On the Source and Rewriting of 1 Corinthians 2.9 in Christian, Jewish and Islamic Traditions (1 Clem 34.8; GosJud 47.10-13; a ḥadīth qudsī)

The article reopens the file of sources, parallels and rewritings of 1 Cor 2.9, a saying that Paul attributes to some written source, when others sources put it into Jesus' mouth (e.g. GosThom 17). A state of research highlights that the hypothesis of an oral source is generally preferred but an accurate study of 1 Clem 34.8, a parallel too often neglected, supports the presence of a written source that existed before 1 Cor 2.9. GosJud 47.10-13 will help to understand the attribution of the saying to Jesus. The last important part of this article studies its parallel in Islamic traditions, a ḥadīth qudsī.

Cellular source and mechanisms of high transcriptome complexity in the Mammalian testis.

Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide investigations of transcriptome complexity in major mammalian organs have been scarce. Here, using extensive RNA-seq data, we show that transcription of the genome is substantially more widespread in the testis than in other organs across representative mammals. Furthermore, we reveal that meiotic spermatocytes and especially postmeiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein-coding and long noncoding RNA genes but also poorly conserves intergenic sequences, suggesting that it may not be of immediate functional relevance. Rather, our analyses of genome-wide epigenetic data suggest that this prevalent transcription, which most likely promoted the birth of new genes during evolution, is facilitated by an overall permissive chromatin in these germ cells that results from extensive chromatin remodeling.

Stable isotope (C, O, S) systematics of the mercury mineralization at Idrija, Slovenia: constraints on fluid source and alteration processes

The world-class Idrija mercury deposit (western Slovenia) is hosted by highly deformed Permocarboniferous to Middle Triassic sedimentary rocks within a complex tectonic structure at the transition between the External Dinarides and the Southern Alps. Concordant and discordant mineralization formed concomitant with Middle Triassic bimodal volcanism in an aborted rift. A multiple isotopic (C, O, S) investigation of host rocks and ore minerals was performed to put constraints on the source and composition of the fluid, and the hydrothermal alteration. The distributions of the delta(13)C and delta(18)O values of host and gangue carbonates are indicative of a fracture-controlled hydrothermal system, with locally high fluid-rock ratios. Quantitative modeling of the delta(13)C and delta(18)O covariation for host carbonates during temperature dependent fluid-rock interaction, and concomitant precipitation of void-filling dolomites points to a slightly acidic hydrothermal fluid (delta(13)Capproximate to-4parts per thousand and delta(18)Oapproximate to+10parts per thousand), which most likely evolved during isotopic exchange with carbonates under low fluid/rock ratios. The delta(34)S values of hydrothermal and sedimentary sulfur minerals were used to re-evaluate the previously proposed magmatic and evaporitic sulfur sources for the mineralization, and to assess the importance of other possible sulfur sources such as the contemporaneous seawater sulfate, sedimentary pyrite, and organic sulfur compounds. The delta(34)S values of the sulfides show a large variation at deposit down to hand-specimen scale. They range for cinnabar and pyrite from -19.1 to +22.8parts per thousand, and from -22.4 to +59.6parts per thousand, respectively, suggesting mixing of sulfur from different sources. The peak of delta(34)S values of cinnabar and pyrite close to 0parts per thousand is compatible with ore sulfur derived dominantly from a magmatic fluid and/or from hydrothermal leaching of basement rocks. The similar stratigraphic trends of the delta(34)S values of both cinnabar and pyrite suggest a minor contribution of sedimentary sulfur (pyrite and organic sulfur) to the ore formation. Some of the positive delta(34)S values are probably derived from thermochemical reduction of evaporitic and contemporaneous seawater sulfates.

Exploration of the contribution of isotope ratio mass spectrometry to the investigation of explosives: A study of black powders and ammonium nitrate fertilisers

The increasing number of bomb attacks involving improvised explosive devices, as well as the nature of the explosives, give rise to concern among safety and law enforcement agencies. The substances used in explosive charges are often everyday products diverted from their primary licit applications. Thus, reducing or limiting their accessibility for prevention purposes is difficult. Ammonium nitrate, employed in agriculture as a fertiliser, is used worldwide in small and large homemade bombs. Black powder, dedicated to hunting and shooting sports, is used illegally as a filling in pipe bombs causing extensive damage. If the main developments of instrumental techniques in explosive analysis have been constantly pushing the limits of detection, their actual contribution to the investigation of explosives in terms of source discrimination is limited. Forensic science has seen the emergence of a new technology, isotope ratio mass spectrometry (IRMS), that shows promising results. Its very first application in forensic science dates back to 1979. Liu et al. analysed cannabis plants coming from different countries [Liu et al. 1979]. This preliminary study highlighted its potential to discriminate specimens coming from different sources. Thirty years later, the keen interest in this new technology has given rise to a flourishing number of publications in forensic science. The countless applications of IRMS to a wide range of materials and substances attest to its success and suggest that the technique is ready to be used in forensic science. However, many studies are characterised by a lack of methodology and fundamental data. They have been undertaken in a top-down approach, applying this technique in an exploratory manner on a restricted sampling. This manner of procedure often does not allow the researcher to answer a number of questions, such as: do the specimens come from the same source, what do we mean by source or what is the inherent variability of a substance? The production of positive results has prevailed at the expense of forensic fundamentals. This research focused on the evaluation of the contribution of the information provided by isotopic analysis to the investigation of explosives. More specifically, this evaluation was based on a sampling of black powders and ammonium nitrate fertilisers coming from known sources. Not only has the methodology developed in this work enabled us to highlight crucial elements inherent to the methods themselves, but also to evaluate both the longitudinal and transversal variabilities of the information. First, the study of the variability of the profile over time was undertaken. Secondly, the variability of black powders and ammonium nitrate fertilisers within the same source and between different sources was evaluated. The contribution of this information to the investigation of explosives was then evaluated and discussed. --------------------------------------------------------------------------------------------------- Le nombre croissant d'attentats à la bombe impliquant des engins explosifs artisanaux, ainsi que la nature des charges explosives, constituent une préoccupation majeure pour les autorités d'application de la loi et les organismes de sécurité. Les substances utilisées dans les charges explosives sont souvent des produits du quotidien, détournés de leurs applications licites. Par conséquent, réduire ou limiter l'accessibilité de ces produits dans un but de prévention est difficile. Le nitrate d'ammonium, employé dans l'agriculture comme engrais, est utilisé dans des petits et grands engins explosifs artisanaux. La poudre noire, initialement dédiée à la chasse et au tir sportif, est fréquemment utilisée comme charge explosive dans les pipe bombs, qui causent des dommages importants. Si les développements des techniques d'analyse des explosifs n'ont cessé de repousser les limites de détection, leur contribution réelle à l'investigation des explosifs est limitée en termes de discrimination de sources. Une nouvelle technologie qui donne des résultats prometteurs a fait son apparition en science forensique: la spectrométrie de masse à rapport isotopique (IRMS). Sa première application en science forensique remonte à 1979. Liu et al. ont analysé des plants de cannabis provenant de différents pays [Liu et al. 1979]. Cette étude préliminaire, basée sur quelques analyses, a mis en évidence le potentiel de l'IRMS à discriminer des spécimens provenant de sources différentes. Trente ans plus tard, l'intérêt marqué pour cette nouvelle technologie en science forensique se traduit par un nombre florissant de publications. Les innombrables applications de l'IRMS à une large gamme de matériaux et de substances attestent de son succès et suggèrent que la technique est prête à être utilisée en science forensique. Cependant, de nombreuses études sont caractérisées par un manque de méthodologie et de données fondamentales. Elles ont été menées sans définir les hypothèses de recherche et en appliquant cette technique de façon exploratoire sur un échantillonnage restreint. Cette manière de procéder ne permet souvent pas au chercheur de répondre à un certain nombre de questions, tels que: est-ce que deux spécimens proviennent de la même source, qu'entend-on par source ou encore quelle est l'intravariabilité d'une substance? La production de résultats positifs a prévalu au détriment des fondamentaux de science forensique. Cette recherche s'est attachée à évaluer la contribution réelle de l'information isotopique dans les investigations en matière d'explosifs. Plus particulièrement, cette évaluation s'est basée sur un échantillonnage constitué de poudres noires et d'engrais à base de nitrate d'ammonium provenant de sources connues. La méthodologie développée dans ce travail a permis non seulement de mettre en évidence des éléments cruciaux relatifs à la méthode d'analyse elle-même, mais également d'évaluer la variabilité de l'information isotopique d'un point de vue longitudinal et transversal. Dans un premier temps, l'évolution du profil en fonction du temps a été étudiée. Dans un second temps, la variabilité du profil des poudres noires et des engrais à base de nitrate d'ammonium au sein d'une même source et entre différentes sources a été évaluée. La contribution de cette information dans le cadre des investigations d'explosifs a ensuite été discutée et évaluée.

Embolic strokes of undetermined source in the athens stroke registry: a descriptive analysis.

BACKGROUND AND PURPOSE: A new clinical construct termed embolic stroke of undetermined source (ESUS) was recently introduced, but no such population has been described yet. Our aim is to provide a detailed descriptive analysis of an ESUS population derived from a large prospective ischemic stroke registry using the proposed diagnostic criteria. METHODS: The criteria proposed by the Cryptogenic Stroke/ESUS International Working Group were applied to the Athens Stroke Registry to identify all ESUS patients. ESUS was defined as a radiologically confirmed nonlacunar brain infarct in the absence of (a) extracranial or intracranial atherosclerosis causing ≥50% luminal stenosis in arteries supplying the ischemic area, (b) major-risk cardioembolic source, and (c) any other specific cause of stroke. RESULTS: Among 2735 patients admitted between 1992 and 2011, 275 (10.0%) were classified as ESUS. In the majority of ESUS (74.2%), symptoms were maximal at onset. ESUS were of moderate severity (median National Institute Health Stroke Scale score, 5). The most prevalent risk factor was arterial hypertension (64.7%), and 50.9% of patients were dyslipidemic. Among potential causes of the ESUS, covert atrial fibrillation (AF) was the most prevalent: in 30 (10.9%) patients, AF was diagnosed during hospitalization for stroke recurrence, whereas in 50 (18.2%) patients AF was detected after repeated ECG monitoring during follow-up. Also, covert AF was strongly suggested in 38 patients (13.8%) but never recorded. CONCLUSIONS: About 10% of patients with first-ever ischemic stroke met criteria for ESUS; covert paroxysmal AF seems to be a frequent cause of ESUS.

Evidence evaluation in fingerprint comparison and automated fingerprint identification systems: modeling between finger variability

In the context of the investigation of the use of automated fingerprint identification systems (AFIS) for the evaluation of fingerprint evidence, the current study presents investigations into the variability of scores from an AFIS system when fingermarks from a known donor are compared to fingerprints that are not from the same source. The ultimate goal is to propose a model, based on likelihood ratios, which allows the evaluation of mark-to-print comparisons. In particular, this model, through its use of AFIS technology, benefits from the possibility of using a large amount of data, as well as from an already built-in proximity measure, the AFIS score. More precisely, the numerator of the LR is obtained from scores issued from comparisons between impressions from the same source and showing the same minutia configuration. The denominator of the LR is obtained by extracting scores from comparisons of the questioned mark with a database of non-matching sources. This paper focuses solely on the assignment of the denominator of the LR. We refer to it by the generic term of between-finger variability. The issues addressed in this paper in relation to between-finger variability are the required sample size, the influence of the finger number and general pattern, as well as that of the number of minutiae included and their configuration on a given finger. Results show that reliable estimation of between-finger variability is feasible with 10,000 scores. These scores should come from the appropriate finger number/general pattern combination as defined by the mark. Furthermore, strategies of obtaining between-finger variability when these elements cannot be conclusively seen on the mark (and its position with respect to other marks for finger number) have been presented. These results immediately allow case-by-case estimation of the between-finger variability in an operational setting.

Major, minor, trace element, Sm-Nd and Sr isotope compositions of mafic rocks from the earliest oceanic crust of the Alpine Tethys

Recent isotopic and biochronologic dating has demonstrated that the Gets nappe contains remnants of the oldest part of the oceanic crust of the Alpine Tethys. The ophiolites are associated with deep sea sediments, platform carbonates and continental crustal elements suggesting a transitional environment between continental and oceanic crust. Therefore, the ophiolites from the Gets nappe provide the opportunity to assess the nature of mantle source and the magma evolution during the final rifting stage of the European lithosphere. Trace clement analyses of mafic rocks can he divided into two sets: (1) P, Zr and Y contents are consistent with those of mid-ocean ridge basalts and REE patterns have a P-MORB affinity. (2) P,Zr Ti and Y contents are compatible with within-plate basalts and are characterized by REE spectra similar to that of T-MORB. Both have Nd isotopic compositions similar to those of synrift magma of the Red Sea and to the Rhine Graben. The model ages are in agreement with an LREE-enriched subcontinental mantle source derived from depleted mantle 800 to 900 Ma ago. Minor, trace element and Sm-Nd compositions suggest that these rocks are basaltic relies of an earliest stage of oceanic spreading i.e. an embryonic ocean. Comparison between REE patterns, Nd and Sr isotope compositions, isotopic and biochronologic ages from different Alpine Tethys ophiolites shows that samples with enriched LREE are from the older ophiolitic suites and are relies of the embryonic ocean floor. Later phases of ocean spreading are characterized by basalts that are depleted in LREE.

Mechanical and elemental characterization of solder joints and welds using a gold-palladium alloy

Purpose. This study was conducted to determine whether newer infrared or laser welding technologies created joints superior to traditional furnace or torch soldering methods of joining metals. It was designed to assess the mechanical resistance, the characteristics of the fractured surfaces, and the elemental diffusion of joints obtained by four different techniques: (1) preceramic soldering with a propane-oxygen torch, (2) postceramic soldering with a porcelain furnace, (3) preceramic and (4) postceramic soldering with an infrared heat source, and (5) laser welding. Material and methods. Mechanical resistance was determined by measuring the ultimate tensile strength of the joint and by determining their resistance to fatigue loading. Elemental diffusion to and from the joint was assessed with microprobe tracings. Scanning electron microscopy micrographs of the fractured surface were also obtained and evaluated. Results. Under monotonic tensile stress, three groups emerged: The laser welds were the strongest, the preceramic joints ranged second, and the postceramic joints were the weakest. Under fatigue stress, the order was as follows: first, the preceramic joints, and second, a group that comprised both postceramic joints and the laser welds. Inspection of the fractographs revealed several fracture modes but no consistent pattern emerged. Microprobe analyses demonstrated minor diffusion processes in the preceramic joints, whereas significant diffusion was observed in the postceramic joints. Clinical Implications. The mechanical resistance data conflicted as to the strength that could be expected of laser welded joints. On the basis of fatigue resistance of the joints, neither infrared solder joints nor laser welds were stronger than torch or furnace soldered joints.

Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1.

Sphingomonas wittichii RW1 is a bacterium isolated for its ability to degrade the xenobiotic compounds dibenzodioxin and dibenzofuran (DBF). A number of genes involved in DBF degradation have been previously characterized, such as the dxn cluster, dbfB, and the electron transfer components fdx1, fdx3, and redA2. Here we use a combination of whole genome transcriptome analysis and transposon library screening to characterize RW1 catabolic and other genes implicated in the reaction to or degradation of DBF. To detect differentially expressed genes upon exposure to DBF, we applied three different growth exposure experiments, using either short DBF exposures to actively growing cells or growing them with DBF as sole carbon and energy source. Genome-wide gene expression was examined using a custom-made microarray. In addition, proportional abundance determination of transposon insertions in RW1 libraries grown on salicylate or DBF by ultra-high throughput sequencing was used to infer genes whose interruption caused a fitness loss for growth on DBF. Expression patterns showed that batch and chemostat growth conditions, and short or long exposure of cells to DBF produced very different responses. Numerous other uncharacterized catabolic gene clusters putatively involved in aromatic compound metabolism increased expression in response to DBF. In addition, only very few transposon insertions completely abolished growth on DBF. Some of those (e.g., in dxnA1) were expected, whereas others (in a gene cluster for phenylacetate degradation) were not. Both transcriptomic data and transposon screening suggest operation of multiple redundant and parallel aromatic pathways, depending on DBF exposure. In addition, increased expression of other non-catabolic genes suggests that during initial exposure, S. wittichii RW1 perceives DBF as a stressor, whereas after longer exposure, the compound is recognized as a carbon source and metabolized using several pathways in parallel.

Endoscopic low-coherence topography measurement for upper airways and hollow samples.

To evaluate the severity of airway pathologies, quantitative dimensioning of airways is of utmost importance. Endoscopic vision gives a projective image and thus no true scaling information can be directly deduced from it. In this article, an approach based on an interferometric setup, a low-coherence laser source and a standard rigid endoscope is presented, and applied to hollow samples measurements. More generally, the use of the low-coherence interferometric setup detailed here could be extended to any other endoscopy-related field of interest, e.g., gastroscopy, arthroscopy and other medical or industrial applications where tri-dimensional topology is required. The setup design with a multiple fibers illumination system is presented. Demonstration of the method ability to operate on biological samples is assessed through measurements on ex vivo pig bronchi.

Role and regulation of polyphosphate in leishmania parasites

Le protozoaire unicellulaire Leishmania est l'agent responsable de la leishmaniose, une maladie parasitaire humaine qui se manifeste par des lésions de la peau, se résolvant le plus souvent spontanément, jusqu'à des lésions viscérales fatales. Le parasite est transmis de l'insecte à l'hôte mammifère lors d'un repas sanguin de la mouche des sables et y réside respectivement sous formes extra- et intracellulaires. On estime que cette maladie touche environ 12 millions de personnes dans 98 pays. Etant donné que les médicaments disponibles à ce jour sont faiblement efficaces et/ou hautement toxiques, il est indispensable de consolider les connaissances sur le fonctionnement et la survie du parasite pour pouvoir développer de nouvelles stratégies de traitements et de préventions. Tous les organismes vivants, dont Leishmania, contiennent du polyphopshate (polyP). Cette molécule chargée négativement est constituée de trois jusqu'à plusieurs centaines de résidus de phosphates reliées par des liaisons à haute énergie. Le polyP sert donc de source d'énergie et de réservoir de phosphate; dans certaines espèces, il joue aussi un rôle dans l'adaptation au stress et la virulence de pathogènes. Ceci nous a amené à étudier le rôle du polyP dans le parasite Leishmania. L'enzyme responsable de la synthèse de polyP a été identifié récemment dans la levure : il s'agit de la chaperone de transport vacuolaire 4 (Vtc4). Nous avons identifié un homologue de Vtc4 chez les Trypanosomatidae, et avons donc décidé d'examiner sa fonction dans le métabolisme du polyP chez Leishmania. En éliminant l'expression de Vtc4 chez L. major et L. guyanensis, nous avons pu démontrer qu'il est indispensable pour la production de polyP chez Leishmania. De plus, nous avons constaté que ces parasites possèdent des chaînes de polyP allant de trois jusqu'à environ 300 résidus de phosphate. Le taux de polyP dans la cellule est précisément régulé et varie entre un très haut niveau durant la phase proliférative des promastigotes à un niveau bas en phase stationnaire tardive, alors que l'expression de Vtc4p reste stable. Dans les amastigotes intracellulaires, seulement des petites quantités de polyP et de Vtc4p sont détectées. En outre, l'absence de Vc4p et de polyP n'a pas d'effet significatif sur les infections in vivo de souris, ce qui indique que le polyP n'est pas nécessaire au développement de la leishmaniose. Ceci suggère que Vtc4p n 'est pas une bonne cible pour le développement de nouveaux traitements contre Leishmania. "Néanmoins, la présence du polyP favorise fortement la survie du parasite suite à un choc de température (37°C) et aide ainsi à sa persistance intracellulaire pendant les premiers jours d'infection de macrophages. En résumé, nos résultats indiquent que si le polyP a peu d'importance pendant l'infection et le développement de la leishmaniose chez la souris, il est par contre crucial pour l'adaptation à des situations de stress comme l'augmentation de la température. Le fait que le polyP a été conservé dans tous les organismes durant l'évolution suggère toutefois que cette molécule joue un rôle fondamental. Etant donné que l'absence de polyP n'a pas d'effet sur la survie des amastigotes, il pourrait être plus important dans la forme promastigote infectant la mouche des sables. - The unicellular protozoan parasite Leishmania is the causative agent of the human disease leishmaniasis, which can range from self-healing skin lesions to fatal visceral lesions. The parasite is transmitted from the insect vector to the mammalian host when the sand fly takes its blood meal and exists in an extra- and an intracellular form, respectively. The disease is estimated to affect 12 million people in 98 countries and currently available drug treatments are of relatively low potency and/or high toxicity. Thus, investigating parasite survival mechanisms and parasite adaptation to the two host environments contributes to the general understanding of Leishmania propagation and might therefore help to develop future treatments or preventions. All living cells, including Leishmania, contain a negatively charged polymer of a few up to several hundred phosphate residues. These so-called polyphosphates (polyPs) serve as an energy source and phosphate reservoir. In some organisms, polyP is also involved in adaptation to stresses and virulence of pathogens. Therefore we were interested in investigating the importance of polyP in Leishmania parasites. Recently, an eukaryotic enzyme responsible for polyP synthesis has been identified as the vacuolar transporter chaperone 4 (Vtc4) in yeast. We, and others, found a Vtc4 homologue in trypanosomatids and decided to examine its potential function in polyP metabolism. By generating VTC4 knock-out cell lines in L. major and Vtc4 knock-down cell lines in L. guyanensis, we were able to demonstrate that Vtc4p is responsible for the total amount of cellular polyP. We also observed that Leishmania polyP chain length ranges from a few up to around 300 residues and that its level is tightly regulated. PolyP abundance is highest during the logarithmic proliferating phase of promastigotes and decreases in the stationary phase, while Vtc4 protein expression remains stable during both phases. In the intracellular amastigote form, only low amounts of polyP and Vtc4p were detectable. Furthermore, absence of Vtc4p and polyP did not have a significant effect on in vivo mouse infections, indicating that polyP is not necessary for Leishmania disease progression. This suggests that Vtc4p would be a poor drug target against Leishmania infection. However, presence of the polymer strongly supported parasite survival during heat shock (37°C) and thereby promoted intracellular persistence during the first days of macrophage infections. Taken together, we found that polyP has little importance in Leishmania {in vivo) infection but that it plays a crucial role during adaptation to stress, such as heat shock. Given that polyP has been preciously conserved in all organisms during evolution it seems to play a fundamental role. Since absence of polyP does not affect amastigote survival, it might be significant for promastigote existence in the sand fly vector.

Activity measurements of 18F and 90Y with commercial radionuclide calibrators for nuclear medicine in Switzerland.

The activity of radiopharmaceuticals in nuclear medicine is measured before patient injection with radionuclide calibrators. In Switzerland, the general requirements for quality controls are defined in a federal ordinance and a directive of the Federal Office of Metrology (METAS) which require each instrument to be verified. A set of three gamma sources (Co-57, Cs-137 and Co-60) is used to verify the response of radionuclide calibrators in the gamma energy range of their use. A beta source, a mixture of (90)Sr and (90)Y in secular equilibrium, is used as well. Manufacturers are responsible for the calibration factors. The main goal of the study was to monitor the validity of the calibration factors by using two sources: a (90)Sr/(90)Y source and a (18)F source. The three types of commercial radionuclide calibrators tested do not have a calibration factor for the mixture but only for (90)Y. Activity measurements of a (90)Sr/(90)Y source with the (90)Y calibration factor are performed in order to correct for the extra-contribution of (90)Sr. The value of the correction factor was found to be 1.113 whereas Monte Carlo simulations of the radionuclide calibrators estimate the correction factor to be 1.117. Measurements with (18)F sources in a specific geometry are also performed. Since this radionuclide is widely used in Swiss hospitals equipped with PET and PET-CT, the metrology of the (18)F is very important. The (18)F response normalized to the (137)Cs response shows that the difference with a reference value does not exceed 3% for the three types of radionuclide calibrators.

Large scale assessment of regulatory evolution and transcriptome complexity in mammals

AbstractIn addition to genetic changes affecting the function of gene products, changes in gene expression have been suggested to underlie many or even most of the phenotypic differences among mammals. However, detailed gene expression comparisons were, until recently, restricted to closely related species, owing to technological limitations. Thus, we took advantage of the latest technologies (RNA-Seq) to generate extensive qualitative and quantitative transcriptome data for a unique collection of somatic and germline tissues from representatives of all major mammalian lineages (placental mammals, marsupials and monotremes) and birds, the evolutionary outgroup.In the first major project of my thesis, we performed global comparative analyses of gene expression levels based on these data. Our analyses provided fundamental insights into the dynamics of transcriptome change during mammalian evolution (e.g., the rate of expression change across species, tissues and chromosomes) and allowed the exploration of the functional relevance and phenotypic implications of transcription changes at a genome-wide scale (e.g., we identified numerous potentially selectively driven expression switches).In a second project of my thesis, which was also based on the unique transcriptome data generated in the context of the first project we focused on the evolution of alternative splicing in mammals. Alternative splicing contributes to transcriptome complexity by generating several transcript isoforms from a single gene, which can, thus, perform various functions. To complete the global comparative analysis of gene expression changes, we explored patterns of alternative splicing evolution. This work uncovered several general and unexpected patterns of alternative splicing evolution (e.g., we found that alternative splicing evolves extremely rapidly) as well as a large number of conserved alternative isoforms that may be crucial for the functioning of mammalian organs.Finally, the third and final project of my PhD consisted in analyzing in detail the unique functional and evolutionary properties of the testis by exploring the extent of its transcriptome complexity. This organ was previously shown to evolve rapidly both at the phenotypic and molecular level, apparently because of the specific pressures that act on this organ and are associated with its reproductive function. Moreover, my analyses of the amniote tissue transcriptome data described above, revealed strikingly widespread transcriptional activity of both functional and nonfunctional genomic elements in the testis compared to the other organs. To elucidate the cellular source and mechanisms underlying this promiscuous transcription in the testis, we generated deep coverage RNA-Seq data for all major testis cell types as well as epigenetic data (DNA and histone methylation) using the mouse as model system. The integration of these complete dataset revealed that meiotic and especially post-meiotic germ cells are the major contributors to the widespread functional and nonfunctional transcriptome complexity of the testis, and that this "promiscuous" spermatogenic transcription is resulting, at least partially, from an overall transcriptionally permissive chromatin state. We hypothesize that this particular open state of the chromatin results from the extensive chromatin remodeling that occurs during spermatogenesis which ultimately leads to the replacement of histones by protamines in the mature spermatozoa. Our results have important functional and evolutionary implications (e.g., regarding new gene birth and testicular gene expression evolution).Generally, these three large-scale projects of my thesis provide complete and massive datasets that constitute valuables resources for further functional and evolutionary analyses of mammalian genomes.

Simultaneous determination of Pu and Am radioisotopes in environmental samples: a tool for determining origin and release date

A radiochemical procedure was developed for the sequential determination of Pu and Am radioisotopes in environmental samples. The radioisotope activities were then used to assess the origin and release date of the environmental plutonium. The radioanalytical procedure is based on the separation of Pu and Am on selective extraction chromatographic resins (Eichrom TEVA and DGA). Alpha sources were prepared by electrodeposition on stainless steel discs, and the alpha emitting radionuclides (238Pu, 239,240Pu and 241Am) were measured by alpha spectrometry. For the determination of the beta emitting 241Pu, the Pu alpha source was leached in hot concentrated nitric acid and the Pu fraction further purified by extraction chromatography on a small column of TEVA resin (100 μg of resin in a pipette tip). 241Pu is then measured by ultra low level liquid scintillation counting. Due to the lack of reference material for 241Pu, the proposed radiochemical method was nevertheless validated using four IAEA reference sediments with information values of 241Pu. The proposed method was then used to determine the 238Pu, 239,240Pu, 241Pu and 241Am activity concentrations in alpine soils of France and Switzerland. The soil is the primary receptor of the atmospheric radioactive fallout and, because of the strong binding interaction with soils particles, the isotopes are little fractionated. Therefore, the activity ratios 241Pu/239+240Pu and 238Pu/239,240Pu in soil samples were used to determine the origin (source) and date of the Pu contamination in the investigated alpine sites. The 241Pu/239,240Pu and 238Pu/239,240Pu activity ratios confirmed that the main origin of Pu in the alpine soils was the global fallout from the nuclear bomb tests (NBT) in the fifties and sixties. Furthermore, the 241Pu/241Am activity ratios were used to determine the age of the Pu contamination, which is also an important data for distinguishing the Pu sources. The estimation of the date of the contamination, by the 241Pu/241Am age-dating method, further confirmed the NBT as the Pu source. However, the 241Pu/241Am dating method was limited to samples where Pu-Am fractionation was insignificant. If any, the contribution of the Chernobyl accident in the studied sites is negligible.

The systematic profiling of false identity documents: method validation and performance evaluation using seizures known to originate from common and different sources

False identity documents constitute a potential powerful source of forensic intelligence because they are essential elements of transnational crime and provide cover for organized crime. In previous work, a systematic profiling method using false documents' visual features has been built within a forensic intelligence model. In the current study, the comparison process and metrics lying at the heart of this profiling method are described and evaluated. This evaluation takes advantage of 347 false identity documents of four different types seized in two countries whose sources were known to be common or different (following police investigations and dismantling of counterfeit factories). Intra-source and inter-sources variations were evaluated through the computation of more than 7500 similarity scores. The profiling method could thus be validated and its performance assessed using two complementary approaches to measuring type I and type II error rates: a binary classification and the computation of likelihood ratios. Very low error rates were measured across the four document types, demonstrating the validity and robustness of the method to link documents to a common source or to differentiate them. These results pave the way for an operational implementation of a systematic profiling process integrated in a developed forensic intelligence model.