Accelerating root system phenotyping of seedlings through a computer-assisted processing pipeline

Background: There are numerous systems and techniques to measure the growth of plant roots. However, phenotyping large numbers of plant roots for breeding and genetic analyses remains challenging. One major difficulty is to achieve high throughput and resolution at a reasonable cost per plant sample. Here we describe a cost-effective root phenotyping pipeline, on which we perform time and accuracy benchmarking to identify bottlenecks in such pipelines and strategies for their acceleration. Results: Our root phenotyping pipeline was assembled with custom software and low cost material and equipment. Results show that sample preparation and handling of samples during screening are the most time consuming task in root phenotyping. Algorithms can be used to speed up the extraction of root traits from image data, but when applied to large numbers of images, there is a trade-off between time of processing the data and errors contained in the database. Conclusions: Scaling-up root phenotyping to large numbers of genotypes will require not only automation of sample preparation and sample handling, but also efficient algorithms for error detection for more reliable replacement of manual interventions

Dying at home in Belgium: a descriptive GP interview study

<p>Abstract</p> <p>Background</p> <p>While increasing attention is being paid to enabling terminal patients to remain at home until death, limited information is available on the circumstances in which people at home actually die. Therefore this study aims to describe patient characteristics, functional and cognitive status and physical and psychological symptom burden in the last three months of life among Belgian patients dying at home, according to their GPs.</p> <p>Methods</p> <p>In 2005, a nationwide and retrospective interview study with GPs took place on people dying at home in Belgium as reported by Sentinel Network of GPs in Belgium. GPs registered all deaths (patients aged 1 year or more) weekly and were interviewed about all patients dying non-suddenly at home, using face-to-face structured interviews.</p> <p>Results</p> <p>Interviews were obtained on 205 patients (90% response rate). Between the second and third month before death, 55% were fully invalid or limited in self-care. In the last week of life, almost all were fully invalid. Fifty four percent were unconscious at some point during the last week; 46% were fully conscious. Most frequently reported symptoms were lack of energy, lack of appetite and feeling drowsy. Conditions most difficult for GPs to manage were shortness of breath, lack of energy and pain.</p> <p>Conclusions</p> <p>Many people dying at home under the care of their GPs in Belgium function relatively well until the last week of life and cognitive status seems to be preserved until the end in many cases. However, symptoms which GPs find difficult to control still manifest in many patients in the final week of life.</p

Hospitalisations at the end of life: using a sentinel surveillance network to study hospital use and associated patient, disease and healthcare factors

<p>Abstract</p> <p>Background</p> <p>Hospital deaths following several hospital admissions or long hospital stays may be indicative of a low quality of dying. Although place of death has been extensively investigated at population level, hospital use in the last months of life and its determinants have been studied less often, especially in Europe and with a general end-of-life patient population. In this study we aim to describe hospital use in the last three months of life in Belgium and identify associated patient, disease and healthcare factors.</p> <p>Methods</p> <p>We conducted a retrospective registration study (13 weeks in 2004) with the Belgian Sentinel Network of General Practitioners, an epidemiological surveillance system representative of all GPs in Belgium, covering 1.75% of the total Belgian patient population. All registered non-sudden or expected deaths of patients (aged one year or older) at the GPs' practices were included. Bivariate and regression analyses were performed.</p> <p>Results</p> <p>The response rate was 87%. The GPs registered 319 deaths that met inclusion criteria. Sixty percent had been hospitalised at least once in the last three months of life, for a median of 19 days. The percentage of patients hospitalised increased exponentially in the last weeks before death; one fifth was admitted in the final week of life. Seventy-two percent of patients hospitalised at least once in the final three months died in hospital. A palliative treatment goal, death from cardiovascular diseases, the expression of a wish to die in an elderly home and palliative care delivery by the GP were associated with lower hospitalisation odds.</p> <p>Conclusion</p> <p>Hospital care plays a large role in the end of patients' lives in Belgium, especially in the final weeks of life. The result is a high rate of hospital deaths, showing the institutionalised nature of dying. Patients' clinical conditions, the expression of preferences and also healthcare characteristics such as being treated as a palliative care patient, seem to be associated with hospital transfers. It is recommended that hospitalisation decisions are only made after careful consideration. Short admissions in the final days of life should be prevented in order to make dying at home more feasible.</p

Euthanasia and other end-of-life decisions: a mortality follow-back study in Belgium

BACKGROUND: This study compares prevalence and types of medical end-of-life decisions between the Dutch-speaking and French-speaking communities of Belgium. This is the first nationwide study that can make these comparisons and the first measurement after implementation of the euthanasia law (2002). METHODS: We performed a mortality follow-back study in 2005-2006. Data were collected via the nationwide Sentinel Network of General Practitioners, an epidemiological surveillance system representative of all Belgian GPs.Weekly, all GPs reported the medical end-of-life decisions among all non-sudden deaths of patients in their practice. We compared the northern Dutch-speaking (60%) and southern French-speaking communities (40%) controlling for population differences. RESULTS: We analysed 1690 non-sudden deaths. An end-of-life decision with possible life-shortening effect was made in 50% of patients in the Dutch-speaking community and 41% of patients in the French-speaking community (OR 1.4; 95%CI, 1.2 to 1.8). Continuous deep sedation until death occurred in 8% and 15% respectively (OR 0.5; 95%CI, 0.4 to 0.7). Community differences regarding the prevalence of euthanasia or physician-assisted suicide were not significant.Community differences were more present among home/care home than among hospital deaths: non-treatment decisions with explicit life-shortening intention were made more often in the Dutch-speaking than in the French-speaking community settings (OR 2.2; 95%CI, 1.2 to 3.9); while continuous deep sedation occurred less often in the Dutch-speaking community settings (OR 0.5; 95%CI, 0.3 to 0.9). CONCLUSION: Even though legal and general healthcare systems are the same for the whole country, there are considerable variations between the communities in type and prevalence of certain end-of-life decisions, even after controlling for population difference

Nationwide monitoring of end-of-life care via the Sentinel Network of General Practitioners in Belgium: the research protocol of the SENTI-MELC study

<p>Abstract</p> <p>Background</p> <p>End-of-life care has become an issue of great clinical and public health concern. From analyses of official death certificates, we have societal knowledge on how many people die, at what age, where and from what causes. However, we know little about how people are dying. There is a lack of population-based and nationwide data that evaluate and monitor the circumstances of death and the care received in the final months of life. The present study was designed to describe the places of end-of-life care and care transitions, the caregivers involved in patient care and the actual treatments and care provided to dying patients in Belgium. The patient, residence and healthcare characteristics associated with these aspects of end-of-life care provision will also be studied. In this report, the protocol of the study is outlined.</p> <p>Methods/Design</p> <p>We designed a nationwide mortality follow-back study with data collection in 2005 and 2006, via the nationwide Belgian Sentinel Network of General Practitioners (GPs) i.e. an existing epidemiological surveillance system representative of all GPs in Belgium, covering 1.75% of the total Belgian population. All GPs were asked to report weekly, on a standardized registration form, every patient (>1 year) in their practice who had died, and to identify patients who had died "non-suddenly." The last three months of these patients' lives were surveyed retrospectively. Several quality control measures were used to ensure data of high scientific quality.</p> <p>Discussion</p> <p>In 2005 and 2006, respectively 1385 and 1305 deaths were identified of which 66% and 63% died non-suddenly. The first results are expected in 2007. Via this study, we will build a descriptive epidemiological database on end-of-life care provision in Belgium, which might serve as baseline measurement to monitor end-of-life care over time. The study will inform medical practice as well as healthcare authorities in setting up an end-of-life care policy. We publish the protocol here to inform others, in particular countries with analogue GP surveillance networks, on the possibilities of performing end-of-life care research. A preliminary analysis of the possible strengths, weaknesses and opportunities of our research is outlined.</p

What determines inclusion in the early phase of the type 2 diabetes care trajectory in Belgium?

In 2009, the Belgian National Institute of Health and Disability Insurance established a care trajectory (CT) for a subgroup of type 2 diabetes mellitus patients (T2DM) based on Wagner's chronic care model. The goal of this CT is to optimise the quality of care using an integrated multidisciplinary approach. This study aims to identify patient-related factors associated with inclusion in a CT and to determine the most frequent reasons for non-inclusion

Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics

Plant root systems are key drivers of plant function and yield. They are also under-explored targets to meet global food and energy demands. Many new technologies have been developed to characterize crop root system architecture (CRSA). These technologies have the potential to accelerate the progress in understanding the genetic control and environmental response of CRSA. Putting this potential into practice requires new methods and algorithms to analyze CRSA in digital images. Most prior approaches have solely focused on the estimation of root traits from images, yet no integrated platform exists that allows easy and intuitive access to trait extraction and analysis methods from images combined with storage solutions linked to metadata. Automated high-throughput phenotyping methods are increasingly used in laboratory-based efforts to link plant genotype with phenotype, whereas similar field-based studies remain predominantly manual low-throughput.DescriptionHere, we present an open-source phenomics platform “DIRT”, as a means to integrate scalable supercomputing architectures into field experiments and analysis pipelines. DIRT is an online platform that enables researchers to store images of plant roots, measure dicot and monocot root traits under field conditions, and share data and results within collaborative teams and the broader community. The DIRT platform seamlessly connects end-users with large-scale compute “commons” enabling the estimation and analysis of root phenotypes from field experiments of unprecedented size.ConclusionDIRT is an automated high-throughput computing and collaboration platform for field based crop root phenomics. The platform is accessible at http://​dirt.​iplantcollaborat​ive.​org/​ and hosted on the iPlant cyber-infrastructure using high-throughput grid computing resources of the Texas Advanced Computing Center (TACC). DIRT is a high volume central depository and high-throughput RSA trait computation platform for plant scientists working on crop roots. It enables scientists to store, manage and share crop root images with metadata and compute RSA traits from thousands of images in parallel. It makes high-throughput RSA trait computation available to the community with just a few button clicks. As such it enables plant scientists to spend more time on science rather than on technology. All stored and computed data is easily accessible to the public and broader scientific community. We hope that easy data accessibility will attract new tool developers and spur creative data usage that may even be applied to other fields of science