Specimens as research objects: reconciliation across distributed repositories to enable metadata propagation

Botanical specimens are shared as long-term consultable research objects in a global network of specimen repositories. Multiple specimens are generated from a shared field collection event; generated specimens are then managed individually in separate repositories and independently augmented with research and management metadata which could be propagated to their duplicate peers. Establishing a data-derived network for metadata propagation will enable the reconciliation of closely related specimens which are currently dispersed, unconnected and managed independently. Following a data mining exercise applied to an aggregated dataset of 19,827,998 specimen records from 292 separate specimen repositories, 36% or 7,102,710 specimens are assessed to participate in duplication relationships, allowing the propagation of metadata among the participants in these relationships, totalling: 93,044 type citations, 1,121,865 georeferences, 1,097,168 images and 2,191,179 scientific name determinations. The results enable the creation of networks to identify which repositories could work in collaboration. Some classes of annotation (particularly those regarding scientific name determinations) represent units of scientific work: appropriate management of this data would allow the accumulation of scholarly credit to individual researchers: potential further work in this area is discussed.Comment: 9 pages, 1 table, 3 figure

Social and Governance Implications of Improved Data Efficiency

Many researchers work on improving the data efficiency of machine learning. What would happen if they succeed? This paper explores the social-economic impact of increased data efficiency. Specifically, we examine the intuition that data efficiency will erode the barriers to entry protecting incumbent data-rich AI firms, exposing them to more competition from data-poor firms. We find that this intuition is only partially correct: data efficiency makes it easier to create ML applications, but large AI firms may have more to gain from higher performing AI systems. Further, we find that the effect on privacy, data markets, robustness, and misuse are complex. For example, while it seems intuitive that misuse risk would increase along with data efficiency -- as more actors gain access to any level of capability -- the net effect crucially depends on how much defensive measures are improved. More investigation into data efficiency, as well as research into the "AI production function", will be key to understanding the development of the AI industry and its societal impacts.Comment: 7 pages, 2 figures, accepted to Artificial Intelligence Ethics and Society 202

Predicting Type 2 Diabetes Complications and Personalising Patient Using Artificial Intelligence Methodology

The prediction of the onset of different complications of disease, in general, is challenging due to the existence of unmeasured risk factors, imbalanced data, time-varying data due to dynamics, and various interventions to the disease over time. Scholars share a common argument that many Artificial Intelligence techniques that successfully model disease are often in the form of a “black box” where the internal workings and complexities are extremely difficult to understand, both from practitioners’ and patients’ perspective. There is a need for appropriate Artificial Intelligence techniques to build predictive models that not only capture unmeasured effects to improve prediction, but are also transparent in how they model data so that knowledge about disease processes can be extracted and trust in the model can be maintained by clinicians. The proposed strategy builds probabilistic graphical models for prediction with the inclusion of informative hidden variables. These are added in a stepwise manner to improve predictive performance whilst maintaining as simple a model as possible, which is regarded as crucial for the interpretation of the prediction results. This chapter explores this key issue with a specific focus on diabetes data. According to the literature on disease modelling, especially on major diseases such as diabetes, a patient’s mortality often occurs due to the associated complications caused by the disease over time and not the disease itself. This is often patient-specific and will depend on what type of cohort a patient belongs to. Another main focus of this study is patient personalisation via precision medicine by discovering meaningful subgroups of patients which are characterised as phenotypes. These phenotypes are explained further using Bayesian network analysis methods and temporal association rules. Overall, this chapter discussed the earlier research of the chapter’s author. It explores Artificial Intelligence (IDA) techniques for modelling the progression of disease whilst simultaneously stratifying patients and doing so in a transparent manner as possible. To this end, it reviews the current literature on some of the most common Artificial Intelligent (AI) methodologies, including probabilistic modelling, association rule mining, phenotype discovery and latent variable discovery by using diabetes as a case study

Nonimmunological alterations of glomerular filtration by s-PAF in the rat kidney

Nonimmunological alterations of glomerular filtration by s-PAF in the rat kidney. Rat kidneys were isolated and perfused with a cell-free perfusion buffer containing 4% albumin. Infusion of platelet activating factor (s-PAF) into the isolated perfused kidney caused a dose-dependent fall in renal vascular resistance (RVR): 12 ± 6% at 10nM s-PAF, 18 ± 3% at 100nM s-PAF and 20 ± 7% at 1 µM. s-PAF. Glomerular filtration rate fell by 32 ± 5% at 10nM, 38 ± 6% at 100nM, and 52 ± 10% at 1 µM. s-PAF (50nM) increased urinary protein excretion after 20 minutes. Because GFR fell to a greater extent than RVR, possible changes in glomerular permeability after s-PAF treatment were assessed morphologically using native ferritin. After s-PAF treatment (100nM), the number of ferritin particles/µm2 increased from 1.2 ± 0.9 (control) to 795 ± 69 in the glomerular basement membrane (GBM) and from 0.2 ± 0.06 (control) to 98 ± 29 in lamina rara externa (LRE). To quantitate changes in fixed anionic charges, polyethylenimine (PEI) was quantitated morphologically in GBM. No significant change between s-PAF treated and untreated kidneys was seen. s-PAF did not alter the sialoglycoprotein pattern in the perfused kidney as assessed by lysozyme staining. These results are in contrast to findings with s-PAF in vivo where in addition to increased glomerular permeability, a reduction of fixed anionic charges is seen. Thus, these results help to differentiate a dual mechanism of s-PAF: 1) a direct action of s-PAF on glomerular epithelial and vascular cells and, 2) an indirect action of s-PAF on glomerular structures via stimulation of release of inflammatory mediators from circulatory cells

Using Bayesian Networks to Investigate the Influence of Subseasonal Arctic Variability on Midlatitude North Atlantic Circulation

Recent enhanced warming and sea ice depletion in the Arctic have been put forward as potential drivers of severe weather in the midlatitudes. Evidence of a link between Arctic warming and midlatitude atmospheric circulation is growing, but the role of Arctic processes relative to other drivers remains unknown. Arctic–midlatitude connections in the North Atlantic region are particularly complex but important due to the frequent occurrence of severe winters in recent decades. Here, dynamic Bayesian networks with hidden variables are introduced to the field to assess their suitability for teleconnection analyses. Climate networks are constructed to analyze North Atlantic circulation variability at 5-day to monthly time scales during the winter months of the years 1981–2018. The inclusion of a number of Arctic, midlatitude, and tropical variables allows for an investigation into the relative role of Arctic influence compared to internal atmospheric variability and other remote drivers. A robust covariability between regions of amplified Arctic warming and two definitions of midlatitude circulation is found to occur entirely within winter at submonthly time scales. Hidden variables incorporated in networks represent two distinct modes of stratospheric polar vortex variability, capturing a periodic shift between average conditions and slower anomalous flow. The influence of the Barents–Kara Seas region on the North Atlantic Oscillation is found to be the strongest link at 5- and 10-day averages, while the stratospheric polar vortex strongly influences jet variability on monthly time scales

Heat transfer between fluids in two phase flow

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1961.MIT Institute Archives copy bound with: Rheology of blood plasma / Paul M. Cox, Jr., Henry L. Gabelnick. 1961.Includes bibliographical references (leaves 38-39).by Allan S. Douglas, Edward L. Tucker.B.S

Consensus and meta-analysis regulatory networks for combining multiple microarray gene expression datasets

Microarray data is a key source of experimental data for modelling gene regulatory interactions from expression levels. With the rapid increase of publicly available microarray data comes the opportunity to produce regulatory network models based on multiple datasets. Such models are potentially more robust with greater confidence, and place less reliance on a single dataset. However, combining datasets directly can be difficult as experiments are often conducted on different microarray platforms, and in different laboratories leading to inherent biases in the data that are not always removed through pre-processing such as normalisation. In this paper we compare two frameworks for combining microarray datasets to model regulatory networks: pre- and post-learning aggregation. In pre-learning approaches, such as using simple scale-normalisation prior to the concatenation of datasets, a model is learnt from a combined dataset, whilst in post-learning aggregation individual models are learnt from each dataset and the models are combined. We present two novel approaches for post-learning aggregation, each based on aggregating high-level features of Bayesian network models that have been generated from different microarray expression datasets. Meta-analysis Bayesian networks are based on combining statistical confidences attached to network edges whilst Consensus Bayesian networks identify consistent network features across all datasets. We apply both approaches to multiple datasets from synthetic and real (Escherichia coli and yeast) networks and demonstrate that both methods can improve on networks learnt from a single dataset or an aggregated dataset formed using a standard scale-normalisation

Bioinformatics tools in predictive ecology: Applications to fisheries

This article is made available throught the Brunel Open Access Publishing Fund - Copygith @ 2012 Tucker et al.There has been a huge effort in the advancement of analytical techniques for molecular biological data over the past decade. This has led to many novel algorithms that are specialized to deal with data associated with biological phenomena, such as gene expression and protein interactions. In contrast, ecological data analysis has remained focused to some degree on off-the-shelf statistical techniques though this is starting to change with the adoption of state-of-the-art methods, where few assumptions can be made about the data and a more explorative approach is required, for example, through the use of Bayesian networks. In this paper, some novel bioinformatics tools for microarray data are discussed along with their ‘crossover potential’ with an application to fisheries data. In particular, a focus is made on the development of models that identify functionally equivalent species in different fish communities with the aim of predicting functional collapse