ELPA: A parallel solver for the generalized eigenvalue problem

For symmetric (hermitian) (dense or banded) matrices the computation of eigenvalues and eigenvectors Ax = λBx is an important task, e.g. in electronic structure calculations. If a larger number of eigenvectors are needed, often direct solvers are applied. On parallel architectures the ELPA implementation has proven to be very efficient, also compared to other parallel solvers like EigenExa or MAGMA. The main improvement that allows better parallel efficiency in ELPA is the two-step transformation of dense to band to tridiagonal form. This was the achievement of the ELPA project. The continuation of this project has been targeting at additional improvements like allowing monitoring and autotuning of the ELPA code, optimizing the code for different architectures, developing curtailed algorithms for banded A and B, and applying the improved code to solve typical examples in electronic structure calculations. In this paper we will present the outcome of this project

The Conserved Nup107-160 Complex Is Critical for Nuclear Pore Complex Assembly

AbstractNuclear pore complexes (NPCs) are large multiprotein assemblies that allow traffic between the cytoplasm and the nucleus. During mitosis in higher eukaryotes, the Nuclear Envelope (NE) breaks down and NPCs disassemble. How NPCs reassemble and incorporate into the NE upon mitotic exit is poorly understood. We demonstrate a function for the conserved Nup107-160 complex in this process. Partial in vivo depletion of Nup133 or Nup107 via RNAi in HeLa cells resulted in reduced levels of multiple nucleoporins and decreased NPC density in the NE. Immunodepletion of the entire Nup107-160 complex from in vitro nuclear assembly reactions produced nuclei with a continuous NE but no NPCs. This phenotype was reversible only if Nup107-160 complex was readded before closed NE formation. Depletion also prevented association of FG-repeat nucleoporins with chromatin. We propose a stepwise model in which postmitotic NPC assembly initiates on chromatin via early recruitment of the Nup107-160 complex

Variations in water use by a mature mangrove of Avicennia germinans, French Guiana

In the tropical intertidal zones, little is known on water uptake by mangroves. Transpiration rates are generally measured at leaf level, but few studies exist on water use at tree or stand levels. The objective of this study was to measure sap flow in trees of different sizes to appreciate the range of variation in water use that may exist in a site dominated by 80% mature Avicennia germinans. The results showed that from the dry to the wet season the mean water use increased from 3.2 to 5.3 dm3 d−1 in small trees (DBH ∼ 13 cm), from 11.5 to 30.8 dm3 d−1 in medium trees (∼24 cm) and from 40.8 to 64.1 dm3 d−1 in large ones (∼45 cm). Sapwood remained active up to a depth of 8 cm with radial variations within the stem. Weak correlations were obtained with VPD and net radiation. This study confirmed that transpiration was larger under low levels of salinity. Water use at stand level (∼1900 living stems ha−1) was estimated to be in the range of 5.8 to 11.8 m3 ha−1 d−1 according to the season

A mixed-methods study on evaluating an updated, francophone version of ETAT+ training in Madagascar

Background: Madagascar needs major efforts to achieve the UN Sustainable Development Goals, despite the considerable reduction of child mortality during past years. In this context, implementation of emergency triage assessment and treatment (ETAT) plays an important role. In recent years, ETAT training activities rarely took place in Madagascar. To strengthen ETAT in Madagascar, a pilot training course was conducted in December 2019 at the University Hospital Mahajanga. Objective: This study aims to evaluate if the ETAT+ pilot training content matches clinical needs in Madagascar and whether participants achieved their learning objectives. Methods: In this cross-sectional mixed-methods study, a 41-item questionnaire was used at the end of the ETAT+ training to evaluate their learning experience from the 12 participants (paediatricians, physicians, nurses and midwives). Six weeks after the training, guided interviews were conducted among five participants to describe how training content could be transferred into clinical practice in five health facilities. Results: Results suggest that this pilot project designed to contribute to the re-establishment of ETAT in Madagascar meets participants’ needs and is adapted to clinical realities in terms of transmitted knowledge, skills and competencies. However, results also show that considerable multidisciplinary efforts are needed to advance ETAT+ implementation in Madagascar. Conclusions: Implementation processes of ETAT training programmes need re-evaluation to assure their validity to contribute to quality of care improvements efficiently. Further operational research is required to evaluate sustainable, innovative implementation strategies adapted to contexts in Madagascar

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

QUBIC, a specific and highly sensitive method for detection of protein–protein interactions, is used to identify new partners for the mitotic spindle components pericentrin and TACC3

From protein sequences to 3D-structures and beyond: the example of the UniProt Knowledgebase

With the dramatic increase in the volume of experimental results in every domain of life sciences, assembling pertinent data and combining information from different fields has become a challenge. Information is dispersed over numerous specialized databases and is presented in many different formats. Rapid access to experiment-based information about well-characterized proteins helps predict the function of uncharacterized proteins identified by large-scale sequencing. In this context, universal knowledgebases play essential roles in providing access to data from complementary types of experiments and serving as hubs with cross-references to many specialized databases. This review outlines how the value of experimental data is optimized by combining high-quality protein sequences with complementary experimental results, including information derived from protein 3D-structures, using as an example the UniProt knowledgebase (UniProtKB) and the tools and links provided on its website (http://www.uniprot.org/). It also evokes precautions that are necessary for successful predictions and extrapolations

Degradation of haloaromatic compounds

An ever increasing number of halogenated organic compounds has been produced by industry in the last few decades. These compounds are employed as biocides, for synthetic polymers, as solvents, and as synthetic intermediates. Production figures are often incomplete, and total production has frequently to be extrapolated from estimates for individual countries. Compounds of this type as a rule are highly persistent against biodegradation and belong, as "recalcitrant" chemicals, to the class of so-called xenobiotics. This term is used to characterise chemical substances which have no or limited structural analogy to natural compounds for which degradation pathways have evolved over billions of years. Xenobiotics frequently have some common features. e.g. high octanol/water partitioning coefficients and low water solubility which makes for a high accumulation ratio in the biosphere (bioaccumulation potential). Recalcitrant compounds therefore are found accumulated in mammals, especially in fat tissue, animal milk supplies and also in human milk. Highly sophisticated analytical techniques have been developed for the detection of organochlorines at the trace and ultratrace level