Domesticating data: Traveling and value-making in the data economy

Data are versatile objects that can travel across contexts. While data's travels have been widely discussed, little attention has been paid to the sites from where and to which data flow. Drawing upon ethnographic fieldwork in two connected data-intensive laboratories and the concept of domestication, we explore what it takes to bring data 'home' into the laboratory. As data come and dwell in the home, they are made to follow rituals, and as a result, data are reshaped and form ties with the laboratory and its practitioners. We identify four main ways of domesticating data. First, through storytelling about the data's origins, data practitioners draw the boundaries of their laboratory. Second, through standardization, staff transform samples into digital data that can travel well while ruling what data can be let into the home. Third, through formatting, data practitioners become familiar with their data and at the same time imprint the data, thus making them belong to their home. Finally, through cultivation, staff turn data into a resource for knowledge production. Through the lens of domestication, we see the data economy as a collection of homes connected by flows, and it is because data are tamed and attached to homes that they become valuable knowledge tools. Such domestication practices also have broad implications for staff, who in the process of 'homing' data, come to belong to the laboratory. To conclude, we reflect on what these domestication processes-which silence unusual behaviours in the data-mean for the knowledge produced in data-intensive research.

Slowing down decay: biological clocks in personalized medicine

This article discusses so-called biological clocks. These technologies, based on aging biomarkers, trace and measure molecular changes in order to monitor individuals' "true" biological age against their chronological age. Drawing on the concept of decay, and building on ethnographic fieldwork in an academic laboratory and a commercial firm, we analyze the implications of the development and commercialization of biological clocks that can identify when decay is "out of tempo." We show how the building of biological clocks rests on particular forms of knowing decay: In the academic laboratory, researchers focus on endo-processes of decay that are internal to the person, but when the technology moves to the market, the focus shifts as staff bracket decay as exo-processes, which are seen as resulting from a person's lifestyle. As the technology of biological clocks travels from the laboratory to the market of online testing of the consumer's biological age, we observe shifting visions of aging: from an inevitable trajectory of decline to a malleable and plastic one. While decay is an inevitable trajectory starting at birth and ending with death, the commercialization of biological clocks points to ways of stretching time between birth and death as individuals "optimize" their biological age through lifestyle changes. Regardless of admitted uncertainties about what is measured and the connection between maintenance and future health outcomes, the aging person is made responsible for their decaying body and for enacting maintenance to slow down decay. We show how the biological clock's way of "knowing" decay turns aging and its maintenance into a life-long concern and highlight the normative implications of framing decay as malleable and in need of intervention.

Democratic research: Setting up a research commons for a qualitative, comparative, longitudinal interview study during the COVID-19 pandemic

The sudden and dramatic advent of the COVID-19 pandemic led to urgent demands for timely, relevant, yet rigorous research. This paper discusses the origin, design, and execution of the SolPan research commons, a large-scale, international, comparative, qualitative research project that sought to respond to the need for knowledge among researchers and policymakers in times of crisis. The form of organization as a research commons is characterized by an underlying solidaristic attitude of its members and its intrinsic organizational features in which research data and knowledge in the study is shared and jointly owned. As such, the project is peer-governed, rooted in (idealist) social values of academia, and aims at providing tools and benefits for its members. In this paper, we discuss challenges and solutions for qualitative studies that seek to operate as research commons.

Renting Valuable Assets: Knowledge and Value Production in Academic Science

This paper explores what it takes for research laboratories to produce valuable knowledge in academic institutions marked by the coexistence of multiple evaluative frameworks. Drawing upon ethnographic fieldwork carried out in two UK-based epigenetics research laboratories, I examine the set of practices through which research groups intertwine knowledge production with the making of scientific, health and wealth value. This includes building and maintaining a portfolio of valuable resources, such as expertise, scientific credibility or data and turning these resources into assets by carefully organising and managing their value. Laboratories then put these assets to productive use within and outside their labs towards the creation or extraction of value. I identify two models for producing value within academic science: a commodity-based model whereby laboratories mobilise their assets to produce results, which can be converted into publications for the accumulation of credibility capital; and a rentier model of accumulation, whereby laboratories own valuable assets, which they rent out to others outside their lab against a revenue. Following recent developments in STS on value production in the bioeconomy, I argue that the concepts of asset and rent are essential analytical tools to get to grips with the origins of value within academic science.

Caring for data: Value creation in a data-intensive research laboratory

Drawing upon ethnographic observations of staff working within a research laboratory built around research and clinical data from twins, this article analyzes practices underlying the production and maintenance of a research database. While critical data studies have discussed different forms of 'data work' through which data are produced and turned into effective research resources, in this paper we foreground a specific form of data work, namely the affective and attentive relationships that humans build with data. Building on STS and feminist scholarship that highlights the importance of care in scientific work, we capture this specific form of data work as care. Treating data as relational entities, we discuss a set of caring practices that staff employ to produce and maintain their data, as well as the hierarchical and institutional arrangements within which these caring practices take place. We show that through acts of caring, that is, through affective and attentive engagements, researchers build long-term relationships with the data they help produce, and feel responsible for its flourishing and growth. At the same time, these practices of care - which we found to be gendered and valued differently from other practices within formal and informal reward systems - help to make data valuable for the institution. In this manner, care for data is an important practice of valuation and valorisation within data-intensive research that has so far received little explicit attention in scholarship and professional research practice.

When more data means better results: Abundance and scarcity in research collaborations in epigenetics

Drawing upon ethnographic findings from an epigenetics research laboratory in the United Kingdom, this paper explores practices of research collaborations in the field of epigenetics, and epigenomics research consortia in particular. I demonstrate that research consortia are key scientific infrastructures that enable the aggregation of masses of data deemed necessary for the production of results and the fostering of epistemic value. Building on STS scholarship on value production, and the concept of asset, I show that the production of valuable research within epigenomics research consortia rests on the active organisation and management of abundance and scarcity. It involves shaping and standardising the masses of data gathered in consortia, while it also entails research teams enclosing their data within their laboratories' walls. As they do so, research teams construct data into scarce and monopolised assets, which they can put to productive use in collaborative endeavours against a revenue. In addition to contributing empirical and critical insights into the ways epigenetics knowledge is formed and negotiated in specific research contexts, this paper offers conceptual tools to examine and problematise knowledge production practices in data-intensive research more broadly. In particular, it points out that while contemporary big biology is marked by the generalised imperative to 'share' data and 'open' science, collaborative endeavours within research consortia are built around forms of exclusions.

Markers as mediators: A review and synthesis of epigenetics literature

Epigenetics, the study of the processes that control gene expression without a change in DNA sequence, highlights the importance of environmental factors in gene regulation. This paper maps the terrain of epigenetics and identifies four main research subfields: gene expression; molecular epigenetics; clinical epigenetics and epigenetic epidemiology. Within and across these fields, we analyse of what is conceptualised as environment and demonstrate the variable ways authors understand epigenetics environments. Then, following an analysis of the discursive strategies employed by epigenetics researchers, we demonstrate how authors portray the interactions between genes, epigenetics, and environment as relationships linking the outside (where the environment is located) with the inside (where the genes are located). We argue that authors assign specific roles to each actor: the environment as the active player initiating the relationship, the genes as recipients, and epigenetics as mediators between environment and genes. Framed as mediators, epigenetic markers can be understood as enablers of communication between environment and genome, capable of processing and organising signals so as to regulate the interactions between the actors of epigenetic relationships. This finding complicates the observation by social science scholars that the interactions between environment and genes can be understood through the concept of signal.

Dihydroxyacetone conversion into lactic acid in an aqueous medium in the presence of metal salts: influence of the ionic thermodynamic equilibrium on the reaction performance

Different Lewis acid aluminium complexes catalyse the successive reactions to convert dihydroxyacetone into lactic acid in an aqueous medium.

Hospital-wide prospective mandatory surveillance of invasive aspergillosis in a French teaching hospital (2000-2002)

A multidisciplinary working group devoted to epidemiological surveillance of invasive aspergillosis (IA) was created in January 2000 in Grenoble University Hospital. This article presents the results of a three-year IA surveillance. The multidisciplinary working group surveyed all hospitalized patients, and the mycology laboratory detected most suspected IA cases. Cases were reviewed monthly by the Aspergillosis Committee, and were classified according to international consensus criteria. Possible nosocomial acquisition was determined. Among the 490 alerts, 74 IA cases were observed: six proven cases (8%), 36 (49%) probable cases and 32 (43%) possible cases. The incidence was 4.4 (95% CI 3.4-5.4) IA/100 000 patient-days. Among the proven and probable IA cases, we observed 10 nosocomial cases and six cases of undetermined origin. No cases were noted in the protected rooms in the haematology unit. Only one cluster of cases (three nosocomial cases) was detected in the haematology unit. Forty-three percent of cases (N=32) were hospitalized in the haematology unit, and all other cases were hospitalized elsewhere. This three-year survey found a high rate of non-nosocomial IA cases and a high frequency of IA cases hospitalized in units other than haematology. Thus, this study shows the importance of IA surveillance in haematology units and all high-risk units.

Funiculitis due to Schistosoma haematobium: uncommon diagnosis using parasitologic analysis of semen

Schistosomal funiculitis is one of the rare localizations of longstanding chronic infection with schistosomiasis. We report a case of a 24-year-old-man who experienced iliac fossa pain and weight loss eight years after his last trip to Mali. Clinical diagnosis of lesions in the genitourinary tract due to schistosomiasis and biologic analysis are required to diagnose this uncommon localization of schistosomiasis.

[Emerging parasitosis ans mycosis: risk and threats for the new millenium]

For multiple reasons, the emergent infectious risks do not stop increasing these last twenty years. The climatic modifications and the human interventions modifying the biotope as well as the rapid spreading of resistant strains to treatments, generate re-emergence or emergence, all the more dramatic as the means of fight are reduced. These emergent or re-emergent diseases are extremely worrisome as their diagnosis and their prevention are often difficult. The important infesting power of parasites and the particularly effective capacities of adaptation of these eucaryotes contributed to the public health problems. Anthropozoonoses and zoonoses constitute a permanent risk the control of which is imaginary. The new pathogenic agents, the unusual clinical demonstrations in the context of deficiency of the host immune functions imply attentiveness and a permanent up to date of the knowledge of the biologist and of the different professionals of health. The risks with which are confronted the humanity during this century underline the necessity of determining mechanisms involved in the pathogenesis. The determination of the specific and vital biologic processes for the microorganism, could allow to define the most appropriated targets and the most effective and original means of fight.

[Role of local immunity in invasive pulmonary aspergillosis]

A LEADING CAUSE OF MORTALITY: Inhalation of fungal spores may cause infection and/or inflammation, which is dependent on the nature of the fungus as well as the individual's immune status. Aspergillus fumigatus is responsible for a dramatic pathology, invasive aspergillosis (IA). IA has become a leading cause of death, mainly among bone marrow transplantation or solid-organ recipients, but also among AIDS patients. IMMUNE RESPONSE: The diversity of immune failure suggests that many lines of immunity are implicated in the A. fumigatus elimination process. Non specific immunity plays a major role in the defence against A. fumigatus, including three major lines: anatomical barriers, humoral components, phagocytic cells. But acquired immunity plays a role with different T-cell subsets and their associated cytokines. FUNGUS-HOST RELATIONSHIPS: The relationship between the fungus and its host is complex and could be again study to improve the prevention and the treatment of IA. The aim of this review is a synthesis of the knowledge about the immunity response against Aspergillus fumigatus in IA.

Emerging pathogens

The ever increasing numbers of immunosuppressed individuals has led to a significant increase in the incidence of opportunistic infections, particularly those caused by fungi. The epidemiology of infections caused by the common fungal pathogens such as Candida albicans, Cryptococcus neoformans and Aspergillus fumigatus has been well documented. However, in addition to these, a number of species which have previously been unrecognized (e.g., C. dubliniensis) or have previously been assumed to be non-pathogenic (e.g., Saccharomyces cerevisiae, Scedosporium spp. and Fusarium spp.) have emerged as agents of human disease. Since these species have only been identified recently as human pathogens, their role in disease is poorly understood. In most cases, identification of these species is problematic and therefore their epidemiology has yet to be elucidated adequately. In addition, several of these species fail to respond to conventional antifungal therapies. In this article, we describe the emergence of two separate yeast species (C. dubliniensis and S. cerevisiae) and two separate groups of moulds (Scedosporium prolificans and Fusarium spp.), as human pathogens. It is apparent from what we already know, that much work has yet to be performed before we have a clear understanding of how these species cause disease and most importantly how they can be controlled.

Hydrocortisone, prednisolone and dexamethasone act on Aspergillus fumigatus in vitro susceptibility to itraconazole

In a previous in vitro investigation from the same laboratory a therapeutic level of hydrocortisone enhanced the itraconazole susceptibility of a single strain of Aspergillus fumigatus. In the present work, the influence of therapeutic levels of hydrocortisone (1 microM), prednisolone (0.125 microM 0.25 microM and 0.5 microM) and dexamethasone (0.25 microM and 0.5 microM) on the itraconazole susceptibility of four A. fumigatus strains, was determined. A. fumigatus conidia were germinated either in the absence or in the presence of a glucocorticoid. The germinated conidia were then spread onto plates and grown either in the presence or in the absence of a glucocorticoid, together with increasing concentrations of itraconazole. The mean colony forming units (CFU) were measured. Two factor analyses of variance showed that hydrocortisone significantly (p <0.001) potentiated the action of itraconazole. The cytotoxic effect of prednisolone on the fungal strains added significantly to the effect of itraconazole (p <0.001). Dexamethasone was also cytotoxic to the fungus but, when used in conjunction with itraconazole, it effectively increased (p <0.01) the number of CFU. This study showed a direct effect of glucocorticoids, currently in use for patient therapy, on in vitro A. fumigatus susceptibility to itraconazole.

[Subcutaneous mycosis due to Scopulariopsis brevicaulis in an immunocompromised patient]

BACKGROUND

Scopulariopsis brevicaulis is a causal agent of onchomycosis. We report the unusual clinical manifestations caused by this opportunist fungus.

CASE REPORT

A 61-year-old man consulted in February 1997 for a budding lesion located on the right medial malleolus. This patient had had a liver transplantation for primary biliary cirrhosis in 1990 and had been taking prednisone and cyclosporine since this time. Cyclosporine had been recently replaced by tacrolimus. The histology examination of a lesion specimen taken from the ankle evidenced a dermal mycosis due to opportunist filamentous fungus. Total excision was performed. The patient then developed nodular lesions of the left elbow during the summer of 1997. Mycology culture of a skin biopsy grew numerous colonies of Scopulariopsis brevicaulis. Excision of the elbow lesion was delayed due to hospitalization for suspected graft rejection and development of insulin-dependent diabetes. The elbow lesion was then resected followed by a skin graft. The mycology examination identified the same causal agent.

DISCUSSION

This liver transplant recipient developed two unusual extra-ungual localizations (ankle and elbow) of a Scopulariopsis brevicaulis infection. Chronic immunosuppression favored development of the infection with a pseudo-epithéliomatous presentation. The histology and mycology examinations were necessary for positive diagnosis.

Diagnosis of malaria in non-endemic countries by the ParaSight-F test

QBC, examination of thin blood smears, and Parasight-F were performed for every case of malaria suspected between May 1997 and December 1998. Data from 310 patients were reported. Fifty had malaria infection diagnosed by QBC and thin blood film, among whom 39 had Plasmodium falciparum infection. Three of these 39 were negative with the Parasight-F test. Eleven patients had a positive ParaSight-F test but microscopic diagnosis methods were negative. Interpretation of these 11 positive ParaSight-F results is proposed to depend on clinical criteria.

Recurrent subcutaneous infection due to Scopulariopsis brevicaulis in a liver transplant recipient

We describe a case of recurrent Scopulariopsis brevicaulis subcutaneous infection, which occurred 6 years after the patient underwent liver transplantation. Combined surgery and long-term oral therapy with terbinafine resulted in a favorable outcome, although this is not the rule in the previously reported S. brevicaulis infections in immunocompromised patients.

[Diagnosis of malaria in non-endemic countries : value, limitations and complementarity of existing methods]

The biological diagnosis of malaria is urgent to avoid rapid and fatal outcome. Every year in France, 5,000 imported malaria cases are observed. Thin stained blood smear microscopical examination remains the reference method of diagnosis; however its performance is linked to the professional competence of the biologists. Thus easier methods have been developed (QBC test). Some of them, limited to the diagnosis of malaria due to Plasmodium falciparum do not require highly skilled personal to perform or interpret (antigen detection on dipsticks, tests Parasight or cardboard, ICT Malaria Pf), but limitations and errors occurred. These different tests must be complementary methods of traditional diagnosis. In association with microscopical examinations, they provide rapid and efficient diagnosis of malaria in non-endemic areas. Relying on our experience, the best association is: QBC + thin blood smear and depending of results antigen detection (ParaSight F, ICT Malaria Pf).

Asymmetric synthesis of 2-methyl cyclohexane carboxylic acids by heterogeneous catalysis: mechanistic aspects

The catalytic hydrogenation of (S)-alkyl-N-(2-methylbenzoyl)pyroglutamates was studied over supported rhodium and ruthenium catalysts at room temperature and a pressure of 5 MPa. The reaction was diastereoselective with the predominant formation of (1S,2R)-2-methylcyclohexane carboxylic acid with a diastereomeric excess (de) of up to 96%. The most stable conformation was determined by means of a combination of modelling calculations, NMR spectroscopy and X-ray structural determination. In this conformation, the carbonyl group of the pyroglutamate auxiliary shields one face of the aromatic ring. The observed selectivity may thus be explained by a preferential adsorption at the unshielded face which avoids steric repulsion by the C=O group to result in a cis hydrogenation. The addition of an amine, the nature of the support (alumina or active carbon) or of the metal (Rh or Ru) were shown to give additional stabilisation of the adsorption at the unshielded face to increase the diastereoisomeric excess.

Aspergillus Fumigatus antigen detection in sera from patients at risk for invasive aspergillosis

We have developed an inhibition enzyme immunoassay (inhibition-EIA) to monitor for the occurrence of invasive aspergillosis (IA) in sera from 45 immunocompromised (IC) patients. The test uses rabbit polyclonal antibodies and a mixture of components from Aspergillus fumigatus, containing three predominant antigens with molecular weights of 18,000, 33,000, and 56,000. Circulating antigens were found in five of seven proven cases of IA due to A. fumigatus. In two of the five positive cases, antigenemia was detected with inhibition-EIA earlier than with X ray or other biological methods. No antigens were detected in the sera from two patients with proven IA due to Aspergillus flavus and Aspergillus terreus nor in the sera from four patients with probable IA. Circulating antigens were not detected in the control group, composed of 30 healthy adult blood donors. Four of the 32 at-risk patients examined, though they displayed no definite evidence of IA, gave a positive result in this test. The sensitivity, specificity, and positive predictive value of inhibition-EIA were 71.4, 94.4, and 71.2%, respectively. The data were compared with those obtained by a latex agglutination assay of galactomannan (GM) that was positive in only one patient with probable IA. The higher sensitivity obtained by inhibition-EIA may well be due to its ability to detect circulating antigens other than GM in the sera of IC patients with IA. Detecting these antigens may improve the diagnosis of IA, as they may serve as markers of this infection.

Identification of amylase crystalloids in cystic lesions of the parotid gland

OBJECTIVE

To identify alpha-amylase crystalloid formations in parotid specimens obtained by fine needle aspiration.

STUDY DESIGN

The study concerned three cases of sialadenitis with crystalloid formation observed between 1993 and 1998. In one of these cases, transmission electron microscopy, mass spectrometry and measurement of amylase activity were used to characterize the nature of the crystalloids.

RESULTS

Light microscopy revealed the same crystalloid structure in all three cases. In one case, where the material was saved, a biochemical method made it possible to reveal high amylase activity, while protein electrophoresis and mass spectrometry were used to identify salivary alpha-amylase.

CONCLUSION

Crystalloids of salivary alpha-amylase can be identified by May-Grünwald-Giemsa and Papanicolaou stain and can be rapidly confirmed through determination of amylase activity.

[Fungal and parasitic nosocomial infections: importance and limitations of disinfection methods]

Due to the increase of opportunistic mycosis and parasitosis for several years, the management of fungal and parasitic risk in hospital has become a necessity and an obligation. The authors remind the main rules and knowledges essential to an optimal management of the fungal and parasitic disinfection in hospital. They summarize the efficiency of different disinfection processes in relation to yeasts, filamentous fungi, Pneumocystis carinii, Cryptosporidia and Microsporidia involved in hospital pathology.

Does hydrocortisone modify the in vitro susceptibility of Aspergillus fumigatus to itraconazole and amphotericin B?

To analyse if hydrocortisone could modify the in vitro susceptibility of Aspergillus fumigatus to antifungal drugs, we developed a procedure to test the susceptibility of an A. fumigatus strain to amphotericin B and itraconazole, grown in the presence and in the absence of hydrocortisone. Conidia were germinated in the presence or the absence of hydrocortisone in Czapek medium without antifungal drug. A dilution of these cultures (5x10(3) conidia ml(-1)) was spread onto Czapek-agarose plates containing both antifungal drug and hydrocortisone. The cfu per plate were enumerated and compared. A therapeutic concentration of hydrocortisone induced a significant increase in the susceptibility to itraconazole. Conversely, the susceptibility to amphotericin B was not significantly modified when this antifungal drug was associated with hydrocortisone.

Specific antibody detection in invasive aspergillosis by analytical isoelectrofocusing and immunoblotting methods

Aspergillus fumigatus antigens have been tested to determine their potential as aids in the diagnosis of invasive aspergillosis (IA). Immunoglobulin G (IgG) antibodies to these antigens were detected by analytical isoelectrofocusing in conjunction with immunoblotting. A total of 12 antigenic fractions, including culture filtrates and surface and mycelial extracts of A. fumigatus, were investigated. Eleven were reactive with serum specimens from patients with aspergilloma, which served as positive controls for the evaluation of a specific IgG response. Eight of 12 antigens showed good responses with serum specimens from patients with allergic bronchopulmonary aspergillosis, which were used to assess the sensitivity of IgG detection. No measurable reactivity was detected in 18 negative control serum specimens, while 11 of 13 patients with proven, highly probable, or probable cases of IA had anti-Aspergillus IgG to multiple antigenic preparations. Patients with IA who were capable of mounting a substantial humoral response to Aspergillus antigens gave an antibody profile with five antigenic preparations which seemed to be characteristic of the disease. Data show that this method is highly sensitive and may allow the selection of fractions which are both highly antigenic and specific for the detection of antibodies to Aspergillus antigens. They also indicate that the use of a spectrum of antigenic molecules is advisable, given the variability observed in the immune responses of individual patients.

Itraconazole in the treatment of aspergillosis: a study of 16 cases

Itraconazole, a new triazole antifungal agent, has marked in vitro activity against filamentous fungi, particularly Aspergillus. We studied three groups of patients suffering from aspergillosis (16 cases): six affected with aspergilloma, three with allergic bronchopulmonary aspergillosis and seven with invasive aspergillosis. The survey consisted in clinical, radiological, mycological and serological evaluations with respect to drug plasma levels. Itraconazole was given at a dosage of 200-400 mg day-1 for periods ranging from 14 to 488 days. Out of the 16 patients, nine responded to therapy (recovery or improvement) and one failed to respond. Three patients improved but experienced relapses and three others could not be evaluated because of liver function disorders, so that treatment had to be stopped prematurely.

Western blot detection of IgG anti-Aspergillus fumigatus elastase in sera of patients with aspergillosis

Anti-Aspergillus fumigatus alkaline protease IgG was investigated by Western blot. Specific IgG antibodies were detected in sera of two of nine patients with proven or highly probable invasive aspergillosis and in sera of one of eight patients with proven or highly probable allergic bronchopulmonary aspergillosis. No response was obtained in sera of 23 control patients. The specific but transient IgG response to this induced enzyme does not recommend its use as sole serodiagnostic aid.

Fungal polysaccharides

Fungal polysaccharides are cell wall components which may act as antigens or as structural substrates. As antigens, the role of mannans in Saccharomyces cerevisiae and Candida albicans, and of glycoproteins in Aspergillus fumigatus are discussed. Analyses on beta-glucan synthetase in Paracoccidioides brasiliensis and the inhibitory effect of Hansenula mrakii killer toxin on beta-glucan biosynthesis are also considered.