81 research outputs found
Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing
Dengue virus is an emerging infectious agent that infects an estimated 50–100 million people annually worldwide, yet current diagnostic practices cannot detect an etiologic pathogen in ∼40% of dengue-like illnesses. Metagenomic approaches to pathogen detection, such as viral microarrays and deep sequencing, are promising tools to address emerging and non-diagnosable disease challenges. In this study, we used the Virochip microarray and deep sequencing to characterize the spectrum of viruses present in human sera from 123 Nicaraguan patients presenting with dengue-like symptoms but testing negative for dengue virus. We utilized a barcoding strategy to simultaneously deep sequence multiple serum specimens, generating on average over 1 million reads per sample. We then implemented a stepwise bioinformatic filtering pipeline to remove the majority of human and low-quality sequences to improve the speed and accuracy of subsequent unbiased database searches. By deep sequencing, we were able to detect virus sequence in 37% (45/123) of previously negative cases. These included 13 cases with Human Herpesvirus 6 sequences. Other samples contained sequences with similarity to sequences from viruses in the Herpesviridae, Flaviviridae, Circoviridae, Anelloviridae, Asfarviridae, and Parvoviridae families. In some cases, the putative viral sequences were virtually identical to known viruses, and in others they diverged, suggesting that they may derive from novel viruses. These results demonstrate the utility of unbiased metagenomic approaches in the detection of known and divergent viruses in the study of tropical febrile illness
Effects of fluoxetine on functional outcomes after acute stroke (FOCUS): a pragmatic, double-blind, randomised, controlled trial
Background
Results of small trials indicate that fluoxetine might improve functional outcomes after stroke. The FOCUS trial aimed to provide a precise estimate of these effects.
Methods
FOCUS was a pragmatic, multicentre, parallel group, double-blind, randomised, placebo-controlled trial done at 103 hospitals in the UK. Patients were eligible if they were aged 18 years or older, had a clinical stroke diagnosis, were enrolled and randomly assigned between 2 days and 15 days after onset, and had focal neurological deficits. Patients were randomly allocated fluoxetine 20 mg or matching placebo orally once daily for 6 months via a web-based system by use of a minimisation algorithm. The primary outcome was functional status, measured with the modified Rankin Scale (mRS), at 6 months. Patients, carers, health-care staff, and the trial team were masked to treatment allocation. Functional status was assessed at 6 months and 12 months after randomisation. Patients were analysed according to their treatment allocation. This trial is registered with the ISRCTN registry, number ISRCTN83290762.
Findings
Between Sept 10, 2012, and March 31, 2017, 3127 patients were recruited. 1564 patients were allocated fluoxetine and 1563 allocated placebo. mRS data at 6 months were available for 1553 (99·3%) patients in each treatment group. The distribution across mRS categories at 6 months was similar in the fluoxetine and placebo groups (common odds ratio adjusted for minimisation variables 0·951 [95% CI 0·839–1·079]; p=0·439). Patients allocated fluoxetine were less likely than those allocated placebo to develop new depression by 6 months (210 [13·43%] patients vs 269 [17·21%]; difference 3·78% [95% CI 1·26–6·30]; p=0·0033), but they had more bone fractures (45 [2·88%] vs 23 [1·47%]; difference 1·41% [95% CI 0·38–2·43]; p=0·0070). There were no significant differences in any other event at 6 or 12 months.
Interpretation
Fluoxetine 20 mg given daily for 6 months after acute stroke does not seem to improve functional outcomes. Although the treatment reduced the occurrence of depression, it increased the frequency of bone fractures. These results do not support the routine use of fluoxetine either for the prevention of post-stroke depression or to promote recovery of function.
Funding
UK Stroke Association and NIHR Health Technology Assessment Programme
Seasonal simulation of water, salinity and nitrate dynamics under drip irrigated mandarin (Citrus reticulata) and assessing management options for drainage and nitrate leaching
Abstract not availableV. Phogat, M.A. Skewes, J.W. Cox, G. Sanderson, J. Alam, J. Šimune
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Seasonal simulation of water, salinity and nitrate dynamics under drip irrigated mandarin (Citrus reticulata) and assessing management options for drainage and nitrate leaching
Estimation of all water fluxes temporally and spatially within and out of the crop root zone, and evaluation of issues like salinity and nutrient leaching, are necessary to fully appraise the efficiency of irrigation systems. Simulation models can be used to investigate these issues over several seasons when the cost of long term monitoring is prohibitive. Model results can be used to advise growers if improvements are required to various aspects of irrigation system operations. In this study, HYDRUS-2D was used to evaluate data measured during one season in a young mandarin ( Citrus reticulata) orchard, irrigated with an intensive surface drip fertigation system. Water contents, salinities, and nitrate concentrations measured weekly in the field were compared with model predictions.The temporal mean absolute error (MAE) values between weekly measured and simulated water contents ranged from 0.01 to 0.04cm3cm-3. However, modelling error (MAE) was slightly larger at 10cm depth (0.04cm3cm-3), as compared to greater depths (0.02-0.03cm3cm-3). Similarly, the errors were larger in the surface soil layer (25cmdepth) for nitrate-nitrogen, NO3--N (1.52mmol(c)L-1), as compared to greater depths. The spatial and temporal soil solution salinity (ECsw) and NO3--N data showed accumulation of salts and nitrate within the soil up until day 150 of the simulation (December, 2006), followed by leaching due to high precipitation and over irrigation at later times. Only 49% of applied water was used by the mandarin trees, while 33.5% was leached. On the other hand, the simulation revealed that a significant amount of applied nitrogen (85%) was taken up by the mandarin trees, and the remaining 15% was leached. The results indicate that the irrigation and fertigation schedule needs modifying as there was overwatering from December onwards.Different permutations and combinations of irrigation and fertigation scheduling were evaluated to optimise the water and nitrogen uptake and to reduce their leaching out of the crop root zone. Slightly higher nitrogen uptake (1.73kgha-1) was recorded when fertigation was applied second to last hour in an irrigation event, as compared to applying it earlier during an irrigation event. Similarly, a 20% reduction in irrigation and N application produced a pronounced reduction in drainage (28%) and N leaching (46.4%), but it also decreased plant N uptake by 15.8% and water uptake by 4.8%, and increased salinity by 25.8%, as compared to the normal practice. This management would adversely impact the sustainability of this expensive irrigation system. However, reducing only irrigation by 30% during the 2nd half of the crop season (January to August) reduced drainage and N leaching by 37.2% and 50.5%, respectively, and increased N uptake by 6.9%. Such management of irrigation would be quite promising for the sustainability of the entire system. It is concluded that judicious manipulations of irrigation and fertilizer applications can be helpful in designing drip irrigation schedules for perennial horticultural crops to achieve improved efficiency of irrigation and fertigation applications and reduced contamination of receiving water bodies. © 2014 Elsevier B.V
Recommended from our members
Seasonal simulation of water, salinity and nitrate dynamics under drip irrigated mandarin (Citrus reticulata) and assessing management options for drainage and nitrate leaching
Estimation of all water fluxes temporally and spatially within and out of the crop root zone, and evaluation of issues like salinity and nutrient leaching, are necessary to fully appraise the efficiency of irrigation systems. Simulation models can be used to investigate these issues over several seasons when the cost of long term monitoring is prohibitive. Model results can be used to advise growers if improvements are required to various aspects of irrigation system operations. In this study, HYDRUS-2D was used to evaluate data measured during one season in a young mandarin ( Citrus reticulata) orchard, irrigated with an intensive surface drip fertigation system. Water contents, salinities, and nitrate concentrations measured weekly in the field were compared with model predictions.The temporal mean absolute error (MAE) values between weekly measured and simulated water contents ranged from 0.01 to 0.04cm3cm-3. However, modelling error (MAE) was slightly larger at 10cm depth (0.04cm3cm-3), as compared to greater depths (0.02-0.03cm3cm-3). Similarly, the errors were larger in the surface soil layer (25cmdepth) for nitrate-nitrogen, NO3--N (1.52mmol(c)L-1), as compared to greater depths. The spatial and temporal soil solution salinity (ECsw) and NO3--N data showed accumulation of salts and nitrate within the soil up until day 150 of the simulation (December, 2006), followed by leaching due to high precipitation and over irrigation at later times. Only 49% of applied water was used by the mandarin trees, while 33.5% was leached. On the other hand, the simulation revealed that a significant amount of applied nitrogen (85%) was taken up by the mandarin trees, and the remaining 15% was leached. The results indicate that the irrigation and fertigation schedule needs modifying as there was overwatering from December onwards.Different permutations and combinations of irrigation and fertigation scheduling were evaluated to optimise the water and nitrogen uptake and to reduce their leaching out of the crop root zone. Slightly higher nitrogen uptake (1.73kgha-1) was recorded when fertigation was applied second to last hour in an irrigation event, as compared to applying it earlier during an irrigation event. Similarly, a 20% reduction in irrigation and N application produced a pronounced reduction in drainage (28%) and N leaching (46.4%), but it also decreased plant N uptake by 15.8% and water uptake by 4.8%, and increased salinity by 25.8%, as compared to the normal practice. This management would adversely impact the sustainability of this expensive irrigation system. However, reducing only irrigation by 30% during the 2nd half of the crop season (January to August) reduced drainage and N leaching by 37.2% and 50.5%, respectively, and increased N uptake by 6.9%. Such management of irrigation would be quite promising for the sustainability of the entire system. It is concluded that judicious manipulations of irrigation and fertilizer applications can be helpful in designing drip irrigation schedules for perennial horticultural crops to achieve improved efficiency of irrigation and fertigation applications and reduced contamination of receiving water bodies. © 2014 Elsevier B.V
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