Technical note: The two step procedure (TSP) for the determination of age at death of adult human remains in forensic cases.

This paper presents the principles and results of TSP (the two step procedure), a comprehensive (combined) method of age estimation in mature human skeletal remains. The first step consists of the examination of the pubic symphysis using the Suchey-Brooks system for a "pre-choice". Then for SBS phases I, II, III, (young adults up to about 40) the age estimate is given using the chronological interval corresponding to each phase. For SBS phase is IV, V or VI (mature adults, about 40 to 60), then (second step) the dental method of Lamendin (using single rooted tooth) will be applied alone. Both methods are fast, easy to learn and to use (requiring no preparation except cleaning soft tissues from the pubic bone) and are not expensive, making TSP usable by all pathologists or anthropologists in any Forensic unit. It is also of great practical use in mass disaster and mass grave situation. After 15 years of use, a literature review and four evaluation studies we confirm that TSP is more accurate than any single method for aging adults and at least as good as more complicated combined methods. Despite its advantages TSP is, like all other aging methods, not efficient in adults over 65 years of age.

Temporal dynamics of the very premature infant gut dominant microbiota.

BACKGROUND: The very-preterm infant gut microbiota is increasingly explored due to its probable role in the development of life threatening diseases. Results of high-throughput studies validate and renew the interest in approaches with lower resolution such as PCR-Temporal Temperature Gel Electrophoresis (TTGE) for the follow-up of dominant microbiota dynamics. We report here an extensive longitudinal study of gut colonization in very preterm infants. We explored by 16S rDNA-based PCR-TTGE a total of 354 stool specimens sampled during routine monitoring from the 1(st) to the 8(th) week of life in 30 very pre-term infants born before 30 weeks of gestational age. RESULTS: Combining comparison with a diversity ladder and sequencing allowed affiliation of 50 Species-Level Operational Taxonomic Units (SLOTUs) as well as semi-quantitative estimation of Operational Taxonomic Units (OTUs). Coagulase-negative staphylococci, mainly the Staphylococcus epidermidis, was found in all the infants during the study period and was the most represented (75.7% of the SLOTUs) from the first days of life. Enterococci, present in 60% of the infants were early, highly represented and persistent colonizers of the premature gut. Later Enterobacteriaceae and the genus Clostridium appeared and were found in 10 (33%) and 21 infants (70%), respectively. We showed a high representation of Veillonella in more than a quarter of the infants and being able to persistently colonize premature gut. The genera Anaerococcus, Aquabacterium, Bacillus, Bifidobacterium, Corynebacterium, Micrococcus, Oceanobacillus, Propionibacterium, Pseudomonas, Rothia, Sarcina, Sneathia and Streptococcus were observed as transient or persistent colonizers, each genus being found in a minority of infants. CONCLUSIONS: Despite low resolution, PCR-TTGE remains complementary to high-throughput sequencing-based approaches because it allows the follow-up of dominant bacteria in gut microbiota in a large longitudinal cohorts of preterm neonates. We described the development of pre-term gut microbiota that should be now replaced regarding the functional role of major OTUs.

Numerical modelling of the V-J combinations of the T cell receptor TRA/TRD locus.

T-Cell antigen Receptor (TR) repertoire is generated through rearrangements of V and J genes encoding alpha and beta chains. The quantification and frequency for every V-J combination during ontogeny and development of the immune system remain to be precisely established. We have addressed this issue by building a model able to account for Valpha-Jalpha gene rearrangements during thymus development of mice. So we developed a numerical model on the whole TRA/TRD locus, based on experimental data, to estimate how Valpha and Jalpha genes become accessible to rearrangements. The progressive opening of the locus to V-J gene recombinations is modeled through windows of accessibility of different sizes and with different speeds of progression. Furthermore, the possibility of successive secondary V-J rearrangements was included in the modelling. The model points out some unbalanced V-J associations resulting from a preferential access to gene rearrangements and from a non-uniform partition of the accessibility of the J genes, depending on their location in the locus. The model shows that 3 to 4 successive rearrangements are sufficient to explain the use of all the V and J genes of the locus. Finally, the model provides information on both the kinetics of rearrangements and frequencies of each V-J associations. The model accounts for the essential features of the observed rearrangements on the TRA/TRD locus and may provide a reference for the repertoire of the V-J combinatorial diversity.

Early postpartum discharge and breastfeeding: an observational study from France.

BACKGROUND: Early postpartum discharge is a recent practice in France, but the influence of a shortened hospital stay on subsequent breastfeeding is unknown. The objective of the present study was to compare the breastfeeding mode after early discharge (ED) and conventional discharge (CD) from a hospital maternity unit. METHODS: An observational study was conducted in a French university hospital among 135 breastfeeding mothers, who delivered between 1 January and 31 July 2006. Forty-five ED mothers were matched with 90 CD mothers on 13 criteria. A structured questionnaire was used to collect data regarding feeding practices at 10 weeks postpartum, the period corresponding to paid maternity leave. RESULTS: Exclusive breast-, mixed, and bottle feedings were reported by, respectively, 35 (77.8%), three (6.7%) and seven (15.5%) ED mothers and 64 (71.1%), 12 (13.3%) and 14 (15.6%) CD mothers (no significant differences). Satisfaction with support for breastfeeding and reasons for switching to mixed or bottle feeding were comparable in the two groups. Multivariate analysis indicated that only the planned duration of breastfeeding and the mother's dissatisfaction with help significantly influenced breastfeeding prevalence. CONCLUSIONS: Early postpartum hospital discharge organized by skilled professionals is compatible with a satisfactory rate of exclusive breastfeeding up to the return to work. Formalized programs of instruction for perinatal professionals would help to reduce early abandonment.

Proximal fixation of thoracic stent-grafts as a function of oversizing and increasing aortic arch angulation in human cadaveric aortas.

PURPOSE: To assess the fixation of 4 commercially available thoracic stent-grafts as a function of oversizing and increasing aortic arch angulation. METHODS: A benchtop pulsatile flow model was devised to test stent-graft anchorage in a 2-cm-long proximal landing zone at varying landing zone angles (70 degrees to 140 degrees ) and stent-graft oversizing (5% to 37%). The experiments were performed using 15 human thoracic cadaveric aortas and 4 stent-grafts with different proximal anchoring mechanisms: TAG, Zenith TX, Valiant, and Relay. The lack of device-wall apposition was measured as a function of landing zone angulation and oversizing during static and dynamic (60 pulses/min, 300/150 mmHg) tests; stent-graft collapse was also investigated. RESULTS: The Valiant stent-graft remained apposed to the aortic wall at each increment of neck angulation and degree of oversizing. Lack of apposition of the proximal anchorage segment (Relay: bare spring; TAG: scalloped flares) was observed with the Relay above 80 degrees landing zone angulation (1-7 mm) and with the TAG above 90 degrees angulation (1-6 mm). The lack of device-wall apposition was greater with Relay than TAG (p = 0.009), but the "body" of these devices always remained well apposed. Lack of "body" apposition (1.0-7.5 mm) was first observed with the Zenith stent-graft above 70 degrees angulation (p<0.001). No stent-graft collapse was seen. An increase in stent-graft oversizing significantly (p<0.01) increased the lack of device-wall apposition for the TAG, Zenith, and Relay devices. CONCLUSION: In the face of severe aortic arch angulation, stent-grafts with hooks do not improve fixation. Major factors in stent-graft design that contribute to secure proximal anchorage seem to be radial force and the presence of a proximal open stent segment.

IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations.

BACKGROUND: Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cell receptor (TR) loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS). Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files) and are difficult to extract. DESCRIPTION: IMGT/GeneInfo is an online information system that provides, through a user-friendly interface, exhaustive information resulting from the complex mechanisms of T cell receptor V-J and V-D-J recombinations. T cells comprise two populations which express the alphabeta and gammadelta TR, respectively. The first version of the system dealt with the Homo sapiens and Mus musculus TRA and TRB loci whose gene rearrangements allow the synthesis of the alphabeta TR chains. In this paper, we present the second version of IMGT/GeneInfo where we complete the database for the Homo sapiens and Mus musculus TRG and TRD loci along with the introduction of a quality control procedure for existing and new data. We also include new functionalities to the four loci analysis, giving, to date, a very informative tool which allows to work on V(D)J genes of all TR loci in both human and mouse species. IMGT/GeneInfo provides more than 59,000 rearrangement combinations with a full gene description which is freely available at http://imgt.cines.fr/GeneInfo. CONCLUSION: IMGT/GeneInfo allows all TR information sequences to be in the same spot, and are now available within two computer-mouse clicks. This is useful for biologists and bioinformaticians for the study of T lymphocyte V(D)J gene rearrangements and their applications in immune response analysis.

IMGT/GeneInfo: enhancing V(D)J recombination database accessibility.

IMGT/GeneInfo is a user-friendly online information system that provides information on data resulting from the complex mechanisms of immunoglobulin (IG) and T cell receptor (TR) V(D)J recombinations. For the first time, it is possible to visualize all the rearrangement parameters on a single page. IMGT/GeneInfo is part of the international ImMunoGeneTics information system (IMGT), a high-quality integrated knowledge resource specializing in IG, TR, major histocompatibility complex (MHC), and related proteins of the immune system of human and other vertebrate species. The IMGT/GeneInfo system was developed by the TIMC and ICH laboratories (with the collaboration of LIGM), and is the first example of an external system being incorporated into IMGT. In this paper, we report the first part of this work. IMGT/GeneInfo_TR deals with the human and mouse TRA/TRD and TRB loci of the TR. Data handling and visualization are complementary to the current data and tools in IMGT, and will subsequently allow the modelling of V(D)J gene use, and thus, to predict non-standard recombination profiles which may eventually be found in conditions such as leukaemias or lymphomas. Access to IMGT/GeneInfo is free and can be found at http://imgt.cines.fr/GeneInfo.

Bio-array images processing and genetic networks modelling.

The new tools available for gene expression studies are essentially the bio-array methods using a large variety of physical detectors (isotopes, fluorescent markers, ultrasounds...). Here we present first rapidly an image-processing method independent of the detector type, dealing with the noise and with the peaks overlapping, the peaks revealing the detector activity (isotopic in the presented example), correlated with the gene expression. After this primary step of bio-array image processing, we can extract information about causal influence (activation or inhibition) a gene can exert on other genes, leading to clusters of genes co-expression in which we extract an interaction matrix M and an associated interaction graph G explaining the genetic regulatory dynamics correlated to the studied tissue function. We give two examples of such interaction matrices and graphs (the flowering genetic regulatory network of Arabidopsis thaliana and the lytic/lysogenic operon of the phage Mu) and after some theoretical rigorous results recently obtained concerning the asymptotic states generated by the genetic networks having a given interaction matrix and reciprocally concerning the minimal (in the sense of having a minimal number of non-zero coefficients) matrices having given stationary stable states.

Genetic regulation networks: circuits, regulons and attractors.

We deal in this paper with the concept of genetic regulation network. The genes expression observed through the bio-array imaging allows the geneticist to obtain the intergenic interaction matrix W of the network. The interaction graph G associated to W presents in general interesting features like connected components, gardens of Eden, positive and negative circuits (or loops), and minimal components having 1 positive and 1 negative loop called regulons. Depending on parameters values like the connectivity coefficient K(W) and the mean inhibition weight I(W), the genetic regulation network can present several dynamical behaviours (fixed configuration, limit cycle of configurations) called attractors, when the observation time increases. We give some examples of such genetic regulation networks and analyse their dynamical properties and their biological consequences.

A differential geometry approach for biomedical image processing.

We show in this paper how simple considerations about bio-arrays images lead to a peak segmentation allowing the genes activity analysis. Bio-arrays images have a particular structure and the aim of the paper is to present a mathematical method allowing their automatic processing. The differential geometry approach used here can be also employed for other types of images presenting grey level peaks corresponding to a functional activity or to a chemical concentration. The mathematical method is based on elementary techniques of differential geometry and dynamical systems theory and provides a simple efficient algorithm when the peaks to segment are isolated.