 39 weeks were £1510 and £1522 less for the mirtazapine group compared with placebo and sertraline respectively.
In terms of reducing depression, mirtazapine and sertraline were not cost-effective for treating depression in dementia. However, mirtazapine does appear likely to have been cost-effective if costing includes the impact on unpaid carers and with quality of life included in the outcome. Unpaid (family) carer costs were lower with mirtazapine than sertraline or placebo. This may have been mediated via the putative ability of mirtazapine to ameliorate sleep disturbances and anxiety. Given the priority and the potential value of supporting family carers of people with dementia, further research is warranted to investigate the potential of mirtazapine to help with behavioural and psychological symptoms in dementia and in supporting carers.
The intertidal zone between land and sea provides some of the most productive and complex of habitats, supporting vast numbers of birds of many species. This chapter explores patterns of use of estuarine mudflats and saltmarshes by birds, drivers of within- and between-estuary variation in use of estuarine resources by these species, and consequences of recent environmental changes on estuaries. A series of case studies of anthropogenic impacts on estuarine habitats and their implications for bird populations is described. Although the primary geographic focus of these examples is western Europe, and particularly Britain, estuaries across the globe are experiencing similar threats and impacts. There are also large intertidal areas outside estuaries that provide rather different environments for birds; these are discussed in Chapter 13.
The estuarine environment and its bird assemblages
Estuarine mudflats and sandflats typically occur in areas of shallow, sheltered tidal water, where currents from rivers and tidal movements slow sufficiently to allow settlement of particles of sediment. Sand and gravel particles are typically large enough to settle out of the water column directly, but the settlement of finer particles of silt and clay is aided by the surface attraction displayed by these fine sediments when in salt water, in a process known as flocculation. The resulting formation of extensive areas of mud and sandflat creates a habitat of extreme importance for many intertidal species and communities (Fig. 12.1).
The largely deforested island of Cebu, Philippines, hosts a forest-dwelling hawk-owl identified in the literature as Ninox philippensis spilonota but which is in fact a Cebu island endemic species, soon to be named. To determine the current distribution and habitat requirements of this hawk-owl, the five largest of 11 remaining forest patches on Cebu were surveyed between March and June 2011, involving 64 post-sunset 500-m walked transects with playback and habitat assessments. Radio-telemetry studies were also conducted on 10 owls but only for 3–5 days per owl as they removed the transmitters. A total of 52 owls were located across all five forests (at 16 sites two owls responded together to playback) but only the largest forest, Alcoy, contained enough transects for analyses of habitat in relation to owl distribution. Alcoy stands on steep-sided hills and some planting of exotic species occurs within it. Owls were detected in forest interior, forest edge and forest-plantation mix in Alcoy, and on ridges and in gullies despite lower tree densities and greater proximity to clearings in the gullies. However, parts of Alcoy experience strong winds, and owl occupancy decreased significantly with increasing wind speed. Home ranges for the 10 radio-tagged owls were estimated to cover ∼10 ha, although given the short tracking periods this may be an underestimate. Suitable forest studied covers roughly 1,670 ha, with six unstudied forests totalling 250 ha, so assuming a pair every 10 ha would give a tentative global population estimate of ∼ 200 pairs of Cebu Hawk-owls, and even fewer if home ranges are larger than estimated. This, coupled with continuing habitat degradation, triggers the IUCN Red List category ‘Endangered’. Tree cavities suitable for nests may be limiting, and nest-box provision could be explored, provided this does not increase predator pressure on other rare species.
To investigate nutrition literacy among adult grocery buyers regarding energy-related labelling terms on food packaging.
Qualitative interviews and quantitative surveys to determine shoppers’ understanding of energy terms (‘energy’, ‘calories’ and ‘kilojoules’) and how energy terms affect perceptions of healthiness and intentions to purchase breakfast cereals, muesli bars and frozen meals.
Individual in-depth interviews and surveys in two metropolitan supermarkets, Sydney, Australia.
Australian adults (interview n 40, survey n 405) aged 18–79 years.
The relationship between energy and perceived healthiness of food varied by product type: higher energy breakfast cereals were perceived to be healthier, while lower energy frozen meals were seen as healthier choices. Likewise, intentions to purchase the higher energy product varied according to product type. The primary reason stated for purchasing higher energy products was for sustained energy. Participants from households of lower socio-economic status were significantly more likely to perceive higher energy products as healthier. From the qualitative interviews, participants expressed uncertainty about their understanding of kilojoules, while only 40 % of participants in intercept surveys correctly answered that kilojoules and calories measured the same thing.
Australian consumers have a poor understanding of energy and kilojoules and tend to perceive higher energy products as healthier and providing sustained energy. This has implications regarding the usefulness of industry front-of-pack labelling initiatives and quick service restaurant menu labelling that provides information on energy content only. Comprehensive and widely communicated education campaigns will be essential to guide consumers towards healthier choices.
Although hospital-acquired infections appear to be a growing threat to the survival of newborns in the developing world, the epidemiology of this problem remains poorly characterized.
During a 10-month period, we conducted prospective longitudinal surveillance for colonization and bloodstream infection caused by gram-negative rods among all infants hospitalized in the 2 largest neonatal intensive care units in Manila, the Philippines. We determined antibiotic susceptibilities and calculated adjusted odds ratios for risk factors for bacteremia by means of multivariate logistic regression.
Of 1,831 neonates enrolled during a 10-month period, 1,017 (55.5%) became newly colonized and 358 (19.6%) became bacteremic with a drug-resistant gram-negative rod, most commonly Klebsiella species, Enterobacter species, Acinetobacter species, and Pseudomonas aeruginosa. Of the invasive isolates, 20% were resistant to imipenem, 41% to trimethoprim-sulfamethoxazole, 52% to amikacin, 63% to ampicillin-sulbactam, 67% to ceftazidime, and 80% to tobramycin. The factors significantly associated with an increased risk of bacteremia were mechanical ventilation and prematurity. Additionally, colonization with a drug-resistant gram-negative rod was an independent risk factor for bacteremia (odds ratio, 1.4 [95% confidence interval, 1.0-1.9]).
Colonization with a drug-resistant gram-negative rod was an independent risk factor for sepsis. If our data are typical, the unusually high intensity of colonization pressure and disease caused by multidrug-resistant gram-negative rods at these 2 neonatal intensive care units indicates an emerging healthcare crisis in the developing world. Improved infection control methods are therefore critically needed in developing countries.
This article describes the testing of a model that proposes that people's beliefs regarding the effectiveness of hazard preparedness interact with social context factors (community participation, collective efficacy, empowerment and trust) to influence levels of hazard preparedness. Using data obtained from people living in coastal communities in Alaska and Oregon that are susceptible to experiencing tsunami, structural equation modelling analyses confirmed the ability of the model to help account for differences in levels of tsunami preparedness. Analysis revealed that community members and civic agencies influence preparedness in ways that are independent of the information provided per se. The model suggests that, to encourage people to prepare, outreach strategies must (a) encourage community members to discuss tsunami hazard issues and to identify the resources and information they need to deal with the consequences a tsunami would pose for them and (b) ensure that the community-agency relationship is complementary and empowering.
Objective: To expand upon the existing psychometric properties of the Comprehensive Assessment of Prospective Memory (CAPM) for use with adults with traumatic brain injury by examining concurrent and criterion validity. Method: Participants were 45 adults with a traumatic brain injury. Participants and their relatives completed Section A of the CAPM and a measure of psychosocial integration. Participants were also administered two neuropsychological tests of prospective memory, the Cambridge Prospective Memory Test (CAM-PROMPT) and the Memory Intentions Screening Test (MIST). Concurrent validity was measured by comparing scores on the CAPM with scores on the CAM-PROMPT and MIST. Criterion validity was examined by correlating CAPM scores with level of psychosocial integration. Results: Participant self-reports on the CAPM were not significantly correlated with the CAM-PROMPT or MIST, but were significantly correlated with level of psychosocial integration. Relative reports on the CAPM were correlated significantly with total score on the MIST and CAM-PROMPT and level of psychological integration. Conclusions: The findings indicate that the concurrent validity of the self-report version of CAPM is low suggesting that self-reports alone do not provide an objective measure for assessing prospective memory function. The relative report version however, demonstrated reasonable concurrent and criterion validity, suggesting that the relative report version of the Section A of the CAPM is a useful means of evaluating frequency of prospective memory failure in adults with traumatic brain injury.
Background: Few smoking cessation interventions have made extensive use of e-mail. Objective: This study set out to document how the e-mail component of an e-mail-based smoking cessation program was received by college smokers. Methods: Participants were randomised after enrolment to receive either a moderately intensive, e-mail-based intervention — the X-Pack Group — or a less intensive program based on a widely available smoking cessation guidebook. Participants were assessed at baseline and 3 months post-enrolment. This analysis is limited to those in the X-Pack Group (n = 48). Results: Twelve e-mails on average were sent out to each participant over the course of 6 months. Ninety-one per cent of participants reported reading all or most of the e-mails and 73% replied to at least one of the e-mails they received. On average, participants were positive about the e-mails received and most reported that they had liked the e-mails because of the social support and encouragement provided. The average time for counsellors to write and send each e-mail from the templates was 12 minutes, with a range from 2 to 60 minutes. Conclusions: These findings offer evidence of feasibility of an e-mail-based smoking cessation intervention in a college population.
Previous studies have established that prospective memory is commonly affected following traumatic brain injury (TBI). This study examines whether demographic factors, injury severity and site, executive function, and metacognitive factors predict prospective memory performance in adults with TBI, using a cross-sectional multivariate correlational model. Prospective memory of 44 adults (mean age = 30 years) with severe TBI was measured by the Cambridge Prospective Memory Test (CAMPROMPT) time-based and event-based scores. Using stepwise multiple regression, the time-based score was predicted by the Controlled Oral Word Association Test (COWAT) Animals subtest score, length of post-traumatic amnesia (PTA) and use of note-taking on the CAMPROMPT. The event-based score was predicted by length of PTA and COWAT Animals score. Therefore, patients with longer periods of PTA and executive function impairment may be expected to display poorer prospective memory. Note-taking was associated with improved performance on time-based prospective memory tasks. (JINS, 2008, 14, 823–831.)