Weaving seams with data: Conceptualizing City APIs as elements of infrastructures

This article addresses the role of application programming interfaces (APIs) for integrating data sources in the context of smart cities and communities. On top of the built infrastructures in cities, application programming interfaces allow to weave new kinds of seams from static and dynamic data sources into the urban fabric. Contributing to debates about “urban informatics” and the governance of urban information infrastructures, this article provides a technically informed and critically grounded approach to evaluating APIs as crucial but often overlooked elements within these infrastructures. The conceptualization of what we term City APIs is informed by three perspectives: In the first part, we review established criticisms of proprietary social media APIs and their crucial function in current web architectures. In the second part, we discuss how the design process of APIs defines conventions of data exchanges that also reflect negotiations between API producers and API consumers about affordances and mental models of the underlying computer systems involved. In the third part, we present recent urban data innovation initiatives, especially CitySDK and OrganiCity, to underline the centrality of API design and governance for new kinds of civic and commercial services developed within and for cities. By bridging the fields of criticism, design, and implementation, we argue that City APIs as elements of infrastructures reveal how urban renewal processes become crucial sites of socio-political contestation between data science, technological development, urban management, and civic participation

Rapid screening for glucose-6-phosphate dehydrogenase deficiency and haemoglobin polymorphisms in Africa by a simple high-throughput SSOP-ELISA method

BACKGROUND: Mutations in the haemoglobin beta-globin (HbB) and glucose-6-phosphate dehydrogenase (G6PD) genes cause widespread human genetic disorders such as sickle cell diseases and G6PD deficiency. In sub-Saharan Africa, a few predominant polymorphic variants of each gene account for a majority of these deficiencies. Examining at a larger scale the clinical importance of these independent genetic disorders, their possible association with malaria pathogenesis and innate resistance, and their relevance for antimalarial drug treatment, would be easier if an accurate screening method with limited costs was available. METHODS: A simple and rapid technique was developed to detect the most prominent single nucleotide polymorphisms (SNPs) in the HbB and G6PD genes. The method is able to detect the different haemoglobin polymorphisms A, S, C and E, as well as G6PD polymorphisms B, A and A- based on PCR-amplification followed by a hybridization step using sequence-specific oligonucleotide probes (SSOPs) specific for the SNP variants and quantified by ELISA. RESULTS: The SSOP-ELISA method was found to be specific, and compared well to the commonly used PCR-RFLP technique. Identical results were obtained in 98% (haemoglobin) and 95% (G6PD) of the tested 90 field samples from a high-transmission area in Tanzania, which were used to validate the new technique. CONCLUSION: The simplicity and accuracy of the new methodology makes it suitable for application in settings where resources are limited. It would serve as a valuable tool for research purposes by monitoring genotype frequencies in relation to disease epidemiology

All-cause versus cause-specific excess deaths for estimating influenza-associated mortality in Denmark, Spain, and the United States

Background: Seasonal influenza-associated excess mortality estimates can be timely and provide useful information on the severity of an epidemic. This methodology can be leveraged during an emergency response or pandemic. Method: For Denmark, Spain, and the United States, we estimated age-stratified excess mortality for (i) all-cause, (ii) respiratory and circulatory, (iii) circulatory, (iv) respiratory, and (v) pneumonia, and influenza causes of death for the 2015/2016 and 2016/2017 influenza seasons. We quantified differences between the countries and seasonal excess mortality estimates and the death categories. We used a time-series linear regression model accounting for time and seasonal trends using mortality data from 2010 through 2017. Results: The respective periods of weekly excess mortality for all-cause and cause-specific deaths were similar in their chronological patterns. Seasonal all-cause excess mortality rates for the 2015/2016 and 2016/2017 influenza seasons were 4.7 (3.3-6.1) and 14.3 (13.0-15.6) per 100,000 population, for the United States; 20.3 (15.8-25.0) and 24.0 (19.3-28.7) per 100,000 population for Denmark; and 22.9 (18.9-26.9) and 52.9 (49.1-56.8) per 100,000 population for Spain. Seasonal respiratory and circulatory excess mortality estimates were two to three times lower than the all-cause estimates. Discussion: We observed fewer influenza-associated deaths when we examined cause-specific death categories compared with all-cause deaths and observed the same trends in peaks in deaths with all death causes. Because all-cause deaths are more available, these models can be used to monitor virus activity in near real time. This approach may contribute to the development of timely mortality monitoring systems during public health emergencies.This study was conducted as part of Sebastian Schmidt's research fellowship, which was financially supported by the Novo Nordic Foundation and A.P. Møller Fonden. The EuroMOMO network has received financial support from the European Centre for Disease Prevention and Control (ECDC) and from the World Health Organization (WHO) Regional Office for Europe.S

Eliciting harms data from trial participants: how perceptions of illness and treatment mediate recognition of relevant information to report

Background: There is no consensus on the ideal methodology for eliciting participant-reported harms, but question methods influence the extent and nature of data detected. This gives potential for measurement error and undermines meta-analyses of adverse effects. We undertook to identify barriers to accurate and complete reporting of harms data, by qualitatively exploring participants’ experiences of illness and treatment, and reporting behaviours; and compared the number and nature of data detected by three enquiry methods. Methods: Participants within antiretroviral/antimalarial interaction trials in South Africa and Tanzania were asked about medical history, treatments and/or adverse events by general enquiries followed by checklists. Those reporting differently between these two question methods were invited to an in-depth interview and focus group discussion. Health narratives were analysed to investigate accuracy and completeness of case record form data and to understand reasons for differential reporting between question methods. Outcomes were the number and nature of data by question method, themes from qualitative analyses and a theoretical interpretation of participants’ experiences. Results: We observed a cumulative increase in sensitivity of detection of all types of reports while progressing from general enquiry, through checklist, to in-depth interview. Questioning detail and terminology influenced participants’ recognition of health issues and treatments. Reporting patterns and vocabulary suggest influence from the relative importance that illnesses and treatments have for participants. Perceptions were often dichotomised (e.g. ‘street’ versus clinic treatments, symptoms experienced versus tests and examinations performed, chronic versus acute illness, persistent versus intermittent symptoms, activity- versus malaria-related symptoms) and this differentiation extended to ideas of relevance to report. South African participants displayed a ‘trial citizenship’, taking responsibility for the impact of their reporting on trial results, and even reaching reporting decisions by consensus. In contrast, Tanzanians perceived their role more as patients than participants; the locus of responsibility for knowing information relevant to the trial fell with trial staff as doctors rather than with themselves. Conclusions: Our observations of how reporting relates to participant perceptions inside and outside trials could help optimise how harms data are elicited. Questions reflecting the different ways that biomedically defined illness and treatment data are perceived by participants may help them understand relevance for reporting. We will theorise how these two disparate trial environments may have influenced how participants understood their role, as this could help researchers achieve empowered participation in similar trials

The incidence of malaria in travellers to South-East Asia: is local malaria transmission a useful risk indicator?

BACKGROUND: The presence of ongoing local malaria transmission, identified though local surveillance and reported to regional WHO offices, by S-E Asian countries, forms the basis of national and international chemoprophylaxis recommendations in western countries. The study was designed to examine whether the strategy of using malaria transmission in a local population was an accurate estimate of the malaria threat faced by travellers and a correlate of malaria in returning travellers. METHODS: Malaria endemicity was described from distribution and intensity in the local populations of ten S-E Asian destination countries over the period 2003-2008 from regionally reported cases to WHO offices. Travel acquired malaria was collated from malaria surveillance reports from the USA and 12 European countries over the same period. The numbers of travellers visiting the destination countries was based on immigration and tourism statistics collected on entry of tourists to the destination countries. RESULTS: In the destination countries, mean malaria rates in endemic countries ranged between 0.01 in Korea to 4:1000 population per year in Lao PDR, with higher regional rates in a number of countries. Malaria cases imported into the 13 countries declined by 47% from 140 cases in 2003 to 66 in 2008. A total of 608 cases (27.3% Plasmodium falciparum (Pf)) were reported over the six years, the largest number acquired in Indonesia, Thailand and Korea. Four countries had an incidence > 1 case per 100,000 traveller visits; Burma (Myanmar), Indonesia, Cambodia and Laos (range 1 to 11.8-case per 100,000 visits). The remaining six countries rates were 1 case per 100,000 visits to consider targeted malaria prophylaxis recommendations to minimize use of chemoprophylaxis for low risk exposure during visits to S-E Asia. Policy needs to be adjusted regularly to reflect the changing risk

Distinct patterns of blood-stage parasite antigens detected by plasma IgG subclasses from individuals with different level of exposure to Plasmodium falciparum infections

International audienceBACKGROUND: In endemic regions naturally acquired immunity against Plasmodium falciparum develops as a function of age and exposure to parasite infections and is known to be mediated by IgG. The targets of protective antibodies remain to be fully defined. Several immunoepidemiological studies have indicated an association of cytophilic anti-parasite IgG with protection against malaria. It has been hypothesized that the initial antibody responses against parasite antigens upon first few Plasmodium falciparum infections is dominated by non-protective IgG2/IgG4 and IgM antibodies, which then gradually develop into protective response dominated by cytophilic IgG1 and IgG3 antibodies. METHODS: Naturally occurring IgG antibodies against P. falciparum blood-stage antigens were analysed from plasma samples collected from four groups of individuals differing in age and level of exposure to P. falciparum infections. Western Blot profiling of blood-stage parasite antigens displaying reactivity with individual plasma samples in terms of their subclass specificities was conducted. Parasite antigens detected by IgG were grouped based on their apparent molecular sizes resolved by SDS-PAGE as high molecular weight (≥ 70 kDa) or low molecular weight (< 70 kDa). The number of discernable low molecular weight parasite antigens detected by different IgG subclass antibodies from each plasma sample was recorded. Using Wilcoxons rank sum test these reactivities were compared amongst groups of individuals with different levels of exposure to P. falciparum infections. RESULTS: IgG4 and IgM antibodies in plasma samples from all groups detected very few parasite antigens. IgG2 antibodies from all groups detected a common pattern of high molecular weight parasite antigens. Cytophilic IgG subclasses in plasma samples from individuals with higher levels of exposure to P. falciparum infections distinctly detected higher numbers of low molecular weight parasite antigens. CONCLUSIONS: In the present study, there was no evidence for switching of antibody responses from non-cytophilic to cytophilic subclasses against blood-stage parasite antigens as a likely mechanism for induction of protective immunity against malaria

Insect cells are superior to Escherichia coli in producing malaria proteins inducing IgG targeting PfEMP1 on infected erythrocytes

<p>Abstract</p> <p>Background</p> <p>The PFD1235w <it>Plasmodium falciparum </it>erythrocyte membrane protein 1 (PfEMP1) antigen is associated with severe malaria in children and can be expressed on the surface of infected erythrocytes (IE) adhering to ICAM1. However, the exact three-dimensional structure of this PfEMP1 and its surface-exposed epitopes are unknown. An insect cell and <it>Escherichia coli </it>based system was used to express single and double domains encoded by the <it>pfd1235w var </it>gene. The resulting recombinant proteins have been evaluated for yield and purity and their ability to induce rat antibodies, which react with the native PFD1235w PfEMP1 antigen expressed on 3D7_PFD1235w-IE. Their recognition by human anti-malaria antibodies from previously infected Tanzanian donors was also analysed.</p> <p>Methods</p> <p>The recombinant proteins were run on SDS-PAGE and Western blots for quantification and size estimation. Insect cell and <it>E. coli</it>-produced recombinant proteins were coupled to a bead-based Luminex assay to measure the plasma antibody reactivity of 180 samples collected from Tanzanian individuals. The recombinant proteins used for immunization of rats and antisera were also tested by flow cytometry for their ability to surface label 3D7_PFD1235w-IE.</p> <p>Results</p> <p>All seven pAcGP67A constructs were successfully expressed as recombinant protein in baculovirus-infected insect cells and subsequently produced to a purity of 60-97% and a yield of 2-15 mg/L. By comparison, only three of seven pET101/D-TOPO constructs expressed in the <it>E. coli </it>system could be produced at all with purity and yield ranging from 3-95% and 6-11 mg/L. All seven insect cell, but only two of the <it>E. coli </it>produced proteins induced antibodies reactive with native PFD1235w expressed on 3D7_PFD1235w-IE. The recombinant proteins were recognized in an age- and transmission intensity-dependent manner by antibodies from 180 Tanzanian individuals in a bead-based Luminex assay.</p> <p>Conclusions</p> <p>The baculovirus based insect cell system was distinctly superior to the <it>E. coli </it>expression system in producing a larger number of different recombinant PFD1235w protein domains and these were significantly easier to purify at a useful yield. However, proteins produced in both systems were able to induce antibodies in rats, which can recognize the native PFD1235w on the surface of IE.</p

Malaria morbidity and immunity among residents of villages with different Plasmodium falciparum transmission intensity in North-Eastern Tanzania

BACKGROUND: The relationship between the burden of uncomplicated malaria and transmission intensity is unclear and a better understanding of this relationship is important for the implementation of intervention programmes. METHODS: A 6-month longitudinal study monitoring risk factors for anaemia and febrile malaria episodes was conducted among individuals aged below 20 years, residing in three villages of different altitude in areas of high, moderate and low malaria transmission intensity in North-Eastern Tanzania. RESULTS: The burden of anaemia and malarial fever fell mainly on the youngest children and was highest in the village with high transmission intensity. Although a considerable percentage of individuals in all villages carried intestinal worms, logistic regression models indicated that Plasmodium falciparum was the only significant parasitic determinant of anaemia. Interestingly, children who carried low-density parasitaemia at the start of the study had a lower risk of contracting a febrile malaria episode but a higher risk of anaemia during the study period, than children who were slide negative at this point in time. CONCLUSION: Young children living in the high transmission village carried a very high anaemia burden, which could be attributed to malaria. The overall incidence of febrile malaria was also highest in the high transmission village particularly among those under five years of age. These data suggest that in rolling back malaria, available resources in prevention programmes should primarily be focussed on young children, particularly those residing in areas of high malaria transmission

A high-resolution geospatial surveillance-response system for malaria elimination in Solomon Islands and Vanuatu

BACKGROUND A high-resolution surveillance-response system has been developed within a geographic information system (GIS) to support malaria elimination in the Pacific. This paper examines the application of a GIS-based spatial decision support system (SDSS) to automatically locate and map the distribution of confirmed malaria cases, rapidly classify active transmission foci, and guide targeted responses in elimination zones. METHODS Customized SDSS-based surveillance-response systems were developed in the three elimination provinces of Isabel and Temotu, Solomon Islands and Tafea, Vanuatu. Confirmed malaria cases were reported to provincial malaria offices upon diagnosis and updated into the respective SDSS as part of routine operations throughout 2011. Cases were automatically mapped by household within the SDSS using existing geographical reconnaissance (GR) data. GIS queries were integrated into the SDSS-framework to automatically classify and map transmission foci based on the spatiotemporal distribution of cases, highlight current areas of interest (AOI) regions to conduct foci-specific targeted response, and extract supporting household and population data. GIS simulations were run to detect AOIs triggered throughout 2011 in each elimination province and conduct a sensitivity analysis to calculate the proportion of positive cases, households and population highlighted in AOI regions of a varying geographic radius. RESULTS A total of 183 confirmed cases were reported and mapped using the SDSS throughout 2011 and used to describe transmission within a target population of 90,354. Automatic AOI regions were also generated within each provincial SDSS identifying geographic areas to conduct response. 82.5% of confirmed cases were automatically geo-referenced and mapped at the household level, with 100% of remaining cases geo-referenced at a village level. Data from the AOI analysis indicated different stages of progress in each province, highlighting operational implications with regards to strategies for implementing surveillance-response in consideration of the spatiotemporal nature of cases as well as logistical and financial constraints of the respective programmes. CONCLUSIONS Geospatial systems developed to guide Pacific Island malaria elimination demonstrate the application of a high resolution SDSS-based approach to support key elements of surveillance-response including understanding epidemiological variation within target areas, implementing appropriate foci-specific targeted response, and consideration of logistical constraints and costs.A.C.A.C. is supported by a Career Development Award from the Australian National Health and Medical Research Council (#631619)

Review of key knowledge gaps in glucose-6-phosphate dehydrogenase deficiency detection with regard to the safe clinical deployment of 8-aminoquinoline treatment regimens: a workshop report.

The diagnosis and management of glucose-6-phosphate dehydrogenase (G6PD) deficiency is a crucial aspect in the current phases of malaria control and elimination, which will require the wider use of 8-aminoquinolines for both reducing Plasmodium falciparum transmission and achieving the radical cure of Plasmodium vivax. 8-aminoquinolines, such as primaquine, can induce severe haemolysis in G6PD-deficient individuals, potentially creating significant morbidity and undermining confidence in 8-aminoquinoline prescription. On the other hand, erring on the side of safety and excluding large numbers of people with unconfirmed G6PD deficiency from treatment with 8-aminoquinolines will diminish the impact of these drugs. Estimating the remaining G6PD enzyme activity is the most direct, accessible, and reliable assessment of the phenotype and remains the gold standard for the diagnosis of patients who could be harmed by the administration of primaquine. Genotyping seems an unambiguous technique, but its use is limited by cost and the large range of recognized G6PD genotypes. A number of enzyme activity assays diagnose G6PD deficiency, but they require a cold chain, specialized equipment, and laboratory skills. These assays are impractical for care delivery where most patients with malaria live. Improvements to the diagnosis of G6PD deficiency are required for the broader and safer use of 8-aminoquinolines to kill hypnozoites, while lower doses of primaquine may be safely used to kill gametocytes without testing. The discussions and conclusions of a workshop conducted in Incheon, Korea in May 2012 to review key knowledge gaps in G6PD deficiency are reported here