Applications of big data approaches to topics in infectious disease epidemiology

The availability of big data (i.e., a large number of observations and variables per observation) and advancements in statistical methods present numerous exciting opportunities and challenges in infectious disease epidemiology. The studies in this dissertation address questions regarding the epidemiology of dengue and sepsis by applying big data and traditional epidemiologic approaches. In doing so, we aim to advance our understanding of both diseases and to critically evaluate traditional and novel methods to understand how these approaches can be leveraged to improve epidemiologic research. In the first study, we examined the ability of machine learning and regression modeling approaches to predict dengue occurrence in three endemic locations. When we utilized models with historical surveillance, population, and weather data, machine learning models predicted weekly case counts more accurately than regression models. When we removed surveillance data, regression models were more accurate. Furthermore, machine learning models were able to accurately forecast the onset and duration of dengue outbreaks up to 12 weeks in advance without using surveillance data. This study highlighted potential benefits that machine learning models could bring to a dengue early warning system. The second study utilized machine learning approaches to identify the rainfall conditions which lead to mosquito larvae being washed away from breeding sites occurring in roadside storm drains in Singapore. We then used conventional epidemiologic approaches to evaluate how the occurrence of these washout events affect dengue occurrence in subsequent weeks. This study demonstrated an inverse relationship between washout events and dengue outbreak risk. The third study compared algorithmic-based and conventional epidemiologic approaches used to evaluate variables for statistical adjustment. We used these approaches to identify what variables to adjust for when estimating the effect of autoimmune disease on 30-day mortality among ICU patients with sepsis. In this study, autoimmune disease presence was associated with an approximate 10-20% reduction in mortality risk. Risk estimates identified with algorithmic-based approaches were compatible with conventional approaches and did not differ by more than 9%. This study revealed that algorithmic-based approaches can approximate conventional selection methods, and may be useful when the appropriate set of variables to adjust for is unknown

Separator fluid volume requirements in multi-infusion settings

INTRODUCTION. Intravenous (IV) therapy is a widely used method for the administration of medication in hospitals worldwide. ICU and surgical patients in particular often require multiple IV catheters due to incompatibility of certain drugs and the high complexity of medical therapy. This increases discomfort by painful invasive procedures, the risk of infections and costs of medication and disposable considerably. When different drugs are administered through the same lumen, it is common ICU practice to flush with a neutral fluid between the administration of two incompatible drugs in order to optimally use infusion lumens. An important constraint for delivering multiple incompatible drugs is the volume of separator fluid that is sufficient to safely separate them. OBJECTIVES. In this pilot study we investigated whether the choice of separator fluid, solvent, or administration rate affects the separator volume required in a typical ICU infusion setting. METHODS. A standard ICU IV line (2m, 2ml, 1mm internal diameter) was filled with methylene blue (40 mg/l) solution and flushed using an infusion pump with separator fluid. Independent variables were solvent for methylene blue (NaCl 0.9% vs. glucose 5%), separator fluid (NaCl 0.9% vs. glucose 5%), and administration rate (50, 100, or 200 ml/h). Samples were collected using a fraction collector until <2% of the original drug concentration remained and were analyzed using spectrophotometry. RESULTS. We did not find a significant effect of administration rate on separator fluid volume. However, NaCl/G5% (solvent/separator fluid) required significantly less separator fluid than NaCl/NaCl (3.6 ± 0.1 ml vs. 3.9 ± 0.1 ml, p <0.05). Also, G5%/G5% required significantly less separator fluid than NaCl/NaCl (3.6 ± 0.1 ml vs. 3.9 ± 0.1 ml, p <0.05). The significant decrease in required flushing volume might be due to differences in the viscosity of the solutions. However, mean differences were small and were most likely caused by human interactions with the fluid collection setup. The average required flushing volume is 3.7 ml. CONCLUSIONS. The choice of separator fluid, solvent or administration rate had no impact on the required flushing volume in the experiment. Future research should take IV line length, diameter, volume and also drug solution volumes into account in order to provide a full account of variables affecting the required separator fluid volume

ESICM LIVES 2017 : 30th ESICM Annual Congress. September 23-27, 2017.

INTRODUCTION. Unplanned readmission to intensive care is highly undesirable in that it contributes to increased variance in care, disruption, difficulty in resource allocation and may increase length of stay and mortality particularly if subject to delays. Unlike the ICU admission from the ward, readmission prediction has received relatively little attention, perhaps in part because at the point of ICU discharge, full physiological information is systematically available to the clinician and so it is expected that readmission should be largely due to unpredictable factors. However it may be that there are multidimensional trends that are difficult for the clinician to perceive that may nevertheless be predictive of readmission. OBJECTIVES. We investigated whether machine learning (ML) techniques could be used to improve on the simple published SWIFT score [1] for the prediction of unplanned readmission to ICU within 48 hours. METHODS. We extracted systolic BP, pulse pressure, heart and respiration rate, temperature, SpO2, bilirubin, creatinine, INR, lactate, white cell count, platelet count, pH, FiO2, and total Glasgow Coma Score from ICU stays of over 2000 adult patients from our hospital electronic patient record system. We trained our own custom multidimensional / time-sensitive algorithmic ML system to predict failed discharges defined as either readmission or unexpected death within 48 hours of discharge. We used 10-fold cross validation to assess performance. We also assessed the effect of augmenting our system by transfer learning (TL) with 44,000 additional cases from the MIMIC III database. RESULTS. The SWIFT score performed relatively poorly with an AUROC of around 0.6 which our ML system trained on local data was also able to match. However when augmented with an additional dataset by TL, the AUROC for the ML system improved statistically and clinically significantly to over 0.7. CONCLUSIONS. Machine learning is able to improve on predictors based on simple multiple logistic regression. Thus there is likely to be information in the trends and in combinations of variables. A disadvantage with this technique is that ML approaches require large amounts of data for training. However, ML approaches can be improved by TL. Basing prediction models on locally derived data augmented by TL is a potentially novel approach to generating tools that customised to the institution yet can exploit the potential power of ML algorithms. REFERENCES [1] Gajic O, Malinchoc M, Comfere TB, et al. The Stability and Workload Index for Transfer score predicts unplanned intensive care unit patient readmission: initial development and validation. Crit Care Med. 2008;36(3):676–82. Grant Acknowledgement This work was internally funded

Advances in Computational Social Science and Social Simulation

Aquesta conferència és la celebració conjunta de la "10th Artificial Economics Conference AE", la "10th Conference of the European Social Simulation Association ESSA" i la "1st Simulating the Past to Understand Human History SPUHH".Conferència organitzada pel Laboratory for Socio­-Historical Dynamics Simulation (LSDS-­UAB) de la Universitat Autònoma de Barcelona.Readers will find results of recent research on computational social science and social simulation economics, management, sociology,and history written by leading experts in the field. SOCIAL SIMULATION (former ESSA) conferences constitute annual events which serve as an international platform for the exchange of ideas and discussion of cutting edge research in the field of social simulations, both from the theoretical as well as applied perspective, and the 2014 edition benefits from the cross-fertilization of three different research communities into one single event. The volume consists of 122 articles, corresponding to most of the contributions to the conferences, in three different formats: short abstracts (presentation of work-in-progress research), posters (presentation of models and results), and full papers (presentation of social simulation research including results and discussion). The compilation is completed with indexing lists to help finding articles by title, author and thematic content. We are convinced that this book will serve interested readers as a useful compendium which presents in a nutshell the most recent advances at the frontiers of computational social sciences and social simulation researc

Neolithic land-use in the Dutch wetlands: estimating the land-use implications of resource exploitation strategies in the Middle Swifterbant Culture (4600-3900 BCE)

The Dutch wetlands witness the gradual adoption of Neolithic novelties by foraging societies during the Swifterbant period. Recent analyses provide new insights into the subsistence palette of Middle Swifterbant societies. Small-scale livestock herding and cultivation are in evidence at this time, but their importance if unclear. Within the framework of PAGES Land-use at 6000BP project, we aim to translate the information on resource exploitation into information on land-use that can be incorporated into global climate modelling efforts, with attention for the importance of agriculture. A reconstruction of patterns of resource exploitation and their land-use dimensions is complicated by methodological issues in comparing the results of varied recent investigations. Analyses of organic residues in ceramics have attested to the cooking of aquatic foods, ruminant meat, porcine meat, as well as rare cases of dairy. In terms of vegetative matter, some ceramics exclusively yielded evidence of wild plants, while others preserve cereal remains. Elevated δ15N values of human were interpreted as demonstrating an important aquatic component of the diet well into the 4th millennium BC. Yet recent assays on livestock remains suggest grazing on salt marshes partly accounts for the human values. Finally, renewed archaeozoological investigations have shown the early presence of domestic animals to be more limited than previously thought. We discuss the relative importance of exploited resources to produce a best-fit interpretation of changing patterns of land-use during the Middle Swifterbant phase. Our review combines recent archaeological data with wider data on anthropogenic influence on the landscape. Combining the results of plant macroremains, information from pollen cores about vegetation development, the structure of faunal assemblages, and finds of arable fields and dairy residue, we suggest the most parsimonious interpretation is one of a limited land-use footprint of cultivation and livestock keeping in Dutch wetlands between 4600 and 3900 BCE.NWOVidi 276-60-004Human Origin

Taphonomy, environment or human plant exploitation strategies?: Deciphering changes in Pleistocene-Holocene plant representation at Umhlatuzana rockshelter, South Africa

The period between ~40 and 20 ka BP encompassing the Middle Stone Age (MSA) and Later Stone Age (LSA) transition has long been of interest because of the associated technological change. Understanding this transition in southern Africa is complicated by the paucity of archaeological sites that span this period. With its occupation sequence spanning the last ~70,000 years, Umhlatuzana Rock Shelter is one of the few sites that record this transition. Umhlatuzana thus offers a great opportunity to study past environmental dynamics from the Late Pleistocene (MIS 4) to the Late Holocene, and past human subsistence strategies, their social organisation, technological and symbolic innovations. Although organic preservation is poor (bones, seeds, and charcoal) at the site, silica phytoliths preserve generally well throughout the sequence. These microscopic silica particles can identify different plant types that are no longer visible at the site because of decomposition or burning to a reliable taxonomical level. Thus, to trace site occupation, plant resource use, and in turn reconstruct past vegetation, we applied phytolith analyses to sediment samples of the newly excavated Umhlatuzana sequence. We present results of the phytolith assemblage variability to determine change in plant use from the Pleistocene to the Holocene and discuss them in relation to taphonomical processes and human plant gathering strategies and activities. This study ultimately seeks to provide a palaeoenvironmental context for modes of occupation and will shed light on past human-environmental interactions in eastern South Africa.NWOVidi 276-60-004Human Origin

Ways and Capacity in Archaeological Data Management in Serbia

Over the past year and due to the COVID-19 pandemic, the entire world has witnessed inequalities across borders and societies. They also include access to archaeological resources, both physical and digital. Both archaeological data creators and users spent a lot of time working from their homes, away from artefact collections and research data. However, this was the perfect moment to understand the importance of making data freely and openly available, both nationally and internationally. This is why the authors of this paper chose to make a selection of data bases from various institutions responsible for preservation and protection of cultural heritage, in order to understand their policies regarding accessibility and usage of the data they keep. This will be done by simple visits to various web-sites or data bases. They intend to check on the volume and content, but also importance of the offered archaeological heritage. In addition, the authors will estimate whether the heritage has adequately been classified and described and also check whether data is available in foreign languages. It needs to be seen whether it is possible to access digital objects (documents and the accompanying metadata), whether access is opened for all users or it requires a certain hierarchy access, what is the policy of usage, reusage and distribution etc. It remains to be seen whether there are public API or whether it is possible to collect data through API. In case that there is a public API, one needs to check whether datasets are interoperable or messy, requiring data cleaning. After having visited a certain number of web-sites, the authors expect to collect enough data to make a satisfactory conclusion about accessibility and usage of Serbian archaeological data web bases