parfm : Parametric Frailty Models in R

Frailty models are getting more and more popular to account for overdispersion and/or clustering in survival data. When the form of the baseline hazard is somehow known in advance, the parametric estimation approach can be used advantageously. Nonetheless, there is no unified widely available software that deals with the parametric frailty model. The new parfm package remedies that lack by providing a wide range of parametric frailty models in R. The gamma, inverse Gaussian, and positive stable frailty distributions can be specified, together with five different baseline hazards. Parameter estimation is done by maximising the marginal log-likelihood, with right-censored and possibly left-truncated data. In the multivariate setting, the inverse Gaussian may encounter numerical difficulties with a huge number of events in at least one cluster. The positive stable model shows analogous difficulties but an ad-hoc solution is implemented, whereas the gamma model is very resistant due to the simplicity of its Laplace transform

Restructurations : Regard sur ses répercussions humaines et organisationnelles

International audienceThis study has been carried out in a multinational company and which is currently undergoing a restructuring. This analysis puts the emphasis on the human and organizational effects generated by this singular context. Drawing on three theoretical concepts, the aim of this study is to check if a degree of " stress perceived " as high associated with an " organizational support perceived " as weak questions the " affective commitment " of the employees leading to bad outcomes for the company in terms of productivity and efficiency. The results confirm our predictions. Indeed, a correlation between a stress perceived as " pathological " , an organizational support perceived as weak and a moderate affective commitment is to be found for the employees surveyed.Réalisée au sein d'une multinationale en restructuration, cette étude met l'accent sur les répercussions humaines et organisationnelles générées par ce contexte singulier. En conjuguant trois concepts théoriques, l'objectif de cette recherche est de vérifier si un " stress perçu " élevé associé à un faible " soutien organisationnel perçu " remet en question " l'implication organisationnelle affective " des salariés, engendrant fatalement des conséquences négatives en termes de productivité et d'efficacité de l'entreprise. Les résultats obtenus confirment nos prédictions, témoignant d'une corrélation entre un stress perçu dit " pathologique " , un faible soutien organisationnel perçu et une implication organisationnelle affective modérée des salariés sondés

IMPACT OF THERMAL TREATMENT ON THE PROPERTIES OF THE PROTEIC FOAMS

The food foams are "whipped" products that have recently experienced significant growth in the food industry. They are appreciated by consumers for their creamy texture, taste and visual aspect. Whey proteins are particularly common ingredients in the formulation of food foams because of their functional properties (foaming properties, interfacial, emulsifying). Denaturation and aggregation of whey proteins further to a heat treatment, allows the improvement of these properties by creating protein aggregates with targeted properties. The objective of this study is to understand the impact of the intensity of heat treatment applied to a protein solution on the aggregation of proteins (proportion, size and morphology of protein assemblies) and on their foaming properties in order to better control the use properties of foamed products stabilized by whey protein aggregates (WPI). In this work, a 2% w/v of whey proteins in the presence of salt (50 mM NaCl) was heated in an Actijoule type tubular heat exchanger at 80, 90 and 100 °C. Native and denatured solutions of WPI were characterized by microcalorimetry ( DSC), size exclusion chromatography (SEC), diffusion light scattering (DLS), electrophoresis (SDS-PAGE), optical microscopy and atomic force microscopy (AFM). To assess the impact of thermal treatment on the foaming ability of protein solutions, a bubbling method has been employed. The experimental results showed that as far as the heating temperature is increased, it promotes the aggregation of proteins into oligomers which then are forming soluble aggregates of about 160 nm in diameter. We have also observed that the increase of this fraction is a continuous function of temperature for solutions treated up to 100 °C. However, the amount of insoluble aggregates formed reaches a maximum when the heat treatment temperature is 90 °C. Finally, we showed by SDS-PAGE that the soluble and insoluble aggregates are stabilized by disulfide bridges and microscopically we found that insoluble aggregates are dense and highly branched. With regard to the foaming properties of proteins, the formation of the foam was very dependent on the thermal treatment applied to protein solutions. Our results demonstrate as well that the time of bubbling is clearly correlated with the proportion of insoluble proteins and for this reason, a thermal treatment at 90 °C that leads to a significant increase of the proportion of insoluble aggregates, retards foam formation. Also, Lactoglobulin and -Lactalbumin monomers existing in the protein solutions before bubbling, appear to play a crucial role. Thus, we observed that native WPI solutions lead to the formation of dry foams, while the WPI solutions heated to temperatures of at least 80 °C lead rather to the formation of wet foams

The 1999-2000 seismic experiment of Macas swarm (Ecuador) in relation with rift inversion in Subandean foothills

International audienceWe propose to explain the origin of the double trend in seismicity of the Macas swarm in the Subandean Cordillera of Cutucú (Ecuador) and characterize the corresponding active deformation of that region. For that purpose, seismological and geological data have been used, with the deployment of a temporary seismological array, with geological field observations and image processing. We found that some earthquakes are aligned on a well known NNE SSW trend corresponding to the orientation of the nodal planes of the reverse focal mechanism of the Mw=7.0 1995 Macas earthquake as for its aftershocks. Nevertheless, many smaller events are aligned on an unexpected NNW SSE trend inside the Cutucú Cordillera. We interpret these two orientations of the Macas swarm as linked to Subandean basement thrusts inherited from the inversion tectonics of a NNE SSW trending Triassic Jurassic rift, which has been uplifted and partly extruded in the Cutucú Cordillera. The present partitioning of this part of the Subandean deformation is controlled by pre-existing NNE SSW to NNW SSE Triassic Jurassic normal faults that have been subsequently compressed transpressed and reactivated into reverse faults. Major boundary faults of the rift were NNE SSW oriented and correspond now to some main Subandean thrusts as confirms the focal mechanism of the 1995 main shock located on the eastern border (Morona frontal thrust) and the orientation of its aftershocks. In the Cutucú Cordillera, the double orientation of present swarm can be interpreted as the result of accommodation of deformation along NNW SSE pre-existing faults inside the inverted rift system, linked to the motion of the Morona frontal NNE SSW thrust

Campesinos y asalariados en la zona bananera de santa marta (1900 - 1935)

Los conflictos sociales marcaron las zonas de producción bananera desarrolladas bajo los auspicios de la United Fruit Company a partir de 1900. La mayoría de los estudios sobre las protestas contra la Compañía se ha centrado en las luchas de los asalariados para conseguir mejores condiciones de trabajo en las plantaciones bananeras. Sin embargo, estos estudios descuidan la existencia del campesinado en tales regiones y su participación en la formación  de las modalidades de protesta local que surgieron

Colony-forming and single-cell picocyanobacteria nitrogen acquisition strategies and carbon fixation in the brackish Baltic Sea

Picocyanobacteria are widespread and globally significant primary producers. In brackish waters, picocyanobacterial populations are composed of diverse species with both single-cell and colony-forming lifestyles. Compared to their marine counterparts, brackish picocyanobacteria are less well characterized and the focus of research has been weighted toward single-cell picocyanobacteria. Here, we investigate the uptake dynamics of single and colony-forming picocyanobacteria using incubations with dual carbon-13 and inorganic (ammonium and nitrate) or organic (urea and amino acids) nitrogen-15 sources during August and September 2020 in the central Baltic Sea. Phytoplankton community and group-specific uptake rates were obtained using an elemental analyzer isotope ratio mass spectrometer (EA-IRMS) and nano secondary-ion mass spectrometry (NanoSIMS). Picocyanobacteria contributed greater than one third of the ammonium, urea, amino acids, and inorganic carbon community uptake/fixation in September but  5% of the average phytoplankton biomass, suggesting that they are periodically important for the ecosystem. Colonial strain identification was not distinguishable using 16S rRNA gene amplicon data, highlighting a need for refined tools for identification of colonial forms. This study shows the significance of single-celled brackish picocyanobacteria to nutrient cycling and the importance of considering uptake and lifestyle strategies when assessing the role of picocyanobacteria in aquatic ecosystems

Glycation marker glucosepane increases with the progression of osteoarthritis and correlates with morphological and functional changes of cartilage in vivo

Background: Changes of serum concentrations of glycated, oxidized, and nitrated amino acids and hydroxyproline and anticyclic citrullinated peptide antibody status combined by machine learning techniques in algorithms have recently been found to provide improved diagnosis and typing of early-stage arthritis of the knee, including osteoarthritis (OA), in patients. The association of glycated, oxidized, and nitrated amino acids released from the joint with development and progression of knee OA is unknown. We studied this in an OA animal model as well as interleukin-1β-activated human chondrocytes in vitro and translated key findings to patients with OA. Methods: Sixty male 3-week-old Dunkin-Hartley guinea pigs were studied. Separate groups of 12 animals were killed at age 4, 12, 20, 28 and 36 weeks, and histological severity of knee OA was evaluated, and cartilage rheological properties were assessed. Human chondrocytes cultured in multilayers were treated for 10 days with interleukin-1β. Human patients with early and advanced OA and healthy controls were recruited, blood samples were collected, and serum or plasma was prepared. Serum, plasma, and culture medium were analyzed for glycated, oxidized, and nitrated amino acids. Results: Severity of OA increased progressively in guinea pigs with age. Glycated, oxidized, and nitrated amino acids were increased markedly at week 36, with glucosepane and dityrosine increasing progressively from weeks 20 and 28, respectively. Glucosepane correlated positively with OA histological severity (r = 0.58, p < 0.0001) and instantaneous modulus (r = 0.52–0.56; p < 0.0001), oxidation free adducts correlated positively with OA severity (p < 0.0009–0.0062), and hydroxyproline correlated positively with cartilage thickness (p < 0.0003–0.003). Interleukin-1β increased the release of glycated and nitrated amino acids from chondrocytes in vitro. In clinical translation, plasma glucosepane was increased 38% in early-stage OA (p < 0.05) and sixfold in patients with advanced OA (p < 0.001) compared with healthy controls. Conclusions: These studies further advance the prospective role of glycated, oxidized, and nitrated amino acids as serum biomarkers in diagnostic algorithms for early-stage detection of OA and other arthritic disease. Plasma glucosepane, reported here for the first time to our knowledge, may improve early-stage diagnosis and progression of clinical OA

The PHD Finger of Human UHRF1 Reveals a New Subgroup of Unmethylated Histone H3 Tail Readers

The human UHRF1 protein (ubiquitin-like containing PHD and RING finger domains 1) has emerged as a potential cancer target due to its implication in cell cycle regulation, maintenance of DNA methylation after replication and heterochromatin formation. UHRF1 functions as an adaptor protein that binds to histones and recruits histone modifying enzymes, like HDAC1 or G9a, which exert their action on chromatin. In this work, we show the binding specificity of the PHD finger of human UHRF1 (huUHRF1-PHD) towards unmodified histone H3 N-terminal tail using native gel electrophoresis and isothermal titration calorimetry. We report the molecular basis of this interaction by determining the crystal structure of huUHRF1-PHD in complex with the histone H3 N-terminal tail. The structure reveals a new mode of histone recognition involving an extra conserved zinc finger preceding the conventional PHD finger region. This additional zinc finger forms part of a large surface cavity that accommodates the side chain of the histone H3 lysine K4 (H3K4) regardless of its methylation state. Mutation of Q330, which specifically interacts with H3K4, to alanine has no effect on the binding, suggesting a loose interaction between huUHRF1-PHD and H3K4. On the other hand, the recognition appears to rely on histone H3R2, which fits snugly into a groove on the protein and makes tight interactions with the conserved aspartates D334 and D337. Indeed, a mutation of the former aspartate disrupts the formation of the complex, while mutating the latter decreases the binding affinity nine-fold

Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea

Frequencies and biomass of Baltic Sea cyanobacterial blooms are expected to be higher in future climate conditions, but also of longer duration as a result of increased sea surface temperature. Concurrently, climate predictions indicate a reduced salinity in the Baltic Sea. These climate-driven changes are expected to alter not solely the phytoplankton community but also the role of microbial communities for nutrient remineralization. Here, we present the response of summer plankton communities (filamentous cyanobacteria, picocyanobacteria, and heterotrophic bacteria) to the interplay of increasing temperature (from 16 to 18°C and 20°C) and reduced salinity (from salinity 6.9 to 5.9) in the Baltic Proper (NW Gotland Sea) using a microcosm approach. Warmer temperatures led to an earlier peak of cyanobacterial biomass, while yields were reduced. These conditions caused a decrease of nitrogen-fixers (Dolichospermum sp.) biomass, while non nitrogen-fixers (Pseudanabaena sp.) increased. Salinity reduction did not affect cyanobacterial growth nor community composition. Among heterotrophic bacteria, Actinobacteria showed preference for high temperature, while Gammaproteobacteria thrived at in situ temperature. Heterotrophic bacteria community changed drastically at lower salinity and resembled communities at high temperature. Picocyanobacteria and heterotrophic bacterial biomass had a pronounced increase associated with the decay of filamentous cyanobacteria. This suggests that shifts in community composition of heterotrophic bacteria are influenced both directly by abiotic factors (temperature and salinity) and potentially indirectly by cyanobacteria. Our findings suggest that at warmer temperature, lower yield of photosynthetic cyanobacteria combined with lower proportion of nitrogen-fixers in the community could result in lower carbon export to the marine food web with consequences for the decomposer community of heterotrophic bacteria