Controlled Authoring of Biological Experiment Reports

We give a demonstration of an application of XRCE's controlled text authoring system MDA to biological experiment reports. This work is the result of a collaboration between XRCE's Docu- ment Content Models team, CNRS's Institut de Biologie Structurale, and Protein'eXpert, a company specialized in biotechnology based in Grenoble. We start with a brief presentation of the partners involved and their respective goals. We then give some technical background on the MDA system. Some novel features of the application are discussed, in particular how MDA can be used for integrating the formalization of an experimental protocol with its associated textual documenta- tion

Semantically-based text authoring and the concurrent documentation of experimental protocols

Colloque avec actes et comité de lecture. internationale./http://portal.acm.org/citation.cfm?id=958220.958256&coll=portal&dl=ACM&type=series&idx=958220&part=Proceedings&WantType=Proceedings&title=Document%20Engineering&CFID=1928112&CFTOKEN=91775967International audienceWe describe an application of controlled text authoring to biological experiment reports. This work is the result of a collaboration between a computational linguistics team and biological experts from a startup company specializing in protein production studies. We start by presenting our semantically-controlled authoring system, MDA (Multilingual Document Authoring), an expressive model for specifying well-formedness conditions both at the level of the document content and at the level of its textual realization. We then discuss the practical needs of experiment documentation in bioengineering. We then go on to describe the prototype we have developed for this application domain, along with a preliminary evaluation. Finally we discuss a promising new idea emerging from the experimentation but which seems of wider applicability: how the authoring system represents a step towards integrating the formalization of an experimental protocol with its associated textual documentation

Recombinant Nox4 cytosolic domain produced by a cell or cell-free base systems exhibits constitutive diaphorase activity

The membrane protein NADPH (nicotinamide adenine dinucleotide phosphate) oxidase Nox4 constitutively generates reactive oxygen species differing from other NADPH oxidases activity, particularly in Nox2 which needs a stimulus to be active. Although the precise mechanism of production of reactive oxygen species by Nox2 is well characterized, the electronic transfer throughout Nox4 remains unclear. Our study aims to investigate the initial electronic transfer step (diaphorase activity) of the cytosolic tail of Nox4. For this purpose, we developed two different approaches to produce soluble and active truncated Nox4 proteins. We synthesized soluble recombinant proteins either by in vitro translation or by bacteria induction. While proteins obtained by bacteria induction demonstrate an activity of 4.4 ± 1.7. nmol/min/nmol when measured against iodonitro tetrazolium chloride and 20.5 ± 2.8. nmol/min/nmol with cytochrome c, the soluble proteins produced by cell-free expression system exhibit a diaphorase activity with a turn-over of 26 ± 2.6. nmol/min/nmol when measured against iodonitro tetrazolium chloride and 48 ± 20.2. nmol/min/nmol with cytochrome c. Furthermore, the activity of the soluble proteins is constitutive and does not need any stimulus. We also show that the cytosolic tail of the isoform Nox4B lacking the first NADPH binding site is unable to demonstrate any diaphorase activity pointing out the importance of this domain. © 2012 Elsevier Inc.

Hepatitis E virus-associated cryoglobulinemia in solid-organ-transplant recipients

International audienceBackground & AimsAn association between hepatitis E virus (HEV) infection and cryoglobulinemia has been suggested. The aims of this study were to assess the prevalence of cryoglobulinemia during HEV infection in solid‐organ–transplant (SOT) recipients, to describe its outcomes under ribavirin therapy and to evaluate its effects on kidney function and histology.MethodsBetween November 2005 and June 2016, 128 cases of HEV infection were diagnosed among SOT recipients followed in our institution. Cryoglobulinemia data obtained from 66 patients during acute‐phase HEV and 51 patients during chronic‐phase HEV were compared to a historical control group of 89 SOT recipients without HEV markers. Cryoglobulins were also monitored in a group of 43 patients treated by ribavirin.ResultsThe prevalence of cryoglobulinemia was increased in HEV‐infected SOT patients during a chronic phase (52.9%) compared to HEV‐infected SOT patients at acute phase (36.4%) (P = .1) and to HEV‐negative SOT patients (23.6%) (P < .001). HEV infection was identified as an independent predictive factor for cryoglobulinemia (OR 2.3, CI 95%: 1.17‐4.55, P = .02). After ribavirin therapy and HEV clearance, the prevalence of cryoglobulin was significantly decreased from 53.5% to 20.9% (P = .003). Kidney function was significantly worse and proteinuria tended to be higher in chronically HEV‐infected patients with cryoglobulinemia compared to those without cryoglobulinemia. Membranoproliferative glomerulonephritis was diagnosed in 2 patients, of which 1 had detectable cryoglobulinemia.ConclusionsIn conclusion, a relationship between HEV and cryoglobulin formation seems to exist. However, the clinical impact of cryoglobulinemia in SOT patients infected with HEV has to be confirmed

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L’acte de lecture : une question pour l’historien des techniques et des civilisations, pour l’ethnologue et l’anthropologue, pour le psychologue et le cognitiviste, pour l’enseignant et le sociologue, pour le bibliothécaire et le critique littéraire, pour le responsable politique enfin. Le philosophe a aussi son mot à dire, il le fait depuis les premiers moments de l’histoire de la philosophie. Le présent numéro étudie la question d’un point de vue philosophique, sous trois aspects : études d’histoire de la philosophie, théories de la lecture, lectures d’objets insolites. Le parcours se conclut sur la figure d’un lecteur exemplaire, récemment disparu : Jean Starobinski