Trajectory Synthesis for Fisher Information Maximization

Estimation of model parameters in a dynamic system can be significantly improved with the choice of experimental trajectory. For general, nonlinear dynamic systems, finding globally "best" trajectories is typically not feasible; however, given an initial estimate of the model parameters and an initial trajectory, we present a continuous-time optimization method that produces a locally optimal trajectory for parameter estimation in the presence of measurement noise. The optimization algorithm is formulated to find system trajectories that improve a norm on the Fisher information matrix. A double-pendulum cart apparatus is used to numerically and experimentally validate this technique. In simulation, the optimized trajectory increases the minimum eigenvalue of the Fisher information matrix by three orders of magnitude compared to the initial trajectory. Experimental results show that this optimized trajectory translates to an order of magnitude improvement in the parameter estimate error in practice.Comment: 12 page

The SWISS-2DPAGE database: what has changed during the last year

Swiss-2DPAGE (http://www.expasy.ch/ch2d/) is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database established in 1993. The current release contains 21 reference maps from human and mouse biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps now have 2480 identified spots, corresponding to 528 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence. During the last year, the SWISS-2DPAGE has undergone major changes. Six new maps have been added, and new functions to access the data have been provided through the ExPASy server. Finally, an important change concerns the database funding sourc

Matrix metalloproteinase 9 and cellular fibronectin plasma concentrations are predictors of the composite endpoint of length of stay and death in the intensive care unit after severe traumatic brain injury

BACKGROUND: The relationship between severe traumatic brain injury (TBI) and blood levels of matrix metalloproteinase-9 (MMP-9) or cellular fibronectin (c-Fn) has never been reported. In this study, we aimed to assess whether plasma concentrations of MMP-9 and c-Fn could have predictive values for the composite endpoint of intensive care unit (ICU) length of stay (LOS) of survivors and mortality after severe TBI. Secondary outcomes were the state of consciousness measured with the Glasgow Coma Scale (GCS) of survivors at 14 days and Glasgow Outcome Scale Extended (GOSE) at 3 months. METHODS: Forty-nine patients with abbreviated injury scores of the head region ≥ 4 were included. Blood was sampled at 6, 12, 24 and 48 hours after injury. MMP-9 and c-Fn concentrations were measured by ELISA. The values of MMP-9 and c-Fn, and, for comparison, the value of the GCS on the field of the accident (fGCS), as predictors of the composite outcome of ICU LOS and death were assessed by logistic regression. RESULTS: There was a linear relationship between maximal MMP-9 concentration, measured during the 6-12-hour period, and maximal c-Fn concentration, measured during the 24-48-hour period. The risk of staying longer than 9 days in the ICU or of dying was increased in patients with a maximal early MMP-9 concentration ≥ 21.6 ng/ml (OR = 5.0; 95% CI: 1.3 to 18.6; p = 0.02) or with a maximal late c-Fn concentration ≥ 7.7 μg/ml (OR = 5.4; 95% CI: 1.4 to 20.8; p = 0.01). A similar risk association was observed with fGCS ≤8 (OR, 4.4; 95% CI, 1.2-15.8; p = 0.02). No relationship was observed between MMP-9, c-Fn concentrations or fGCS and the GCS at 14 days of survivors and GOSE at 3 months. CONCLUSIONS: Plasma MMP-9 and c-Fn concentrations in the first 48 hours after injury are predictive for the composite endpoint of ICU LOS and death after severe TBI but not for consciousness at 14 days and outcome at 3 months

Evaluation of the ability of Bifidobacterium longum to metabolize human intestinal mucus

The ability of Bifidobacterium longum to use intestinal mucus as a metabolizable source was characterized. Bifidobacterium longum biotype longum NCIMB8809 was grown in a chemically semi-defined medium supplemented with human intestinal mucus, and the cytoplasmic protein profiles and several glycosyl hydrolase activities were analysed and compared with those obtained from the same bacterium grown in the absence of mucus. We were able to identify 22 different proteins in the cytoplasmic fraction, of which nine displayed a different concentration in the presence of mucus. Among the proteins whose concentrations varied, we found specific enzymes that are involved in the response to different environmental conditions, and also proteins that mediate interaction with mucus in bacteria. Significant changes in some glycoside-hydrolysing activities were also detected. In addition, stable isotope labelling of amino acids in cell culture demonstrated that B. longum incorporates leucine from the glycoprotein matrix of mucin within its proteins. This study provides the first proteomic data regarding the interaction of B. longum with intestinal mucus, and contributes to the understanding of the behaviour of this intestinal species in its natural ecological nich

A multiparameter panel method for outcome prediction following aneurysmal subarachnoid hemorrhage

Purpose: Accurate early anticipation of long-term irreversible brain damage during the acute phase of patients with aneurysmal subarachnoid hemorrhage (aSAH) remains difficult. Using a combination of clinical scores together with brain injury-related biomarkers (H-FABP, NDKA, UFD1 and S100β), this study aimed at developing a multiparameter prognostic panel to facilitate early outcome prediction following aSAH. Methods: Blood samples of 141 aSAH patients from two separated cohorts (sets of 28 and 113 patients) were prospectively enrolled and analyzed with 14months of delay. Patients were admitted within 48h following aSAH onset. A venous blood sample was withdrawn within 12h after admission. H-FABP, NDKA, UFD1, S100β and troponin I levels were determined using classical immunoassays. The World Federation of Neurological Surgeons (WFNS) at admission and the Glasgow Outcome Score (GOS) at 6months were evaluated. Results: In the two cohorts, blood concentration of H-FABP, S100β and troponin I at admission significantly predicted unfavorable outcome (GOS 1-2-3). A multivariate analysis identified a six-parameter panel, including WFNS, H-FABP, S100β, troponin I, NDKA and UFD-1; when at least three of these parameters were simultaneously above cutoff values, prediction of unfavorable outcome reached around 70% sensitivity in both cohorts for 100% specificity. Conclusion: The use of this panel, including four brain injury-related proteins, one cardiac marker and a clinical score, could be a valuable tool to identify aSAH patients at risk of poor outcom

Les contaminants métalliques traqués par la spectrométrie atomique dans le bioéthanol

International audienceDans le cadre de la transition énergétique, l'utilisation de biocarburants à base de carbone renouvelable est une des alternatives permettant de limiter l'émission de CO 2 fossile. La diversité des sources potentielles de biomasse requiert en revanche une caractérisation des polluants inorganiques éventuels qui pourraient s'avérer nuisibles. Dans cette optique, une investigation sur les teneurs en contaminants métalliques dans différentes sources de bioéthanol a été menée en collaboration avec l'Université d'Alicante. Nous avons constaté des teneurs systématiquement inférieures au mg/kg sur la totalité des échantillons analysés, lesquels représentent un panel important des bioéthanols utilisés en tant que base de carburant ou base pétrochimique. La source de ces très faibles teneurs a été investiguée en suivant le schéma de fabrication du bioéthanol à partir de betteraves et les résultats montrent que la plupart des métaux présents dans le bioéthanol ont comme source la biomasse de départ. L'étape de distillation est particulièrement efficace pour éliminer ces contaminants : les concentrations sont divisées par 10000. Abstract : As part of the energy transition, the use of renewable biofuels is one of the alternatives to limit the emission of fossil CO 2. Anyhow, the assessment of the environmental benefit provided by the use of biofuels requires a thorough characterization of the inorganic pollutants potentially present in the biomass used as a source of biofuel. With this in mind, an investigation on the levels of metallic contaminants in different bio-ethanol samples was conducted in collaboration with the University of Alicante. The samples chosen were appropriate to be used either as a fuel themselves or blended with fossil fuels. We have found that metallic species were present at concentrations below the mg/kg level in virtually all the bioethanol samples under study. The source of these very low levels of contaminants has been investigated following the bioethanol production scheme from beet and the results show that most of the metals present in bioethanol are also present in the original biomass. From all the procedures required to obtain the biofuel, the distillation of the syrup resulting from the fermentation step is particularly effective in removing these contaminants : Concentrations of metallic species in bioethanol is divided 10,000 times

Partial Hydrolyzed Protein as a Protein Source for Infant Feeding: Do or Don't?

Exclusive breastfeeding until the age of six months is the recommended feeding method for all infants. However, this is not possible for every infant. Therefore, a second choice of feeding, as close as possible to the gold standard, is needed. For historical reasons, this has been cow's-milk-based feeding. This paper discusses if this second-choice feeding method should contain intact protein or partially hydrolyzed proteins. The limited data available indicates that mother's milk is relatively rich in bioactive peptides. Whether partially hydrolyzed protein might be a protein source closer to human milk protein content than intact cow's milk needs further research. However, more research on protein and bioactive peptides in mother's milk should be a priority for future scientific development in this field. Results of such research will also provide an answer to the question of which option would be the best second choice for infant feeding if sufficient breast milk is not available

Ubiquitin Fusion Degradation Protein 1 as a Blood Marker for The Early Diagnosis of Ischemic Stroke

Background: Efficacy of thrombolysis in acute ischemic stroke is strongly related to physician’s ability to make an accurate diagnosis and to intervene within 3–6 h after event onset. In this context, the discovery and validation of very early blood markers have recently become an urgent, yet unmet, goal of stroke research. Ubiquitin fusion degradation protein 1 is increased in human postmortem CSF, a model of global brain insult, suggesting that its measurement in blood may prove useful as a biomarker of stroke.Methods: Enzyme-linked immunosorbent assay (ELISA) was used to measure UFD1 in plasma and sera in three independent cohorts, European (Swiss and Spanish) and North-American retrospective analysis encompassing a total of 123 consecutive stroke and 90 control subjects.Results: Highly significant increase of ubiquitin fusion degradation protein 1 (UFD1) was found in Swiss stroke patients with 71% sensitivity (95% CI, 52–85.8%), and 90% specificity (95% CI, 74.2–98%) (N = 31, p < 0.0001). Significantly elevated concentration of this marker was then validated in Spanish (N = 39, p < 0.0001, 95% sensitivity (95% CI, 82.7–99.4%)), 76% specificity (95% CI, 56.5–89.7%)) and North-American stroke patients (N = 53, 62% sensitivity (95% CI, 47.9–75.2%), 90% specificity (95% CI, 73.5–97.9%), p < 0.0001). Its concentration was increased within 3 h of stroke onset, on both the Swiss (p < 0.0001) and Spanish (p = 0.0004) cohorts.Conclusions: UFD1 emerges as a reliable plasma biomarker for the early diagnosis of stroke, and in the future, might be used in conjunction with clinical assessments, neuroimaging and other blood markers.Abbreviations: AUC: area under curve; BBB: blood–brain barrier; CO: cut-off; CSF: cerebrospinal fluid; CT: computerized tomography; H-FABP: heart-fatty acid binding protein; MMP9: matrix metalloproteinase 9; MRI: magnetic resonance imaging; NDKA: nucleotide diphosphate kinase A; OR: odds ratio; RFU: relative fluorescence units; ROC: receiver operating characteristic; rtPA: recombinant tissue plasminogen activator; SE: sensitivity; SP: specificity; TIA: transient ischemic attack; UFD1: ubiquitin fusion degradation protein

The Next Generation Virgo Cluster Survey. X. Properties of Ultra-Compact Dwarfs in the M87, M49 and M60 Regions

We use imaging from the Next Generation Virgo cluster Survey (NGVS) to present a comparative study of ultra-compact dwarf (UCD) galaxies associated with three prominent Virgo sub-clusters: those centered on the massive, red-sequence galaxies M87, M49 and M60. We show how UCDs can be selected with high completeness using a combination of half-light radius and location in color-color diagrams ($u^*iK_s$ or $u^*gz$). Although the central galaxies in each of these sub-clusters have nearly identical luminosities and stellar masses, we find large differences in the sizes of their UCD populations, with M87 containing ~3.5 and 7.8 times more UCDs than M49 and M60, respectively. The relative abundance of UCDs in the three regions scales in proportion to sub-cluster mass, as traced by X-ray gas mass, total gravitating mass, number of globular clusters, and number of nearby galaxies. We find that the UCDs are predominantly blue in color, with ~85% of the UCDs having colors similar to blue GCs and stellar nuclei of dwarf galaxies. We present evidence that UCDs surrounding M87 and M49 may follow a morphological sequence ordered by the prominence of their outer, low surface brightness envelope, ultimately merging with the sequence of nucleated low-mass galaxies, and that envelope prominence correlates with distance from either galaxy. Our analysis provides evidence that tidal stripping of nucleated galaxies is an important process in the formation of UCDs.Comment: 37 pages, 40 figures. To appear in The Astrophysical Journa