MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics

MOTIVATION

The term clustering designates a comprehensive family of unsupervised learning methods allowing to group similar elements into sets called clusters. Geometrical clustering of molecular dynamics (MD) trajectories is a well-established analysis to gain insights into the conformational behavior of simulated systems. However, popular variants collapse when processing relatively long trajectories because of their quadratic memory or time complexity. From the arsenal of clustering algorithms, HDBSCAN stands out as a hierarchical density-based alternative that provides robust differentiation of intimately related elements from noise data. Although a very efficient implementation of this algorithm is available for programming-skilled users (HDBSCAN*), it cannot treat long trajectories under the de facto molecular similarity metric RMSD.

RESULTS

Here, we propose MDSCAN, an HDBSCAN-inspired software specifically conceived for non-programmers users to perform memory-efficient RMSD-based clustering of long MD trajectories. Methodological improvements over the original version include the encoding of trajectories as a particular class of vantage-point tree (decreasing time complexity), and a dual-heap approach to construct a quasi-minimum spanning tree (reducing memory complexity). MDSCAN was able to process a trajectory of 1 million frames using the RMSD metric in about 21 h with <8 GB of RAM, a task that would have taken a similar time but more than 32 TB of RAM with the accelerated HDBSCAN* implementation generally used.

AVAILABILITY AND IMPLEMENTATION

The source code and documentation of MDSCAN are free and publicly available on GitHub (https://github.com/LQCT/MDScan.git) and as a PyPI package (https://pypi.org/project/mdscan/).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics

MOTIVATION

Density Peaks is a widely spread clustering algorithm that has been previously applied to Molecular Dynamics (MD) simulations. Its conception of cluster centers as elements displaying both a high density of neighbors and a large distance to other elements of high density, particularly fits the nature of a geometrical converged MD simulation. Despite its theoretical convenience, implementations of Density Peaks carry a quadratic memory complexity that only permits the analysis of relatively short trajectories.

RESULTS

Here, we describe DP+, an exact novel implementation of Density Peaks that drastically reduces the RAM consumption in comparison to the scarcely available alternatives designed for MD. Based on DP+, we developed RCDPeaks, a refined variant of the original Density Peaks algorithm. Through the use of DP+, RCDPeaks was able to cluster a one-million frames trajectory using less than 4.5 GB of RAM, a task that would have taken more than 2 TB and about 3× more time with the fastest and less memory-hunger alternative currently available. Other key features of RCDPeaks include the automatic selection of parameters, the screening of center candidates and the geometrical refining of returned clusters.

AVAILABILITY AND IMPLEMENTATION

The source code and documentation of RCDPeaks are free and publicly available on GitHub (https://github.com/LQCT/RCDPeaks.git).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics

MOTIVATION

Classical Molecular Dynamics (MD) is a standard computational approach to model time-dependent processes at the atomic level. The inherent sparsity of increasingly huge generated trajectories demands clustering algorithms to reduce other post-simulation analysis complexity. The Quality Threshold (QT) variant is an appealing one from the vast number of available clustering methods. It guarantees that all members of a particular cluster will maintain a collective similarity established by a user-defined threshold. Unfortunately, its high computational cost for processing big data limits its application in the molecular simulation field.

RESULTS

In this work, we propose a methodological parallel between QT clustering and another well-known algorithm in the field of Graph Theory, the Maximum Clique Problem. Molecular trajectories are represented as graphs whose nodes designate conformations, while unweighted edges indicate mutual similarity between nodes. The use of a binary-encoded RMSD matrix coupled to the exploitation of bitwise operations to extract clusters significantly contributes to reaching a very affordable algorithm compared to the few implementations of QT for MD available in the literature. Our alternative provides results in good agreement with the exact one while strictly preserving the collective similarity of clusters.

AVAILABILITY AND IMPLEMENTATION

The source code and documentation of BitQT are free and publicly available on GitHub (https://github.com/LQCT/BitQT.git) and ReadTheDocs (https://bitqt.readthedocs.io/en/latest/), respectively.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

MCSS-Based Predictions of Binding Mode and Selectivity of Nucleotide Ligands

Computational fragment-based approaches are widely used in drug design and discovery. One of their limitations is the lack of performance of docking methods, mainly the scoring functions. With the emergence of fragment-based approaches for single-stranded RNA ligands, we analyze the performance in docking and screening powers of an MCSS-based approach. The performance is evaluated on a benchmark of protein-nucleotide complexes where the four RNA residues are used as fragments. The screening power can be considered the major limiting factor for the fragment-based modeling or design of sequence-selective oligonucleotides. We show that the MCSS sampling is efficient even for such large and flexible fragments. Hybrid solvent models based on some partial explicit representations improve both the docking and screening powers. Clustering of the n best-ranked poses can also contribute to a lesser extent to better performance. A detailed analysis of molecular features suggests various ways to optimize the performance further.

RNA Back and Forth: Looking through Ribozyme and Viroid Motifs

Current cellular facts allow us to follow the link from chemical to biochemical metabolites, from the ancient to the modern world. In this context, the "RNA world" hypothesis proposes that early in the evolution of life, the ribozyme was responsible for the storage and transfer of genetic information and for the catalysis of biochemical reactions. Accordingly, the hammerhead ribozyme (HHR) and the hairpin ribozyme belong to a family of endonucleolytic RNAs performing self-cleavage that might occur during replication. Furthermore, regarding the widespread occurrence of HHRs in several genomes of modern organisms (from mammals to small parasites and elsewhere), these small ribozymes have been regarded as living fossils of a primitive RNA world. They fold into 3D structures that generally require long-range intramolecular interactions to adopt the catalytically active conformation under specific physicochemical conditions. By studying viroids as plausible remains of ancient RNA, we recently demonstrated that they replicate in non-specific hosts, emphasizing their adaptability to different environments, which enhanced their survival probability over the ages. All these results exemplify ubiquitous features of life. Those are the structural and functional versatility of small RNAs, ribozymes, and viroids, as well as their diversity and adaptability to various extreme conditions. All these traits must have originated in early life to generate novel RNA populations.

Self-assembly Controls Self-cleavage of HHR from ASBVd (-): a Combined SANS and Modeling Study

In the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (-) RNAs thus generated are processed by cleavage to unit-length where ASBVd (-) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (-) and its derived 79-nt HHR (-). A joint thermodynamic analysis of SANS and catalytic data indicates the rate-determining step corresponds to the dimer/monomer transition. 2D and 3D models of monomeric and dimeric HHR (-) suggest that the inter-molecular contacts stabilizing the dimer (between HI and HII domains) compete with the intra-molecular ones stabilizing the active conformation of the full-length HHR required for an efficient self-cleavage. Similar competing intra- and inter-molecular contacts are proposed in ASBVd (-) though with a remoter region from an extension of the HI domain.

Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea

A structural and functional classification of H/ACA and H/ACA-like motifs is obtained from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide:target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs in archaea.

[Propranolol and lactatemia during hypovolemic shock: a case report]

Lactate production results from anaerobic glycolysis. This pathway is recruited physiologically during intense and sustained muscular contractions. Hyperlactatemia may develop when tissue oxygenation is jeopardized such as in shock, its absence having been, however, sometimes reported in sepsis in which interactions between infectious agents and the organism's cells might blunt or disrupt hyperlactatemia development. During the course of acute rotavirus gastroenteritis, a 9-month-old girl developed severe dehydration (capillary-refill time, 5 s) leading to hypovolemic shock without signs of sepsis and with hypotension at 62/21 mmHg Surprisingly, the child failed to develop hyperlactatemia during shock. An etiologic search to understand why hyperlactatemia did not occur revealed that this patient had been receiving propranolol since the age of four months for the treatment of a Cyrano hemangioma. Via its inhibitory action on β-adrenergic receptors, propranolol antagonizes the stimulation of glycolysis by catecholamines, which may be rationally proposed to have contributed to preventing hyperlactatemia during hypovolemic shock in this patient. Mechanisms by which propranolol can mediate this antihyperlactatemia action are further illustrated and discussed.

Comparative study of two box H/ACA ribonucleoprotein pseudouridine-synthases: relation between conformational dynamics of the guide RNA, enzyme assembly and activity

Multiple RNA-guided pseudouridine synthases, H/ACA ribonucleoprotein particles (RNPs) which contain a guide RNA and four proteins, catalyze site-specific post-transcriptional isomerization of uridines into pseudouridines in substrate RNAs. In archaeal particles, the guide small RNA (sRNA) is anchored by the pseudouridine synthase aCBF5 and the ribosomal protein L7Ae. Protein aNOP10 interacts with both aCBF5 and L7Ae. The fourth protein, aGAR1, interacts with aCBF5 and enhances catalytic efficiency. Here, we compared the features of two H/ACA sRNAs, Pab21 and Pab91, from Pyrococcus abyssi. We found that aCBF5 binds much more weakly to Pab91 than to Pab21. Surprisingly, the Pab91 sRNP exhibits a higher catalytic efficiency than the Pab21 sRNP. We thus investigated the molecular basis of the differential efficiencies observed for the assembly and catalytic activity of the two enzymes. For this, we compared profiles of the extent of lead-induced cleavages in these sRNAs during a stepwise reconstitution of the sRNPs, and analyzed the impact of the absence of the aNOP10–L7Ae interaction. Such probing experiments indicated that the sRNAs undergo a series of conformational changes upon RNP assembly. These changes were also evaluated directly by circular dichroism (CD) spectroscopy, a tool highly adapted to analyzing RNA conformational dynamics. In addition, our results reveal that the conformation of helix P1 formed at the base of the H/ACA sRNAs is optimized in Pab21 for efficient aCBF5 binding and RNP assembly. Moreover, P1 swapping improved the assembly of the Pab91 sRNP. Nonetheless, efficient aCBF5 binding probably also relies on the pseudouridylation pocket which is not optimized for high activity in the case of Pab21.

RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi

The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transcripts. Unlike other archaea, such as Sulfolobus and Halobacteriales, P. abyssi produces few leaderless mRNA transcripts. Antisense transcription is widespread (215 transcripts) and targets protein-coding genes that appear to evolve more rapidly than average genes. We identify at least three novel H/ACA-like guide RNAs among the newly characterized non-coding RNAs. Long 5′ UTRs in mRNAs of ribosomal proteins and amino-acid biosynthesis genes strongly suggest the presence of cis-regulatory leaders in these mRNAs. We selected a high-interest subset of non-coding RNAs based on their strong promoters, high GC-content, phylogenetic conservation, or abundance. Some of the novel small RNAs and long 5′ UTRs display high GC contents, suggesting unknown structural RNA functions. However, we were surprised to observe that most of the high-interest RNAs are AU-rich, which suggests an absence of stable secondary structure in the high-temperature environment of P. abyssi. Yet, these transcripts display other hallmarks of functionality, such as high expression or high conservation, which leads us to consider possible RNA functions that do not require extensive secondary structure.

Noradrenaline use for septic shock in children: doses, routes of administration and complications

AIM

To report our 10 year experience with noradrenaline use in children with septic shock focusing on doses, routes of administration and complications.

METHODS

Retrospective single-centre review of children with septic shock who received noradrenaline between 2000 and 2010.

RESULTS

We identified 144 children with septic shock treated with noradrenaline, in 22% as the first-line drug. The median volume resuscitation before vasoactive agent administration was 50 mL/kg interquartile range [IQR: 30-70]. Mean doses of noradrenaline ranged from 0.5 ± 0.4 μg/kg per min (starting dose) to 2.5 ± 2.2 μg/kg per min (maximum dose). Noradrenaline was administered via peripheral venous access or intra-osseous route in 19% of cases for a median duration of 3 h [IQR: 2-4] without any adverse effects. The use of noradrenaline increased over the study period. Mortality rate was 45% with a significant decrease over the study period. Adverse effects included arrhythmia in two children and hypertension in eight children. None of these arrhythmias required treatment and hypertension resolved with the noradrenaline dose reduction.

CONCLUSION

Higher doses of noradrenaline than those suggested in the literature may be necessary to reverse hypotension and hypoperfusion. The use of noradrenaline through peripheral venous access or intra-osseous route was safe, without any adverse effects.

Modeling the RNA 2'OH activation: possible roles of metal ion and nucleobase as catalysts in self-cleaving ribozymes

The RNA 2'OH activation as taking place in the first chemical step of self-cleaving ribozymes is studied theoretically by DFT and MP2 methods using a continuum solvation model (CPCM). The reaction of proton transfer is studied in the presence of two kinds of catalysts: a fully hydrated metal ion (Mg(2+)) or partially hydrated nucleobase (guanine), taken separately or together leading to three different modes of activation. The metal ion is either directly bound (inner-sphere) or indirectly bound (outer-sphere) to the 2'OH group and a hydroxide ion acts as a general or specific base; the nucleobase is taken in anionic or in neutral enol-tautomeric forms playing itself the role of general base. The presence of a close metal ion (outer-sphere) lowers the pK(a) value of the 2'OH group by several log units in both metal-ion and nuleobase catalysis. The direct metal coordination to the 2'OH group (inner-sphere) further stabilizes the developing negative charge on the nucleophile. The switching from the inner-sphere to the outer-sphere coordination appears to be driven by the energy cost for reorganizing the first coordination shell rather than by the electrostatic repulsion between the ligands. The metal-ion catalysis is more effective with a specific base in the dianionic mechanism. On the other hand, the nucleobase catalysis is more effective in the monoanionic mechanism and in the presence of a metal ion acting as a cofactor through nonspecific electrostatic interactions. The results establish a baseline to study the possible roles of metal and nucleobase catalysts and their environment in more realistic models for self-cleaving ribozymes.

Recognising haemorrhagic rash in children with fever: a survey of parents' knowledge

BACKGROUND

Early recognition and treatment of meningococcal disease improves its outcome. Haemorrhagic rash is one of the most specific signs that parents can learn to recognise.

OBJECTIVE

To determine the percentage of parents able to recognise a haemorrhagic rash and perform the tumbler test.

METHODS

123 parents of children consulting for mild injuries were interviewed about the significance and recognition of haemorrhagic rash in febrile children.

RESULTS

Although 88% of parents undressed their children when they were febrile, it was never to look specifically for a skin rash. Only 7% (95% CI 3% to 12%) were able to recognise a petechial rash and knew the tumbler test.

CONCLUSION

Information campaigns about the significance of haemorrhagic rash and about the tumbler test are needed.

[Noninvasive mechanical ventilation in paediatric intensive care units: which indications in 2010?]

Noninvasive ventilation (NVI) is increasingly used in paediatrics, although there is a high variety of practices and a paucity of published data in paediatrics. The last French consensus conference recognized a specific role of NVI for infants suffering from acute bronchiolitis with apnoea, and acute respiratory failure due to laryngotracheomalacia and cystic fibrosis. NVI is feasible and can be beneficial in paediatric acute respiratory failure during neuromuscular diseases. Like in adults, its place in other diseases such as acute bronchoalveolitis without apnoea, acute respiratory failure during neuromuscular diseases, status asthmaticus, acute respiratory distress syndrome (ARDS) and postextubation respiratory failure is growing, even though not always defined. All these adult recommendations have not been validated in the pediatric setting, and, thus, taking the paediatric characteristics into account is essential. In 2010, NVI had an important place in PICU, and must be managed by a trained team whose practice is regularly evaluated.

Deficiency of the tRNATyr:Psi 35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery

Up to now, Psi formation in tRNAs was found to be catalysed by stand-alone enzymes. By computational analysis of archaeal genomes we detected putative H/ACA sRNAs, in four Sulfolobales species and in Aeropyrum pernix, that might guide Psi 35 formation in pre-tRNA(Tyr)(GUA). This modification is achieved by Pus7p in eukarya. The validity of the computational predictions was verified by in vitro reconstitution of H/ACA sRNPs using the identified Sulfolobus solfataricus H/ACA sRNA. Comparison of Pus7-like enzymes encoded by archaeal genomes revealed amino acid substitutions in motifs IIIa and II in Sulfolobales and A. pernix Pus7-like enzymes. These conserved RNA:Psi-synthase- motifs are essential for catalysis. As expected, the recombinant Pyrococcus abyssi aPus7 was fully active and acted at positions 35 and 13 and other positions in tRNAs, while the recombinant S. solfataricus aPus7 was only found to have a poor activity at position 13. We showed that the presence of an A residue 3' to the target U residue is required for P. abyssi aPus7 activity, and that this is not the case for the reconstituted S. solfataricus H/ACA sRNP. In agreement with the possible formation of Psi 35 in tRNA(Tyr)(GUA) by aPus7 in P. abyssi and by an H/ACA sRNP in S. solfataricus, the A36G mutation in the P. abyssi tRNA(Tyr)(GUA) abolished Psi 35 formation when using P. abyssi extract, whereas the A36G substitution in the S. solfataricus pre-tRNA(Tyr) did not affect Psi 35 formation in this RNA when using an S. solfataricus extract.

[Interfaces for pediatric noninvasive ventilation (excluding neonate)]

The quality of noninvasive ventilation in pediatrics is interface-dependent. Several types of interfaces are currently available: nasal and oral masks, nasal pillows and helmets. Despite material improvements in material design, shape, size and components, interfaces are still not adapted for most children. The ideal interface must fit the child's characteristics and the disease requirements. For instance, a nasal canula is recommended for infants younger than 3 months of age. If necessary, nasal masks can be used as oronasal masks. Repeated and careful evaluations are indicated to ensure interface adequacy and to detect cutaneous injuries and facial deformities. Training is required for medical and paramedical personnel. Pediatrics studies, comparing interfaces, are needed to build evidence-based recommendations.

Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs

How far do H/ACA sRNPs contribute to rRNA pseudouridylation in Archaea was still an open question. Hence here, by computational search in three Pyrococcus genomes, we identified seven H/ACA sRNAs and predicted their target sites in rRNAs. In parallel, we experimentally identified 17 Ψ residues in P. abyssi rRNAs. By in vitro reconstitution of H/ACA sRNPs, we assigned 15 out of the 17 Ψ residues to the 7 identified H/ACA sRNAs: one H/ACA motif can guide up to three distinct pseudouridylations. Interestingly, by using a 23S rRNA fragment as the substrate, one of the two remaining Ψ residues could be formed in vitro by the aCBF5/aNOP10/aGAR1 complex without guide sRNA. Our results shed light on structural constraints in archaeal H/ACA sRNPs: the length of helix H2 is of 5 or 6 bps, the distance between the ANA motif and the targeted U residue is of 14 or 15 nts, and the stability of the interaction formed by the substrate rRNA and the 3′-guide sequence is more important than that formed with the 5′-guide sequence. Surprisingly, we showed that a sRNA–rRNA interaction with the targeted uridine in a single-stranded 5′-UNN-3′ trinucleotide instead of the canonical 5′-UN-3′ dinucleotide is functional.

A dedicated computational approach for the identification of archaeal H/ACA sRNAs

Whereas dedicated computational approaches have been developed for the search of C/D sRNAs and snoRNAs, as yet no dedicated computational approach has been developed for the search of archaeal H/ACA sRNAs. Here we describe a computational approach allowing a fast and selective identification of H/ACA sRNAs in archaeal genomes. It is easy to use, even for biologists having no special expertise in computational biology. This approach is a stepwise knowledge-based approach, combining the search for common structural features of H/ACA motifs and the search for their putative target sequences. The first step is based on the ERPIN software. It depends on the establishment of a secondary structure-based "profile." We explain how this profile is built and how to use ERPIN to optimize the search for H/ACA motifs. Several examples of applications are given to illustrate how powerful the method is, its limits, and how the results can be evaluated. Then, the possible target rRNA sequences corresponding to the identified H/ACA motifs are searched by use of a descriptor-based method (RNAMOT). The principles and the practical aspects of this method are also explained, and several examples are given here as well to help users in the interpretation of the results.

Two-metal-ion mechanism for hammerhead-ribozyme catalysis

The hammerhead ribozyme is one of the best studied ribozymes, but it still presents challenges for our understanding of RNA catalysis. It catalyzes a transesterification reaction that converts a 5',3' diester to a 2',3' cyclic phosphate diester via an S(N)2 mechanism. Thus, the overall reaction corresponds to that catalyzed by bovine pancreatic ribonuclease. However, an essential distinguishing aspect is that metal ions are not involved in RNase catalysis but appear to be important in ribozymes. Although various techniques have been used to assign specific functions to metals in the hammerhead ribozyme, their number and roles in catalysis is not clear. Two recent theoretical studies on RNA catalysis examined the reaction mechanism of a single-metal-ion model. A two-metal-ion model, which is supported by experiment and based on ab initio and density functional theory calculations, is described here. The proposed mechanism of the reaction has four chemical steps with three intermediates and four transition states along the reaction pathway. Reaction profiles are calculated in the gas phase and in solution. The early steps of the reaction are found to be fast (with low activation barriers), and the last step, corresponding to the departure of the leaving group, is rate limiting. This two-metal-ion model differs from the models proposed previously in that the two metal ions function not only as Lewis acids but also as general acids/bases. Comparison with experiment shows good agreement with thermodynamic and kinetic data. A detailed analysis based on natural bond orbitals (NBOs) and natural energy decomposition (NEDA) provides insights into the role of metal ions and other factors important for catalysis.

Are the GFRUP's recommendations for withholding or withdrawing treatments in critically ill children applicable? Results of a two-year survey

OBJECTIVE

To evaluate feasibility of the guidelines of the Groupe Francophone de Réanimation et Urgence Pédiatriques (French-speaking group of paediatric intensive and emergency care; GFRUP) for limitation of treatments in the paediatric intensive care unit (PICU).

DESIGN

A 2-year prospective survey.

SETTING

A 12-bed PICU at the Hôpital Jeanne de Flandre, Lille, France.

PATIENTS

Were included when limitation of treatments was expected.

RESULTS

Of 967 children admitted, 55 were included with a 2-day median delay. They were younger than others (24 v 60 months), had a higher paediatric risk of mortality (PRISM) score (14 v 4), and a higher paediatric overall performance category (POPC) score at admission (2 v 1); all p<0.002. 34 (50% of total deaths) children died. A limitation decision was made without meeting for 7 children who died: 6 received do-not-resuscitate orders (DNROs) and 1 received withholding decision. Decision-making meetings were organised for 31 children, and the following decisions were made: 12 DNROs (6 deaths and 6 survivals), 4 withholding (1 death and 3 survivals), with 14 withdrawing (14 deaths) and 1 continuing treatment (survival). After limitation, 21 (31% of total deaths) children died and 10 survived (POPC score 4). 13 procedures were interrupted because of death and 11 because of clinical improvement (POPC score 4). Parents' opinions were obtained after 4 family conferences (for a total of 110 min), 3 days after inclusion. The first meeting was planned for 6 days after inclusion and held on the 7th day after inclusion; 80% of parents were immediately informed of the decision, which was implemented after half a day.

CONCLUSIONS

GFRUPs procedure was applicable in most cases. The main difficulties were anticipating the correct date for the meeting and involving nurses in the procedure. Children for whom the procedure was interrupted because of clinical improvement and who survived in poor condition without a formal decision pointed out the need for medical criteria for questioning, which should systematically lead to a formal decision-making process.

Évaluation de la prescription antibiotique dans un service de réanimation pédiatrique

The antibiotic prescription in intensive care units is frequent using often broad-spectrum antibiotics; its quality has never been evaluated in paediatric intensive care units.

OBJECTIVES

To describe the modalities of antibiotic prescriptions in a paediatric intensive care unit and confront them to the literature guidelines and bacteriological data.

METHODS

From January 1st to March 31st 2005, 52 consecutive prescriptions regarding 45 children, with a total of 47 hospitalisations were prospectively analysed.

RESULTS

Confirmed diagnosis of bacterial infection was retained for 50 of the 52 patients: community acquired infection in 35 cases (70%) and a nosocomial infection in 15 cases. Ten children died during the antibiotic treatment (22%), with 5 deaths related to the infection (11%). Monotherapy represented 56% of the prescriptions of antibiotics. The initial antibiotic treatment was empirical in 42 of 52 cases (81%). The empirical prescriptions were documented afterward in 48% of cases. One or more microorganisms were isolated for 60% of the initial prescriptions. Misuses in antibiotic doses (in excess [10%] or by insufficiency [13%]), number of daily administration (4%), and way of administration and/or length of treatment were observed. Seventy-seven percent of the initial prescriptions seemed to be adapted to the identified or suspected bacteria, but only 63% adequate to recommendations.

CONCLUSION

Almost 2/3rd of the antibiotic prescriptions were adequate to the recommendations. The implementation of standardized and specific protocols should contribute to improve the quality of these prescriptions.

Analysis of sequence and structural features that identify the B/C motif of U3 small nucleolar RNA as the recognition site for the Snu13p-Rrp9p protein pair

The eukaryal Snu13p/15.5K protein binds K-turn motifs in U4 snRNA and snoRNAs. Two Snu13p/15.5K molecules bind the nucleolar U3 snoRNA required for the early steps of preribosomal processing. Binding of one molecule on the C'/D motif allows association of proteins Nop1p, Nop56p, and Nop58p, whereas binding of the second molecule on the B/C motif allows Rrp9p recruitment. To understand how the Snu13p-Rrp9p pair recognizes the B/C motif, we first improved the identification of RNA determinants required for Snu13p binding by experiments using the systematic evolution of ligands by exponential enrichment. This demonstrated the importance of a U.U pair stacked on the sheared pairs and revealed a direct link between Snu13p affinity and the stability of helices I and II. Sequence and structure requirements for efficient association of Rrp9p on the B/C motif were studied in yeast cells by expression of variant U3 snoRNAs and immunoselection assays. A G-C pair in stem II, a G residue at position 1 in the bulge, and a short stem I were found to be required. The data identify the in vivo function of most of the conserved residues of the U3 snoRNA B/C motif. They bring important information to understand how different K-turn motifs can recruit different sets of proteins after Snu13p association.

Ventilation non invasive des nourrissons ayant une infection respiratoire sévère présumée à virus respiratoire syncitial : faisabilité et critères d'échec

Beneficial effect of continuous positive airway pressure (CPAP) during non invasive ventilation (NIV) has been reported in infants with respiratory syncytial virus (RSV) infection, but no study has analyzed the predictors of its failure.

OBJECTIVE

To evaluate the feasibility of NIV and to determine NIV failure criteria.

POPULATION AND METHODS

All infants hospitalized in one PICU with presumed RSV infection between 2002 and 2006 were prospectively included. When respiratory support was needed, NIV was first started according to a pre-established protocol.

RESULTS

One hundred and one infants, 43 females, 58 males, median age 49 days (range: 10-334), median weight 3.9 kg (range: 2,4-12) were included. RSV infection was confirmed in 84/101. Sixty-seven infants were transported by the paediatric medical transport system, 27 with NIV and 15 with invasive ventilation (IV). Fifteen infants were in IV at admission, 69 received NIV during their PICU stay (12 secondarily requiring IV) and 17 were never ventilated. A significant decrease in PCO2 with increase in pH was observed within 2 hours of NIV. Parameters associated with NIV failure were apneas, high values of admission PCO2 and H24 PRISM score. The 17 non-ventilated infants were older and had a lower severity score than those who were ventilated.

CONCLUSION

In infants with RSV and needing respiratory support, NIV represented the sole method of respiratory support in 68% of cases. NIV failure criteria were apneas, high values of admission PCO2 and H24 PRISM score.

Nucleophilic Attack on Phosphate Diesters: A Density Functional Study of In−Line Reactivity in Dianionic, Monoanionic, and Neutral Systems

A density functional study of the hydrolysis reaction of phosphodiesters with a series of attacking nucleophiles in the gas phase and in solution is presented. The nucleophiles HOH, HO-, CH3OH, and CH3O- were studied in reactions with ethylene phosphate, 2'3'-ribose cyclic phosphate and in their neutral (protonated) and monoanionic forms. Stationary-point geometries for the reactions were determined at the density functional B3LYP/6-31++G(d,p) level followed by energy refinement at the B3LYP/6-311++G(3df,2p) level. Solvation effects were estimated by using a dielectric approximation with the polarizable continuum model (PCM) at the gas-phase optimized geometries. This series of reactions characterizes factors that influence the intrinsic reactivity of the model phosphate compounds, including the effect of nucleophile, protonation state, cyclic structure, and solvent. The present study of the in-line mechanism for phosphodiester hydrolysis, a reaction of considerable biological importance, has implications for enzymatic mechanisms. The analysis generally supports the associative mechanism for phosphate ester hydrolysis. The results highlight the importance for the reaction barrier of charge neutralization resulting from the protonation of the nonbridging phosphoryl oxygens and the role of internal hydrogen transfer in the gas-phase mechanism. It also shows that solvent stabilization has a profound influence on the relative barrier heights for the dianionic, monoanionic, and neutral reactions. The calculations provide a comprehensive data set for the in-line hydrolysis mechanisms that can be used for the development of improved semiempirical quantum models for phosphate hydrolysis reactions.

[Withholding or withdrawing life saving treatment in pediatric intensive care unit: GFRUP guidelines]

Several recent French studies have revealed that 40% of death in pediatric intensive care units are associated with withdrawal or limitation of life saving treatments. Because such decisions are common, the Groupe francophone de réanimation et urgences pédiatriques (GFRUP) has decided to publish recommendations in order to help paediatricians dealing with those difficult issues and to improve their decisions. In a first part of the document the ethical principles that imply those guidelines are recalled, followed by definitions of the terms currently employed. The second part contains guidelines regarding decision making process, the way it is applied and organisation of relatives as well as paramedical and medical staff support when the death of a child occurs.

The ERPIN server: an interface to profile-based RNA motif identification

ERPIN is an RNA motif identification program that takes an RNA sequence alignment as an input and identifies related sequences using a profile-based dynamic programming algorithm. ERPIN differs from other RNA motif search programs in its ability to capture subtle biases in the training set and produce highly specific and sensitive searches, while keeping CPU requirements at a practical level. In its latest version, ERPIN also computes E-values, which tell biologists how likely they are to encounter a specific sequence match by chance-a useful indication of biological significance. We present here the ERPIN online search interface (http://tagc.univ-mrs.fr/erpin/). This web server automatically performs ERPIN searches for different RNA genes or motifs, using predefined training sets and search parameters. With a couple of clicks, users can analyze an entire bacterial genome or a genomic segment of up to 5Mb for the presence of tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and other motifs. Search results are displayed with sequence, score, position, E-value and secondary structure graphics. An example of a complete genome scan is provided, as well as an evaluation of run times and specificity/sensitivity information for all available motifs.