Unearthing the Infrastructure: Humans and Sensors in Field-Based Scientific Research

Distributed sensing systems for studying scientific phenomena are critical applications of information technologies. By embedding computational intelligence in the environment of study, sensing systems allow researchers to study phenomena at spatial and temporal scales that were previously impossible to achieve. We present an ethnographic study of field research practices among researchers in the Center for Embedded Networked Sensing (CENS), a National Science Foundation Science & Technology Center devoted to developing wireless sensing systems for scientific and social applications. Using the concepts of boundary objects and trading zones, we trace the processes of collaborative research around sensor technology development and adoption within CENS. Over the 10-year lifespan of CENS, sensor technologies, sensor data, field research methods, and statistical expertise each emerged as boundary objects that were understood differently by the science and technology partners. We illustrate how sensing technologies were incompatible with field-based environmental research until researchers “unearthed” their infrastructures, explicitly reintroducing human skill and expertise into the data collection process and developing new collaborative languages that emphasized building dynamic sensing systems that addressed human needs. In collaborating around a dynamic sensing model, the sensing systems became embedded not in the environment of study, but in the practices of the scientists. Status and citation: This is the revised and accepted version, prior to publisher’s copy editing. Please quote the final version: Mayernik, Matthew S., Wallis, Jillian C., & Borgman, Christine L. (In press). Unearthing the infrastructure: Humans and sensors in field-based scientific research. Journal of Computer Supported Cooperative Work. doi: 10.1007/s10606-012-9178-

Process evaluation for complex interventions in health services research: Analysing context, text trajectories and disruptions

Background: Process evaluations assess the implementation and sustainability of complex healthcare interventions within clinical trials, with well-established theoretical models available for evaluating intervention delivery within specific contexts. However, there is a need to translate conceptualisations of context into analytical tools which enable the dynamic relationship between context and intervention implementation to be captured and understood. Methods: In this paper I propose an alternative approach to the design, implementation and analysis of process evaluations for complex health interventions through a consideration of trial protocols as textual documents, distributed and enacted at multiple contextual levels. As an example, I conduct retrospective analysis of a sample of field notes and transcripts collected during the ESTEEM study - a cluster randomised controlled trial of primary care telephone triage. I draw on theoretical perspectives associated with Linguistic Ethnography to examine the delivery of ESTEEM through staff orientation to different texts. In doing so I consider what can be learned from examining the flow and enactment of protocols for notions of implementation and theoretical fidelity (i.e. intervention delivered as intended and whether congruent with the intervention theory). Results: Implementation of the triage intervention required staff to integrate essential elements of the protocol within everyday practice, seen through the adoption and use of different texts that were distributed across staff and within specific events. Staff were observed deploying texts in diverse ways (e.g. reinterpreting scripts, deviating from standard operating procedures, difficulty completing decision support software), providing numerous instances of disruption to maintaining intervention fidelity. Such observations exposed tensions between different contextual features in which the trial was implemented, offering theoretical explanations for the main trial findings. Conclusions: The value of following how trial protocols produce new texts is that we can observe the flow of 'the intervention as intended' across a series of events which are enacted to meet specific demands of intervention delivery. Such observations are not solely premised on identifying routines or practices of implementation, but where 'protocols as intended' breaks down. In doing so, I discuss whether it is here where we might expose the 'active ingredients' of interventions in action

Human rights, health and the state in Bangladesh

BACKGROUND: This paper broadly discusses the role of the State of Bangladesh in the context of the health system and human rights. The interrelation between human rights, health and development are well documented. The recognition of health as a fundamental right by WHO and subsequent approval of health as an instrument of welfare by the Universal Declaration of Human Rights (UDHR) and the International Covenant on Social, Economic and Cultural Rights (ICSECR) further enhances the idea. Moreover, human rights are also recognized as an expedient of human development. The state is entrusted to realize the rights enunciated in the ICSECR. DISCUSSION: In exploring the relationship of the human rights and health situation in Bangladesh, it is argued, in this paper, that the constitution and major policy documents of the Bangladesh government have recognized the health rights and development. Bangladesh has ratified most of the international treaties and covenants including ICCPR, ICESCR; and a signatory of international declarations including Alma-Ata, ICPD, Beijing declarations, and Millennium Development Goals. However the implementation of government policies and plans in the development of health institutions, human resources, accessibility and availability, resource distribution, rural-urban disparity, the male-female gap has put the health system in a dismal state. Neither the right to health nor the right to development has been established in the development of health system or in providing health care. SUMMARY: The development and service pattern of the health system have negative correlation with human rights and contributed to the underdevelopment of Bangladesh. The government should take comprehensive approach in prioritizing the health rights of the citizens and progressive realization of these rights

Rapidity and Centrality Dependence of Proton and Anti-proton Production from Au+Au Collisions at sqrt(sNN) = 130GeV

We report on the rapidity and centrality dependence of proton and anti-proton transverse mass distributions from Au+Au collisions at sqrt(sNN) = 130GeV as measured by the STAR experiment at RHIC. Our results are from the rapidity and transverse momentum range of |y|<0.5 and 0.35 <p_t<1.00GeV/c. For both protons and anti-protons, transverse mass distributions become more convex from peripheral to central collisions demonstrating characteristics of collective expansion. The measured rapidity distributions and the mean transverse momenta versus rapidity are flat within |y|<0.5. Comparisons of our data with results from model calculations indicate that in order to obtain a consistent picture of the proton(anti-proton) yields and transverse mass distributions the possibility of pre-hadronic collective expansion may have to be taken into account.Comment: 4 pages, 3 figures, 1 table, submitted to PR

Specific Gene Expression Responses to Parasite Genotypes Reveal Redundancy of Innate Immunity in Vertebrates

Vertebrate innate immunity is the first line of defense against an invading pathogen and has long been assumed to be largely unspecific with respect to parasite/pathogen species. However, recent phenotypic evidence suggests that immunogenetic variation, i.e. allelic variability in genes associated with the immune system, results in host-parasite genotype-by-genotype interactions and thus specific innate immune responses. Immunogenetic variation is common in all vertebrate taxa and this reflects an effective immunological function in complex environments. However, the underlying variability in host gene expression patterns as response of innate immunity to within-species genetic diversity of macroparasites in vertebrates is unknown. We hypothesized that intra-specific variation among parasite genotypes must be reflected in host gene expression patterns. Here we used high-throughput RNA-sequencing to examine the effect of parasite genotypes on gene expression patterns of a vertebrate host, the three-spined stickleback (Gasterosteus aculeatus). By infecting naïve fish with distinct trematode genotypes of the species Diplostomum pseudospathaceum we show that gene activity of innate immunity in three-spined sticklebacks depended on the identity of an infecting macroparasite genotype. In addition to a suite of genes indicative for a general response against the trematode we also find parasite-strain specific gene expression, in particular in the complement system genes, despite similar infection rates of single clone treatments. The observed discrepancy between infection rates and gene expression indicates the presence of alternative pathways which execute similar functions. This suggests that the innate immune system can induce redundant responses specific to parasite genotypes

Vascular regrowth following photodynamic therapy in the chicken embryo chorioallantoic membrane

Photodynamic therapy (PDT) induces damage to the endothelium, which can lead to increased vascular permeability and, under intensive PDT conditions, even to platelet aggregation, vasoconstriction, and blood flow stasis. Eventually, ischemia, hypoxia, and inflammation can occur, resulting in angiogenesis. We studied the sequence of the vascular events after Visudyne®-PDT in the chicken chorioallantoic membrane (CAM) at day 11 of development. Using epi-fluorescence microscopy, we monitored the regrowth of capillaries in the PDT treated area. Immediately after irradiation, the treatment resulted in blood flow arrest. And 24 h post PDT, sprouting of new blood vessels was observed at the edge of the PDT zone. Neovessels looping out from the edge of the PDT zone gave rise to specialized endothelial tip structures guiding the vessels towards the center of the treated area. At 48 h almost all of the treated area was repopulated with functional but morphologically altered vasculature. These observations also showed reperfusion of some of the vessels that had been closed by the PDT treatment. CAM samples were immunohistochemically stained for Ki-67 showing proliferation of endothelial cells in the PDT area. Also, several markers of immature and angiogenic blood vessels, such as αVβ3-integrin, vimentin and galectin-1, were found to be enhanced in the PDT area, while the endothelial maturation marker intercellular adhesion molecule (ICAM)-1 was found to be suppressed. These results demonstrate that the new vascular bed is formed by both neo-angiogenesis and reperfusion of existing vessels. Both the quantitative real-time RT–PCR profile and the response to pharmacological treatment with Avastin®, an inhibitor of angiogenesis, suggest that angiogenesis occurs after PDT. The observed molecular profiling results and the kinetics of gene regulation may enable optimizing combination therapies involving PDT for treatment of cancer and other diseases

The genomic basis of adaptive evolution in threespine sticklebacks

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.National Human Genome Research Institute (U.S.)National Human Genome Research Institute (U.S.) (NHGRI CEGS Grant P50-HG002568

Phosphatidylserine Targets Single-Walled Carbon Nanotubes to Professional Phagocytes In Vitro and In Vivo

Broad applications of single-walled carbon nanotubes (SWCNT) dictate the necessity to better understand their health effects. Poor recognition of non-functionalized SWCNT by phagocytes is prohibitive towards controlling their biological action. We report that SWCNT coating with a phospholipid “eat-me” signal, phosphatidylserine (PS), makes them recognizable in vitro by different phagocytic cells - murine RAW264.7 macrophages, primary monocyte-derived human macrophages, dendritic cells, and rat brain microglia. Macrophage uptake of PS-coated nanotubes was suppressed by the PS-binding protein, Annexin V, and endocytosis inhibitors, and changed the pattern of pro- and anti-inflammatory cytokine secretion. Loading of PS-coated SWCNT with pro-apoptotic cargo (cytochrome c) allowed for the targeted killing of RAW264.7 macrophages. In vivo aspiration of PS-coated SWCNT stimulated their uptake by lung alveolar macrophages in mice. Thus, PS-coating can be utilized for targeted delivery of SWCNT with specified cargoes into professional phagocytes, hence for therapeutic regulation of specific populations of immune-competent cells

Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments