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The unmet clinical need for accurate point-of-care (POC) diagnostic tests able to discriminate bacterial from viral infection demands a solution that can be used both within healthcare settings and in the field and that can also stem the tide of antimicrobial resistance. Our approach to solve this problem is to combine the use of Host-gene signatures with our Lab-on-a-chip (LoC) technology enabling low-cost LoC expression analysis to detect Infectious Disease.Host-gene expression signatures have been extensively study as a potential tool to be implemented in the diagnosis of infectious disease. On the other hand LoC technologies using Ion-sensitive field-effect transistor (ISFET) arrays, in conjunction with isothermal chemistries, are offering a promising alternative to conventional lab-based nucleic acid amplification instruments, owing to their portable and affordable nature. Currently, the data analysis of ISFET arrays are restricted to established methods by averaging the output of every sensor to give a single time-series. This simple approach makes unrealistic assumptions, leading to insufficient performance for applications that require accurate quantification such as RNA host transcriptomics. In order to reliably quantify host-gene expression on our LoC platform enabling the classification of bacterial and viral infection on chip, we propose a novel data-driven algorithm for extracting time-to-positive values from ISFET arrays. The algorithm proposed is based on modelling sensor drift with adaptive signal processing and clustering sensors based on their behaviour with unsupervised learning methods. Results show that the approach correctly outputs a time-to-positive for all the reactions, with a high correlation to RT-qLAMP (0.85, R2 = 0.98, p < 0.01), resulting in a classification accuracy of 100 % (CI, 95 - 100). By leveraging more advanced data processing methods for ISFET arrays, this work aims to bridge the gap between translating assays from microarray analysis (expensive lab-based discovery method) to ISFET arrays (cheap point-of-care diagnostics) providing benefits on tackling infectious disease outbreak and diagnostic testing in hard-to-reach areas of the world.

Background: Emergency admissions for infection often lack initial diagnostic certainty. COVID-19 has highlighted a need for novel diagnostic approaches to indicate likelihood of viral infection in a pandemic setting. We sought to derive and validate a blood transcriptional signature to detect viral infections including COVID-19 among adults with suspected infection presenting to the Emergency Department (ED). Methods: Blood RNA sequencing was performed on a discovery cohort of adults attending the ED with suspected infection who had subsequently-confirmed viral, bacterial, or no infection diagnoses. Differentially expressed host genes were subjected to feature selection to derive the most parsimonious discriminating signature. RT-qPCR validation of the signature was then performed in a prospective cohort of ED patients presenting with undifferentiated fever, and a second case-control cohort of ED patients with COVID-19 or bacterial infection. Signature performance was assessed by calculating area under receiver-operating characteristic curves (AUC-ROCs), sensitivities, and specificities. Findings: A 3-gene transcript signature was derived from the discovery cohort of 56 bacterial and 27 viral infection cases. In the validation cohort of 200 cases, the signature differentiated bacterial from viral infections with an AUC-ROC of 0.976 (95% CI: 0.919-1.000), sensitivity 97.3% and specificity of 100%. The AUC-ROC for C-reactive protein (CRP) and leucocyte count (WCC) was 0.833 (95% CI: 0.694-0.944) and 0.938 (95% CI: 0.840-0.986) respectively. The signature achieved higher net benefit in decision curve analysis than either CRP or WCC for discriminating viral infections from all other cases. In the second validation analysis the signature discriminated 35 bacterial infections from 34 SARS-CoV-2 positive COVID-19 infections with AUC-ROC of 0.953 (95% CI: 0.893-0.992), sensitivity 88.6% and specificity of 94.1%. Interpretation: This novel 3-gene signature discriminates viral infections including COVID-19 from other emergency infection presentations in adults, outperforming both WCC and CRP, thus potentially providing significant clinical utility in managing acute presentations with infection.

In recent years agricultural research has developed field practices that promote soil conservation, but how widely are such practices used in Canada? This question has been difficult to answer because no comprehensive inventory of these practices was available. To remedy this, Agriculture and Agri-Food Canada's Centre for Land and Biological Resources Research and the Prairie Farm Rehabilitation Administration (PFRA) worked with the Agricultural Division of Statistics Canada to design a new land management module for the Canada Census of Agriculture. This module was first introduced in the 1991 Census, and results are presented in this report. The objectives of this report are: to record how agricultural land is used and managed in Canada, to produce a study that will serve as a baseline for all subsequent monitoring of land management practices through the census, and to provide information useful for environmental studies of soil and water quality.

This report covers the period from the fall of 1973 to the summer of 1977 during which time a variety of research and monitoring activities were taking place under the auspices of the I.J.C. Pollution from Land Use Activities Reference Group (PLUARG), Task C, Agricultural Watershed Studies. Two distinct studies were undertaken on the topic of the environmental impact of feedlots and manure storages. They were carried out consecutively, the first was concerned with surface water, the second with groundwater. The reports of these two studies are presented in this volume as two separate sections. Only the discussion of implications for remedial measures and the list of references are common to the two studies, and these appear at the end of the document.

Pilot watershed studies were undertaken in six major drainage basins in the Great Lakes basin, in eleven smaller agricultural watersheds in southern Ontario, in one forested watershed area in northern Ontario, west of the Lake Superior basin, and at a few other locations where specific sources of contaminants were evaluated. The pilot watersheds were selected to represent major land use activities, geology, and climatic conditions. Studies were undertaken to determine contaminants being produced from urban, agricultural, and forested land uses and special land-use activities such as orchards, private waste disposal systems, and spray irrigation of municipal sewage effluents. In addition, investigations into the effects of streambank erosion on water quality were conducted in each country. The results of studies of particular land uses and management practices, and pollutant generation, transport and reaction processes are contained in detailed reports by individual investigators or groups of investigators. They are published in either the PLUARG technical report series or as reports of the funding agencies. Combined, they provide a wealth of information on diffuse sources of pollutants and the processes affecting them. To strengthen co-ordination and provide a means for reviewing the major results from the watershed studies, Task C established a Synthesis and Extrapolation Work Group (SEWG) in 1976. The members of the Synthesis and Extrapolation Work Group, supported by the efforts of several investigators who accepted the task of integrating results on agricultural sources of pollutants, prepared this Task C Summary Report. It highlights the findings, shows the range of effects and causes of variations in pollutant loadings, and provides maps showing the results of extrapolation of loading information for suspended sediment, total phosphorus, and total nitrogen contributed by agricultural and urban land uses. In the report, they describe other contaminants such as organic toxicants, metals, and micro-organisms and go on to present principles, factors and practices needed in considering and implementing remedial and preventative measures to reduce diffuse sources of pollutants. Unit area loadings derived for the major land uses and an evaluation of the factors which influence these loads were used in developing the priority management concept discussed in the PLUARG Final Report.

Land used for agriculture makes up one of the largest environmental units managed in Canada today. New technology and genetic improvements to plants and animals have increased farm productivity dramatically over the past three decades. Land management is the main factor that often determines whether the environmental effects of agriculture are positive or negative. Little attention has been paid to the possible environmental consequences of many newly developed, intensified farming activities. Land deterioration and the resulting environmental problems may be difficult to recognize on individual farms because the processes involved are so widely distributed and insidious. When problems are recognized, many people are unaware that anything can be done to rectify them. The agricultural community should take precautions to protect the environment from any degradation arising from its activities. Farmers should act on their own behalf and develop an understanding of the impact that various farming practices can have on the environment. This publication is intended as an introduction to the subject, and readers are encouraged to seek more detailed information related to their own situations from regional specialists. Some agricultural practices can cause water and air pollution and the deterioration of the land. Of these three problems, by far the most well documented is how agriculture can affect water quality. Water pollution is therefore dealt with here in more detail than are the other two topics.

The purpose of this study was to make preliminary estimates of the on-farm and off-farm costs of agricultural land degradation in Atlantic and Central Canada, and British Columbia excluding the Peace Region. The types of degradation examined are water erosion, wind erosion, acidity and soil compaction. The main costs which are estimated are the values of crop yield reductions, added inputs (fertilizers, pesticides, etc.) required to offset physical losses, and reduced crop quality. An attempt is also made to quantify the off- farm damage from agricultural land degradation in the study area. The study was carried out in two parts. The first consisted of a procedure to estimate the location, area and severity of erosion, acidification and compaction within 16 subregions of the study area. Newfoundland, Nova Scotia and Prince Edward Island were each treated as separate subregions. Two subregions were created for New Brunswick , three each for Quebec and British Columbia, and five for Ontario. A large electronic data base of physical soil characteristics and land use in the study area was compiled to which standard 'models' of the degradation processes, expected to be operative in the study area, were applied. This exercise yielded the likely extent, location and severity of degradation in the subregions. The second part consisted of estimating crop yield reductions and other economic costs of soil degradation under each type and class of degradation in each subregion. These estimates were obtained by analysing the opinions of a select group of experts in the provinces covered by the study. Questionnaires, group consensus meetings and telephone follow-ups were employed.

This monograph presents a general qualitative assessment of the kind, location and extent of land degradation in the agricultural regions of Canada. In so doing it establishes an information base from which to consider research needs and priorities related to the quantitative assessment of soil deterioration across the country and the development of land management techniques for combatting it. "Land degradation" is considered to be the process or processes of deterioration of soil edaphic qualities relative to their natural or most productive previous state.

The subject of this report is the "overview" analysis of the monitoring data collected during the 1975-1977 intensive study phase of the Agricultural Watershed Studies. The report outlines the methodology and rational for the selection of suitable monitoring sites, the methods used for water quality and quantity data acquisition, the estimation of watershed characteristics, and the statistical analyses of the variance within the data sets. Finally, some conclusions are drawn which are applied to an extrapolation model which attempts to determine areas of the lower Canadian Great Lakes Basin which fall into selected ranges of pollutant contribution rates to streams. Research Branch, Agriculture Canada Ontario Ministry of Agriculture and Food Ontario Ministry of the Environment