Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings.

In order to advance precision medicine, detailed clinical features ought to be described in a way that leverages current knowledge. Although data collected from biomedical research is expanding at an almost exponential rate, our ability to transform that information into patient care has not kept at pace. A major barrier preventing this transformation is that multi-dimensional data collection and analysis is usually carried out without much understanding of the underlying knowledge structure. Here, in an effort to bridge this gap, Electronic Health Records (EHRs) of individual patients are connected to a heterogeneous knowledge network called Scalable Precision Medicine Oriented Knowledge Engine (SPOKE). Then an unsupervised machine-learning algorithm creates Propagated SPOKE Entry Vectors (PSEVs) that encode the importance of each SPOKE node for any code in the EHRs. We argue that these results, alongside the natural integration of PSEVs into any EHR machine-learning platform, provide a key step toward precision medicine

A proteomic analysis of drought stress in barley (hordeum vulgare)

Drought is a major threat to world agriculture. In order to identify proteins associated with plant drought tolerance, barley varieties bred in the UK (Golden Promise) and Iraq (Basrah) were compared. The variety Basrah showed physiological adaptations to drought when compared to Golden Promise, for example relative water content after one week of drought was much higher for Basrah than for Golden Promise in the leaves as well as the roots. Also the water loss rate was significantly different between the two varieties, with the Basrah variety loosing water at about half the rate of Golden Promise. DIGE analyses were carried out on proteins from roots and leaves under control and drought conditions. 24 leaf and 45 root proteins were identified by MALDI-TOF MS spectrometry. The relative expression patterns of the identified proteins fell into a number of distinct classes. The variety Basrah is characterised by constitutive expression or higher drought-induced expression levels of proteins regulating ROS production and protein folding. Photosynthetic enzymes, by contrast, were downregulated in Basrah. Enzyme assays showed a good correlation between DIGE-derived protein abundance estimates and enzyme activity in extracts. Overall this study shows that the enhanced drought tolerance of variety Basrah is driven by an enhanced regulation of ROS under drought. A number of transcription factors with enhanced expression in Basrah under drought conditions were also identified; it is hypothesised that these may contribute to the drought tolerant phenotype and thus make interesting targets for barley breeding experiments.Scotch Whisky Associatio

The Effects of Combined Movement and Storytelling Intervention on Motor Skills in South Asian and White Children Aged 5–6 Years Living in the United Kingdom

Early motor development has an important role in promoting physical activity (PA) during childhood and across the lifespan. Children from South Asian backgrounds are less active and have poorer motor skills, thus identifying the need for early motor skill instruction. This study examines the effect of a movement and storytelling intervention on South Asian children’s motor skills. Following ethics approval and consent, 39 children (46% South Asian) participated in a 12-week movement and storytelling intervention. Pre and post, seven motor skills (run, jump, throw, catch, stationary dribble, roll, and kick) were assessed using Children’s Activity and Movement in Preschool Study protocol. At baseline, South Asian children had poorer performance of motor skills. Following the intervention, all children improved their motor skills, with a bigger improvement observed for South Asian children. Early intervention provided remedial benefits to delays in motor skills and narrowed the motor skills gap in ethnic groups

The social care needs of people affected by cancer: a qualitative study in Lincolnshire

Background People affected by cancer (PABC) can have a range of social care needs at different stages of the patient pathway. These may include emotional, practical, personal, as well as information and financial needs. The UK charity, Macmillan Cancer Support want to refocus their current social care provision and, (where need is evidenced) develop new services to better address the social care needs of PABC in Lincolnshire. In order to do this effectively Macmillan together with the Bromhead Medical Charity has commissioned the University of Lincoln to undertake this research, with a view to developing a thorough understanding of the needs of PABC in Lincolnshire to ensure that service developments are acceptable, appropriate and accessible, and in line with the specific requirements of the local population. Aim (1)To examine the social care needs of PABC in Lincolnshire (2)To provide recommendations regarding future service development and delivery. Methods A qualitative study utilising in-depth interviews (n=10). Interviews were analysed using the Framework method of qualitative data analysis (Ritchie and Spencer, 1994). Results All reported the need for emotional support (in particular around the initial diagnosis and surrounding period). This was fulfilled by friends, family, support groups and Macmillan health professionals. The need for practical and personal care support varied amongst those we interviewed with this often being dependent on the type and frequency of treatment. For most, family and friends shouldered the burden of this as opposed to social services. Some participants relied on personal income to pay for treatment and fund additional costs associated with their illness. Furthermore, expenses were also attributed to friends and family of the patient. In addition we received reports of negative experiences when dealing with the Department of Work and Pensions (DWP) and claiming for Employment Support Allowance (ESA). Information and advice was important throughout the cancer journey; the preferred format (physical or online) was influenced by personal preference. For some, they felt well informed whilst others would have liked more information. Conclusion In line with national research (Macmillan, 2015), this study shows similarities in that respondents reported a range of supportive care needs in relation to emotional, practical and personal, financial and information support. Our study offers an in-depth analysis of the social care needs of PABC in a local setting. The small sample and failure to recruit across all stages of the cancer journey would limit the extent to which the findings could be extrapolated to the wider population. At the same time, it is hoped that the recommendations offer valuable insight into areas that could further be developed to meet the needs of PABC throughout the count

Water quality effects of intermittent water supply in Arraiján, Panama

Intermittent drinking water supply is common in low- and middle-income countries throughout the world and can cause waterquality to degrade in the distribution system.In this study,we characterized waterquality in one study zone with continuous supply and three zoneswith intermittentsupply in the drinking waterdistribution network in Arraija!n,Panama.Low orzero pressuresoccurred in allzones,and negative pressuresoccurred in the continuouszone and two ofthe intermittentzones.Despite hydraulic conditions that created risks for backflow and contaminant intrusion, only four of 423 (0.9%) grab samplescollected atrandom timeswere positive fortotalcoliform bacteria and only one waspositive for E.coli.Only nine of 496 (1.8%) samples had turbidity >1.0 NTU and all samples had !0.2 mg/L free chlorine residual.In contrast,water quality was often degraded during the first-flush period (when supply first returned after an outage).Still, routine and first-flush water quality under intermittent supply was much better in Arraija!n than that reported in a previous study conducted in India.Better waterquality in Arraija!n could be due to betterwaterquality leaving the treatmentplant,shortersupply outages,highersupply pressures,a more consistentand higherchlorine residual,and fewercontaminant sourcesnearpipes.The resultsillustrate thatintermittentsupply and itseffectson waterquality can vary greatly between and within distribution networks.The study also demonstrated thatmonitoring techniques designed specifically for intermittentsupply,such as continuous pressure monitoring and sampling the firstflush,can detectwaterquality threats and degradation thatwould notlikely be detected with conventionalmonitoring.Intermittent drinking water supply is common in low- and middle-income countries throughout the world and can cause waterquality to degrade in the distribution system.In this study,we characterized waterquality in one study zone with continuous supply and three zoneswith intermittentsupply in the drinking waterdistribution network in Arraija!n,Panama.Low orzero pressuresoccurred in allzones,and negative pressuresoccurred in the continuouszone and two ofthe intermittentzones.Despite hydraulic conditions that created risks for backflow and contaminant intrusion, only four of 423 (0.9%) grab samplescollected atrandom timeswere positive fortotalcoliform bacteria and only one waspositive for E.coli.Only nine of 496 (1.8%) samples had turbidity >1.0 NTU and all samples had !0.2 mg/L free chlorine residual.In contrast,water quality was often degraded during the first-flush period (when supply first returned after an outage).Still, routine and first-flush water quality under intermittent supply was much better in Arraija!n than that reported in a previous study conducted in India.Better waterquality in Arraija!n could be due to betterwaterquality leaving the treatmentplant,shortersupply outages,highersupply pressures,a more consistentand higherchlorine residual,and fewercontaminant sourcesnearpipes.The resultsillustrate thatintermittentsupply and itseffectson waterquality can vary greatly between and within distribution networks.The study also demonstrated thatmonitoring techniques designed specifically for intermittentsupply,such as continuous pressure monitoring and sampling the firstflush,can detectwaterquality threats and degradation thatwould notlikely be detected with conventionalmonitoring

GIS interfaced OECD/PIARC QRA model for road transportation of hazardous goods

International audienceWithin the framework of a research project carried out for both the OECD and the PIARC, INERIS developed a Quantitative Risk Assessment Model (QRA model) for the transport of Hazardous Goods on roads including tunnel sections. This work was also carried out with the collaboration of WS-Atkins (UK) and the University of Waterloo (Canada). INERIS, which was the leading developer of this original model, launched a new research project in order to facilitate the generation of data necessary for a given risk study. A new version of the model is in development. These new developments have been funded by the French Ministry of Ecology and Sustainable Growth and the French Ministry of Equipment, Transport and Buildings, Tourism and the Sea. These new developments have been processed in order to enhance the user-interface performance of the original models (QRAM 3.20 and 3.60) and to extend the QRAM capacities to the study of longer routes. These objectives has been reached by the introduction of a linked Geographical Information System (GIS). In between the original model (QRA v3.20) has been used for the application of the French regulation (circular 2000-82, 30th november 2000). Up to now approximately twenty tunnel safety cases have been studied in order to choose the lowest risky route between the open air route and the tunnel one. Doing that the risk level for the road transportation of hazardous goods has been reduced. In order to have in one hand a global view of the various developments of the QRAM and in an other hand to linked these models to the European regulation framework the present paper deals with the following topics : The present regulation for the transport of dangerous goods by road in Europe, The methodology governing the QRAM, The lessons from the French application of the QRAM, The new developments for a GIS interfaced QRAM, The application of the QRAM at European and International level

Imaging the Developing Heart: Synchronized Timelapse Microscopy During Developmental Changes

How do you use imaging to analyse the development of the heart, which not only changes shape but also undergoes constant, high-speed, quasi-periodic changes? We have integrated ideas from prospective and retrospective optical gating to capture long-term, phase-locked developmental time-lapse videos. In this paper we demonstrate the success of this approach over a key developmental time period: heart looping, where large changes in heart shape prevent previous prospective gating approaches from capturing phase-locked videos. We use the comparison with other approaches to in vivo heart imaging to highlight the importance of collecting the most appropriate data for the biological question.Comment: Carl J. Nelson and Charlotte Buckley and John J. Mullins and Martin A. Denvir and Jonathan Taylor, "Imaging the Developing Heart: Synchronized Timelapse Microscopy During Developmental Changes", Proc. SPIE (10499), 10499-41 (2018). Copyright 2018 Society of Photo Optical Instrumentation Engineers (SPIE

The influence of left ventricular hypertrophyon survival in patients with coronaryartery disease: do race and gender matter?

AbstractObjectivesWe sought to determine the overall prognostic importance of left ventricular hypertrophy (LVH) among patients with coronary artery disease (CAD), as well as to determine whether this risk varies as a function of race or gender.BackgroundLeft ventricular hypertrophy is more prevalent among blacks and women than their counterparts. Blacks and women also have higher mortality with coronary disease.MethodsWe studied records of 2,461 patients (19% black, 42% women) diagnosed with CAD at cardiac catheterization between 1990 and 1998 from a single academic center. Left ventricular hypertrophy was defined using standard echocardiographic measures. Cox proportional hazards models were used for adjusted survival analyses. Mean patient follow-up was three years.ResultsPatients with LVH were older (68 vs. 65 years, p < 0.01), more often women (54% vs. 36%, p < 0.01), and black (25% vs. 16%, p < 0.01), and had higher unadjusted three-year mortality rates than patients without LVH (42% vs. 34%, p < 0.01). Left ventricular hypertrophy remained an independent predictor of mortality after adjusting for other clinical risk factors (hazard ratio 1.56, 95% confidence interval 1.35 to 1.80) with prognostic importance equivalent to that of left ventricular ejection fraction. Although the relative risk of LVH did not vary by race or gender, the attributable risk of LVH was greater in blacks and women.ConclusionsClinicians should consider the prognostic importance of LVH when assessing risk in patients with CAD. Because LVH is more common among black and women patients with CAD, it partially accounts for racial and gender differences in survival

Experiencing the double-edged sword of desegregation: Charlotte-Mecklenburg school graduates from 1995--1998

The purpose of this study is to gain insight into the long-term effects of desegregated schooling within a firmly established K-12th grade desegregated school system. Long-term outcomes include: educational and occupational attainment, comfort with diverse individuals, positive attitudes towards race relations, sense of civic engagement, and increased interaction with other racial groups (such as living and working in diverse environments). Previous studies have examined the long-term outcomes of desegregated schooling for graduates who attended desegregated high schools, yet these students attended segregated schools from K-9th grade. Charlotte-Mecklenburg Schools were desegregated from roughly 1975-2002, when its mandatory court order was lifted. This study examines experiences of graduates from 1995-1998, a cohort of students who attended desegregated schools from K-12th grade. This dissertation conducted a comparative case study analysis of a racially desegregated school, racially identifiable White school, and racially identifiable Black school. In 1997, Independence High School was racially desegregated at the school level, with the school demographics mirroring the greater Charlotte community. In contrast, Garinger High School was racially segregated Black, while North Mecklenburg High School was racially segregated White. This dissertation focuses on graduates of three schools and seeks to answer the following general question: How do graduates of Independence High School, Garinger High School, and North Mecklenburg High School from 1995-1998 describe and make sense of their schooling experiences, particularly in regards to interracial contact, racial identity development and diverse understandings of greater society? From this overarching question stem several subsidiary questions: (1) Were there differences in long-term outcomes of graduates between the three schools? (2) Were graduates aware that Charlotte-Mecklenburg Schools were under a court-ordered desegregation plan during their years of schooling? Did graduates see themselves as part of a segregated or desegregated school? (3) Did the racial composition and organizational structure of schools affect opportunities for interracial contact and racial identity development? (4) Did experiences with desegregated schooling lead students to develop a greater sensitivity to the complexities of race and social class as adults? This study utilizes critical theory as a general theoretical lens and focuses specifically on racial identity development theory to better understand the experiences of graduates. Qualitative and quantitative data are used to present a holistic view of the three schools. An overall context of the schooling experience is described using an existing quantitative dataset collected in 1997, and yearbook analysis provides information regarding opportunities for interracial contact in each school. A revised version of the Diversity Assessment Questionnaire (Civil Rights Project, 2001) was distributed to research participants to determine the long-term outcomes of individual high school experiences. From these surveys, a representative sample of twelve graduates per school, for a total of 36, were selected for in-depth interviews. Results indicate that individuals did experience desegregation in dramatically different ways based on the racial composition of their school, with the racially desegregated school and the racially isolated Black school having more positive outcomes than the racially isolated White school. Graduates of all schools were unclear regarding the definition of desegregation and the majority of graduates did not know they attended schools under a court-mandated desegregation plan. Results indicate that desegregation efforts in Charlotte, NC had countless intended and unintended consequences and as such were perceived in dramatically different ways by graduates. Collectively, desegregation provided a positive experience with long-lasting positive outcomes for graduates