[Emergency free flap in reconstruction of the lower limb: About 23 cases over 11 years]. / Reconstruction des pertes de substance des membres inférieurs par lambeau libre en urgence : à propos de 23 cas sur 11 ans.

OBJECTIVES: To study the coverage period influence and various parameters concerning the microsurgical act on the patient clinical outcomes. METHODS: We report 23 cases of reconstruction of lower limb loss of substance by free flap operated from 2010 to 2021. Among them, 9 patients were operated on as an emergency versus 14 in the secondary or late phase of the trauma. RESULTS: The average age of injured patients operated on emergency was 42 years (17-68 years) and 34 years for the patients who undergo deferred surgery (17-57 years). The sex ratio (female/male) was 22% in patients operated on urgently and 7% in patients operated on later. Regarding the type of free flap, it was Serratus anterior muscle flap in 10 cases, Latissismus dorsi flap in 9 cases, ALT flap in 3 cases and Gracilis muscle flap in 1 case. There were 2 failures of vascularized free transfer (8.7%) with complete necrosis of the flap and 3 revision surgeries on venous thrombosis which finally made it possible to obtain 3 flap successes. We analyze the results (complications/osteitis) according to the time to coverage. CONCLUSIONS: In our study, we did not find any significant difference between the groups operated in emergency and at a distance concerning the rate of infection and failure of the flaps.

A functional magnetic resonance proof of concept pilot trial of cognitive rehabilitation in multiple sclerosis.

BACKGROUND: Cognitive impairment is frequent in multiple sclerosis (MS) and lacks effective treatment. Cognitive rehabilitation is widely applied in neurorehabilitation settings. Functional magnetic resonance imaging (fMRI) may help in investigating changes in brain activity and provide a tool to assess the efficacy of rehabilitation. AIM: To investigate the effect on brain activity as measured by fMRI of a cognitive rehabilitation programme in patients with MS and cognitive impairment. METHOD: Fifteen patients with MS and cognitive impairment and five healthy subjects were recruited. Neuropsychological assessments were performed in patients with MS at study entry and after rehabilitation to assess cognitive changes. fMRI scans were performed at week -5 (baseline), week 0 (immediately before rehabilitation) and week 5 (immediately after rehabilitation). The fMRI paradigm was the Paced Auditory Serial Addition Test (PASAT). The cognitive rehabilitation programme was composed of 15 computer-aided drill and practice sessions and five non-computer-aided cognitive stimulation group sessions (over 5 weeks). Strict guidelines ensured comparability of all rehabilitation interventions. RESULTS: Patients had increased brain fMRI activity after rehabilitation in several cerebellar areas when compared with healthy subjects. After rehabilitation, patients had significantly improved their performance on the backward version of the Digit Span Test (p = 0.007) and on a composite score of neuropsychological outcomes (p = 0.009). CONCLUSION: The results of the present study indicate that this cognitive rehabilitation programme increases brain activity in the cerebellum of cognitively impaired patients with MS. The role of fMRI in the assessment of neurorehabilitation schemes warrants further investigation.

La malaria en el mundo en 2010: ¿qué hay de nuevo acerca de esta vieja enfermedad? / Malaria in the world in 2010: What’s new about this old scourge?

El paludismo se mantiene en 2010 como uno de los grandes problemas de salud pública a nivel global. Endémico en 108 países del mundo, causa a día de hoy 250 millones de episodios clínicos y 863 000 muertes anuales, principalmente en el continente africano. El incremento en la última década de los fondos internacionales destinados a financiar actividades de control del paludismo ha condicionado un despliegue sin precedentes de herramientas de control disponibles. Así, millones de redes mosquiteras han sido distribuidas entre las poblaciones más vulnerables de África, y nuevos fármacos más potentes y eficaces han reemplazado en todos los países endémicos a los que habían quedado obsoletos. Como resultado de estos esfuerzos, y por primera vez en muchos años, estamos asistiendo a un cambio en las tendencias epidemiológicas de esta enfermedad, con una disminución de su incidencia global y, como consecuencia, una reducción de su morbimortalidad asociada. Estos progresos han espoleado a la comunidad científica a replantear de nuevo la posibilidad de erradicar esta enfermedad a nivel global. Sin embargo, y a pesar del optimismo imperante, este objetivo será imposible sin la aparición de herramientas de control nuevas y más eficaces, y no parece realista plantearlo a corto plazo. Estos esfuerzos deberán acompañarse de una agenda científica de investigación que sirva a la vez de guía para el diseño de nuevas intervenciones, pero también de mecanismo de monitorización de los progresos obtenidos. Para que el paludismo sea erradicado, también será necesario mantener un compromiso a largo plazo acompañado en paralelo de grandes esfuerzos para reforzar los frágiles sistemas de salud existentes en los países donde la enfermedad es un problema. Este artículo intentará revisar el estado actual del paludismo, en el nuevo contexto de los esfuerzos por su eliminación global (AU)

Malaria remains in 2010 a major global public health problem. The disease is endemic in 108 countries around the world, causing up to 250 million clinical episodes and 863,000 deaths annually, mainly in Africa. In the last decade, the increase of international funding available to finance malaria control activities has conditioned an unprecedented uptake of the different control tools available. Thus, millions of mosquito nets have been distributed among the most vulnerable populations in Africa, and new more potent and effective drugs have replaced those that had become obsolete in most endemic countries. As a result of these efforts, and for the first time in many years, we are witnessing a change in the epidemiology of this disease, with a decrease in its overall impact, and consequently a reduction in its associated morbidity and mortality. These developments have encouraged the scientific community to reconsider the possibility of eradicating the disease globally. However, despite the prevailing optimism, this goal will be impossible without the development of new and more effective control tools, and does not seem realistic to envisage them in the short-term. These efforts must be accompanied by a scientific research agenda that will serve both as a guideline for the design of new interventions, and also as a mechanism for monitoring the progress made. If malaria is to be eradicated, long-term commitments will be necessary, in parallel with greater efforts to strengthen the fragile health systems in countries where the disease is a problem. This article reviews the malaria situation in the light of the current efforts for its global elimination (AU)

Brain volumetry counterparts of cognitive impairment in patients with multiple sclerosis.

BACKGROUND: Cognitive impairment is frequent in multiple sclerosis (MS). Tissue-specific atrophy measures have been shown to correlate with cognitive performance in several studies. Voxel-based morphometry (VBM) aims to identify regional differences in the local composition of brain tissue and makes possible to correlate these findings with cognitive impairment patterns. AIM: To investigate the associations between cognitive impairment in MS and tissue-specific atrophy and regional distribution of grey matter. METHOD: 15 patients with MS and cognitive impairment were included. Demographic (age and years of schooling) and clinical (Multiple Sclerosis Functional Composite-MSFC and subtests, Expanded Disability Status Scale-EDSS, disease duration) variables were recorded and neuropsychological assessments performed (Trail Making Test A and B-TMTA and B, Symbol Digit Modalities Test-SDMT, Digit Span Test-DST and Rey's Auditory Verbal Learning Test Delayed Recall-RAVLT-DR). Magnetic resonance (MR) 3D sequences (MPRAGE) were performed on all subjects and tissue-specific volumes (SIENAx and SPM2 software) and VBM grey matter probability maps (SPM2) were obtained. RESULTS: Moderate correlations were obtained between tissue volumes obtained with SPM2 and SIENAx. Using SIENAx moderate correlations were obtained between normalised brain volume (NBV) and disease duration (rho=-0.575, p=0.025) and RAVLT-DR (rho=0.518, p=0.048). Using SPM2 moderate correlations were obtained between white matter and brain parenchymal fractions (WMF and BPF) and RAVLT-DR (rho=0.572 and 0.539, p=0.026 and 0.038), between grey matter fraction (GMF) and Z scores on the Paced Auditory Serial Addition Test (PASAT) (rho=0.570, p=0.026), and between BPF and disease duration (rho=-0.6, p=0.018). Significant correlations were observed only between regional grey matter probability maps and grey matter (and to a much lesser extent white matter) volumes from SPM2. CONCLUSION: Quantitative tissue-specific atrophy measures may display better correlations with patients' variables than regional grey matter atrophy distribution obtained using VBM methodology. These results should be confirmed in larger samples.

EVA: continuous automatic evaluation of protein structure prediction servers.

UNLABELLED: Evaluation of protein structure prediction methods is difficult and time-consuming. Here, we describe EVA, a web server for assessing protein structure prediction methods, in an automated, continuous and large-scale fashion. Currently, EVA evaluates the performance of a variety of prediction methods available through the internet. Every week, the sequences of the latest experimentally determined protein structures are sent to prediction servers, results are collected, performance is evaluated, and a summary is published on the web. EVA has so far collected data for more than 3000 protein chains. These results may provide valuable insight to both developers and users of prediction methods. AVAILABILITY: http://cubic.bioc.columbia.edu/eva. CONTACT: eva@cubic.bioc.columbia.edu

DBAli: a database of protein structure alignments.

SUMMARY: The DBAli database includes approximately 35000 alignments of pairs of protein structures from SCOP (Lo Conte et al., Nucleic Acids Res., 28, 257-259, 2000) and CE (Shindyalov and Bourne, Protein Eng., 11, 739-747, 1998). DBAli is linked to several resources, including Compare3D (Shindyalov and Bourne, http://www.sdsc.edu/pb/software.htm, 1999) and ModView (Ilyin and Sali, http://guitar.rockefeller.edu/ModView/, 2001) for visualizing sequence alignments and structure superpositions. A flexible search of DBAli by protein sequence and structure properties allows construction of subsets of alignments suitable for a number of applications, such as benchmarking of sequence-sequence and sequence-structure alignment methods under a variety of conditions. AVAILABILITY: http://guitar.rockefeller.edu/DBAli/

Classification of protein disulphide-bridge topologies.

The preferential occurrence of certain disulphide-bridge topologies in proteins has prompted us to design a method and a program, KNOT-MATCH, for their classification. The program has been applied to a database of proteins with less than 65% homology and more than two disulphide bridges. We have investigated whether there are topological preferences that can be used to group proteins and if these can be applied to gain insight into the structural or functional relationships among them. The classification has been performed by Density Search and Hierarchical Clustering Techniques, yielding thirteen main protein classes from the superimposition and clustering process. It is noteworthy that besides the disulphide bridges, regular secondary structures and loops frequently become correctly aligned. Although the lack of significant sequence similarity among some clustered proteins precludes the easy establishment of evolutionary relationships, the program permits us to find out important structural or functional residues upon the superimposition of two protein structures apparently unrelated. The derived classification can be very useful for finding relationships among proteins which would escape detection by current sequence or topology-based analytical algorithms.

Protein structure modeling for structural genomics.

The shapes of most protein sequences will be modeled based on their similarity to experimentally determined protein structures. The current role, limitations, challenges and prospects for protein structure modeling (using information about genes and genomes) are discussed in the context of structural genomics.

Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor.

The detection of osmotic stimuli is essential for all organisms, yet few osmoreceptive proteins are known, none of them in vertebrates. By employing a candidate-gene approach based on genes encoding members of the TRP superfamily of ion channels, we cloned cDNAs encoding the vanilloid receptor-related osmotically activated channel (VR-OAC) from the rat, mouse, human, and chicken. This novel cation-selective channel is gated by exposure to hypotonicity within the physiological range. In the central nervous system, the channel is expressed in neurons of the circumventricular organs, neurosensory cells responsive to systemic osmotic pressure. The channel also occurs in other neurosensory cells, including inner-ear hair cells, sensory neurons, and Merkel cells.

Comparative protein structure modeling of genes and genomes.

Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. The number of protein sequences that can be modeled and the accuracy of the predictions are increasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software. Further advances are necessary in recognizing weak sequence-structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences. The use of individual comparative models in biology is already rewarding and increasingly widespread. A major new challenge for comparative modeling is the integration of it with the torrents of data from genome sequencing projects as well as from functional and structural genomics. In particular, there is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes. Such large-scale modeling is likely to encourage new kinds of applications for the many resulting models, based on their large number and completeness at the level of the family, organism, or functional network.

Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints.

The structures of two species of potato carboxypeptidase inhibitor with nonnative disulfide bonds were determined by molecular dynamics simulations in explicit solvent using disulfide bond constraints that have been shown to work for the native species. Ten structures were determined; five for scrambled A (disulfide bonds between Cys8-Cys27, Cys12-Cys18, and Cys24-Cys34) and five for the scrambled C (disulfide bonds Cys8-Cys24, Cys12-Cys18, and Cys27-Cys34). The two scrambled species were both more solvent exposed than the native structure; the scrambled C species was more solvent exposed and less compact than the scrambled A species. Analysis of the loop regions indicates that certain loops in scrambled C are more nativelike than in scrambled A. These factors, combined with the fact that scrambled C has one native disulfide bond, may contribute to the observed faster conversion to the native structure from scrambled C than from scrambled A. Results from the PROCHECK program using the standard parameter database and a database specially constructed for small, disulfide-rich proteins indicate that the 10 scrambled structures have correct stereochemistry. Further, the results show that a characteristic feature of small, disulfide-rich proteins is that they score poorly using the standard PROCHECK parameter database. Proteins 2000;40:482-493.

Patterns of attentional impairment following closed head injury: a collaborative European study.

A comprehensive assessment of both selective (focused attention, divided attention) and intensive (alertness and vigilance) attentional processes was performed on 106 patients with closed head injury using a computerised battery for the evaluation of attention. All patients were tested at least five months after their accident. A high percentage of patients were pathological in tests mapping the selective components of attention while only a minority were impaired on tests mapping the intensive components of attention. Three different subgroups of patients with consistent performance patterns were evidenced. The psychometric characteristics of the battery and its possible clinical usefulness are discussed.

Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2.

Knowledge-based energy profiles combined with secondary structure prediction have been applied to molecular modelling refinement. To check the procedure, three different models of human procarboxypeptidase A2 (hPCPA2) have been built using the 3D structures of procarboxypeptidase A1 (pPCPA1) and bovine procarboxypeptidase A (bPCPA) as templates. The results of the refinement can be tested against the X-ray structure of hPCPA2 which has been recently determined. Regions miss-modelled in the activation segment of hPCPA2 were detected by means of pseudo-energies using Prosa II and modified afterwards according to the secondary structure prediction. Moreover, models obtained by automated methods as COMPOSER, MODELLER and distance restraints have also been compared, where it was found possible to find out the best model by means of pseudo-energies. Two general conclusions can be elicited from this work: (1) on a given set of putative models it is possible to distinguish among them the one closest to the crystallographic structure, and (2) within a given structure it is possible to find by means of pseudo-energies those regions that have been defectively modelled.

ASAP: analysis of peptide composition.

SUMMARY: ASAP is a web tool designed to search for specific dipeptides, tripeptides and tetrapeptides in a protein sequence database. The server allows for: (a) identification of frequent and infrequent peptides and the creation of peptide probability tables for a given database of sequences (GenerNet program), (b) determination of the compatibility of an amino-acid sequence to the given peptide probability tables (ClonErrNet program); and (c) comparison of different protein databases based on peptide composition (CompNet program). ASAP server can be useful in protein engineering and/or protein classification studies.

Effects of counter-ions and volume on the simulated dynamics of solvated proteins. Application to the activation domain of procarboxypeptidase B.

Molecular dynamics (MD) simulations of the globular activation domain of porcine procarboxypeptidase B (ADBp) and its isolated alpha-helix 1 were performed in order to understand the effects of adding salts and using periodic boundary conditions (this being reflected in the box size) along the simulations. alpha-Helix 1 was chosen because it is the most charged element of the secondary structure within ADBp. Different types of MD simulations with the GROMOS package were performed, studying either the whole activation domain or the isolated alpha-helix 1 with different water box sizes and counter-ionic shells. The analyses of the trajectories show that simulations of solvated proteins are highly sensitive to the presence of counter-ions and less sensitive to the volume of the water box. The differences in protein potential energies, r.m.s. deviations and radius of gyration between the simulations with and without counter-ions demonstrate that during such studies secondary structures of proteins are more stable when their charges are carefully neutralized. This stresses the need for such a procedure when analysing significantly charged proteins. The results also showed that the enlargement of the water box helps in the stabilization of the system.

Protein similarities beyond disulphide bridge topology.

Structural superimposition is an important procedure to analyse the relationships between proteins. A new approach and program, KNOT-MATCH, has been developed for automated structural superimposition of proteins by means of their disulphide bridge topology. As a result of the superimposition, regular secondary structures, loops and clusters of residues become correctly aligned. This fact allows us to find out important structural overlaps of residues, sometimes with functional significance, not only among proteins belonging to the same family but also between apparently non-related proteins. Different disulphide-rich protein families, such as EGF-like, defensin-like and plant protease inhibitors, have been self or cross analysed with this approach. Some amino acids that have been experimentally determined to be structural and/or functional key residues for these proteins are conserved in the three-dimensional space after superimposition by KNOT-MATCH. The program can be very useful for finding relationships among proteins that would be hidden to the current alignment methods based on sequence and on main-chain topology.

Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints.

The folding of the potato carboxypeptidase inhibitor (PCI) from partially unfolded conformations by the introduction of native disulfide bond constraints was studied by molecular dynamics simulations in explicit solvent. PCI consists of a globular core (Cys8 to Cys34), two flexible terminal regions (Glu1 to Ile7 and Glu35 to Gly39) and three loop regions characteristic of the family of proteins known as knottins. To generate unfolded conformations, two high temperature (600 K) simulations were performed; one with the native disulfide bonds intact (N600), and one with the disulfide bonds broken (ND600). For comparison purposes, two simulations at 300 K were done; one with the native disulfide bonds (N300), and one with the disulfide bonds broken (ND300). The N300 simulation reached an energetic equilibrium within a few picoseconds and maintained a stable structure during the 500 ps simulation. The three other simulations led to partial unfolding. The largest changes were observed in ND600 simulation with an rms deviation of over 5 A and radius of gyration 12.5% larger than the crystal structure value. Six structures from the ND600 simulation and one from the N600 simulation were used as starting structures for nine refolding simulations with somewhat different protocols for reforming the native disulfide bonds; in all cases the disulfides were reformed at 600 K and the temperature was decreased to 300 K for equilibration of the folded structures. Except for one structure that was significantly misfolded (final rms of 6.64 A with respect to N300), the other folding simulations recovered the native simulation structure (N300) to within rms differences ranging from 1.8 to 3.2 A for the main-chain of the core, relative to the N300, the X-ray and the NMR structures. Of particular interest is the internal and overall refolding behavior of the three loop regions. The more unfolded starting structures led to smaller rms values for the folded structures. Several energetic and solvation models were used to evaluate the X-ray, NMR, N300 and refolded structures. Although most models can distinguish the X-ray, NMR and N300 from the refolded structures, there is no correlation between the rms values of the latter and their estimated stability. Implications of the present results for protein folding by simulations and database search methods are discussed.