Automated Traffic/Truck Weight Monitoring Equipment (Weigh-in-Motion), HR-282, 1988

This report documents work undertaken in the demonstration of a low-cost Automatic Weight and Classification System (AWACS). An AWACS procurement specification and details of the results of the project are also included. The intent of the project is to support and encourage transferring research knowledge to state and local agencies and manufacturers through field demonstrations. Presently available, Weigh-in-Motion and Classification Systems are typically too expensive to permit the wide deployment necessary to obtain representative vehicle data. Piezo electric technology has been used in the United Kingdom and Europe and is believed to be the basic element in a low-cost AWACS. Low-cost systems have been installed at two sites, one in Portland Cement Concrete (PCC) pavement in Iowa and the other in Asphaltic Cement Concrete (ACC) pavement in Minnesota to provide experience with both types of pavement. The systems provide axle weights, gross vehicle weight, axle spacing, vehicle classification, vehicle speed, vehicle count, and time of arrival. In addition, system self-calibration and a method to predict contact tire pressure is included in the system design. The study has shown that in the PCC pavement, the AWACS is capable of meeting the needs of state and federal highway agencies, producing accuracies comparable to many current commercial WIM devices. This is being achieved at a procurement cost of substantially less than currently available equipment. In the ACC pavement the accuracies were less than those observed in the PCC pavement which is concluded to result from a low pavement rigidity at this site. Further work is needed to assess the AWACS performance at a range of sites in ACC pavements.

Mutations in tubulin genes are frequent causes of various foetal malformations of cortical development including microlissencephaly.

Complex cortical malformations associated with mutations in tubulin genes are commonly referred to as "Tubulinopathies". To further characterize the mutation frequency and phenotypes associated with tubulin mutations, we studied a cohort of 60 foetal cases. Twenty-six tubulin mutations were identified, of which TUBA1A mutations were the most prevalent (19 cases), followed by TUBB2B (6 cases) and TUBB3 (one case). Three subtypes clearly emerged. The most frequent (n = 13) was microlissencephaly with corpus callosum agenesis, severely hypoplastic brainstem and cerebellum. The cortical plate was either absent (6/13), with a 2-3 layered pattern (5/13) or less frequently thickened (2/13), often associated with neuroglial overmigration (4/13). All cases had voluminous germinal zones and ganglionic eminences. The second subtype was lissencephaly (n = 7), either classical (4/7) or associated with cerebellar hypoplasia (3/7) with corpus callosum agenesis (6/7). All foetuses with lissencephaly and cerebellar hypoplasia carried distinct TUBA1A mutations, while those with classical lissencephaly harbored recurrent mutations in TUBA1A (3 cases) or TUBB2B (1 case). The third group was polymicrogyria-like cortical dysplasia (n = 6), consisting of asymmetric multifocal or generalized polymicrogyria with inconstant corpus callosum agenesis (4/6) and hypoplastic brainstem and cerebellum (3/6). Polymicrogyria was either unlayered or 4-layered with neuronal heterotopias (5/6) and occasional focal neuroglial overmigration (2/6). Three had TUBA1A mutations and 3 TUBB2B mutations. Foetal TUBA1A tubulinopathies most often consist in microlissencephaly or classical lissencephaly with corpus callosum agenesis, but polymicrogyria may also occur. Conversely, TUBB2B mutations are responsible for either polymicrogyria (4/6) or microlissencephaly (2/6).

Characterization of BMP signaling in breast development and tumorigenesis

Résumé L'influence des hormones reproductives sur le développement du cancer du sein a été établie au travers de nombreuse études épidémiologiques. Nous avons précédemment démontré que le gène Wnt-4 est un médiateur essentiel de la progestérone dans le développement lobulo-alvéolaire de l'épithélium mammaire. De plus, le rôle de la voie de signalisation Wnt dans la tumorigénèse de la glande mammaire mutine est largement établi. Pour comprendre sa fonction dans le cancer du sein, nous avons activée cette voie en surexprimant le gène Wnt-1 dans des cellules épithéliales primaires de sein, au moyen d'un rétrovirus. Ceci a conduit à la transformation oncogénique de ces cellules et à l'obtention d'un modèle de carcinogénèse du sein dénommé Wnt-1 HMEC. L'analyse de l'expression des gènes induits par la surexpression de Wnt-1 dans ces cellules, a permis d'identifier les gènes BMP4 et 7. Alors que des analyses de RT-PCR ont montré leur forte expression dans les cellules Wnt-1-HMECs, la présence d'une grande quantité de la protéine BMP7 a été constatée dans les tumeurs dérivées de ces cellules. L'importante phosphorylation des Smad 1, 5, S dans les Wnt-1 HMECs indique l'activation de la voie BMP, possiblement due à la stimulation ce celle-ci par BMP7. L'activation de la voie Wnt par la ß-Caténine, conduit à la transcription de BMP7, identifiant ainsi ce gène comme un gène cible de la voie canonique. La pertinence de nos observations a par ailleurs été confirmée par le fait que BMP7 est surexprimé dans les tumeurs de seins humains. Afin d'élucider la fonction de la voie BMP dans le sein, nous avons utilisé le modèle mutin. L'expression du gène BMP7 dans les souris transgéniques MMTV Wnt-1 s'est avérée élevée, démontrant qu'il est aussi un gène cible de la voie Wnt in-vivo. L'expression de l'ARN messager .codant pour la protéine BMP7 est induite lors du développement lobulo-alvéolaire, qui se fait sous l'influence de la progestérone et de Wnt-4. Ensemble, ces observations corroborent le fait qu'une stimulation avec de la progestérone suffit à induire la transcription du gène dans les 24h. Nos résultats coïncident d'autre part avec le fait que BMP7 est exprimé dans la couche myoépithéliale de l'épithélium où la voie Wnt est activée. L'analyse de souris reportrices de l'activité de la voie BMP, suggère une activation dans la couche luminale de l'épithélium durant tout le développement de la glande mammaire. Curieusement, cette même voie est active dans le mésenchyme lors de la mammogénèse embryonnaire. Finalement, nos analyses d'immunofluorescence démontrent la capacité de prolifération des cellules ayant activé BMP, ainsi que leur nette ségrégation d'avec les cellules exprimant le récepteur à la progestérone. Nos résultats démontrent que le gène BMP7 est un gène cible de la voie Wnt canonique dans le sein. Son expression dans la couche myoépitheliale est induite par Wnt-4, lui-même sécrété par les cellules luminales sensibles à la progestérone. La sécrétion de la protéine BMP7 conduit finalement à l'activation de la voie BMP dans les cellules négatives pour le récepteur à la progestérone. Abstract Epidemiological studies highlight the repetitive exposure to circulating progesterone as a major risk in the development of breast cancer. Work in our laboratory showed that Wnt-4 is an essential mediator of progesterone-driven side-branch formation, while Wnt signaling has long been established as strongly oncogenic in the mouse mammary gland. To address the role of Wnt in breast tumorigenesis we activated the pathway in primary human breast epithelial cells by means of refroviral Wnt-1 expression. This resulted in a Wnt1-induced breast carcinogenesis model, being referred to as Wnt-1-HMECs. Gene expression profiling revealed the Bone Morphogenetic Protein 4 and 7 (BMP4 and 7) a mong the most upregulated gene by ectopic Wnt-1 expression in primary HMECs. RT-PCR analysis confirmed elevated BMP4 and 7 mRNA levels in Wnt-1-infected HMECs, as well as strong BMP7 expression in the tumors derived from these cells. Smad 1, 5, 8 phosphorylation was high in Wnt-1HMECs whereas below detection limit in primary HMECs suggesting that the increased expression of BMP-7 results in activation of downstream signaling. Ectopic expressíon of a stabilized form of ßcatenin in primary HMECs resulted in increased transcription of BMP-7 suggesting that it is a target of canonical Wnt signaling. The clinical relevance of our observations was confirmed by the finding of BMP7 being upregulated in human breast tumor samples. To elucidate the role of BMP ligands in the breast in-vivo, we made use of the mouse model. Expression of the BMP7 gene was found to be increased in MMTV-Wnt-1 transgenic animals, suggesting that BMP7 may also be a Wnt 1 target gene in vivo. Expression of BMP7 was upregulated in mid-pregnancy which coincides with progesterone/Wnt induced side branching. BMP7 was induced within 24 hours by progesterone. Consistent with it being a target of canonical Wnt signaling, we demonstrated preferential expression of this ligand in the myoepithelial cells, the target cells of Wnt signals. In-vivo analysis of BMP signaling using a reporter mouse revealed the activation of the pathway in the luminal layer of the epithelium throughout postnatal development. Interestingly, during embryonic mammogenesis the pathway was found to be active in the mesenchyme. Immunofluorescence studies demonstrated that cells with BMP activity can proliferate. They also revealed a clear segregation between progesterone receptor positive cells and cells with active BMP signaling. Together our observations suggest that BMP-7 is a canonical Wnt signaling target both in HMECs and in the mouse mammary gland in-vivo. It is expressed in the myoepithelium possibly in response to Wnt-4, which is secreted by steroid receptor positive cells in response to progesterone. BMP-7 in turn may impinge on lumina) epithelial cells and activate BMP signaling in PR negative cells.

Further delineation of the facial 13q14 deletion syndrome in 13 retinoblastoma patients.

Thirteen years ago, Motegi and colleagues (J Med Genet 1987;24:696-697) summarized the specific facial phenotype of six Japanese retinoblastoma patients with interstitial 13q14 deletions. Among a series of 228 propositi with retinoblastoma referred to the Lausanne Retinoblastoma Clinic for treatment and genetic counseling between 1986 and 1997, 13 (5.7%) were diagnosed with a cytogenetic de-novo 13q14 deletion. We confirm the presence of the reported facial phenotype in our population of Caucasian patients and describe additional clinical traits, thus extending the facial phenotype associated with the 13q14 deletion. Del(13q14) comprises, among others, cranial anomalies, frontal bossing, deeply grooved and long philtrum, depressed and broad nasal bridge, bulbous tip of the nose, thick lower lip, thin upper lip, broad cheeks, and large ears and lobules. Recognition of this particular facial appearance was instrumental in the genetic diagnosis of 13q deletions and in the presymptomatic diagnosis of retinoblastoma in a significant number of our cases. Identification of this phenotype in a retinoblastoma patient allows for efficient diagnosis of recurrence in his progeny and/or sibship, while its ignorance will compromise genetic counseling due to the possible difficulties in detecting large deletions by standard molecular mutation analysis. Recognition of this syndrome in newborns without known familial risk for retinoblastoma is even more important as it is a clear warning sign that indicates immediate ophthalmic examination.

Syndromes vertigineux en pratique ambulatoire [Dizziness in a general practice]

The symptoms of vertigo are frequent complaints. With the anamnestic features and the quite long and tiresome clinical examination alone, the general practitioner should make the difference between a benign peripheral and a potentially fatal central pathology. A good knowledge of the anamnestic and clinical particularities and the diagnostic manoeuvres of the main types of vertigo allows in about two thirds of the cases to distinguish their origin. If a central origin is suspected or if the etiology is uncertain, the patient should be referred to a neurologist for further examination and radiological investigations.

Rift-related inheritance in orogens: a case study from the Austroalpine nappes in Central Alps (SE-Switzerland and N-Italy)

The Austroalpine nappe systems in SE-Switzerland and N-Italy preserve remnants of the Adriatic rifted margin. Based on new maps and cross-sections, we suggest that the complex structure of the Campo, Grosina/Languard, and Bernina nappes is inherited largely from Jurassic rifting. We propose a classification of the Austroalpine domain into Upper, Middle and Lower Austroalpine nappes that is new because it is based primarily on the rift-related Jurassic structure and paleogeography of these nappes. Based on the Alpine structures and pre-Alpine, rift-related geometry of the Lower (Bernina) and Middle (Campo, Grosina/Languard) Austroalpine nappes, we restore these nappes to their original positions along the former margin, as a means of understanding the formation and emplacement of the nappes during initial reactivation of the Alpine Tethyan margin. The Campo and Grosina/Languard nappes can be interpreted as remnants of a former necking zone that comprised pre-rift upper and middle crust. These nappes were juxtaposed with the Mesozoic cover of the Bernina nappe during Jurassic rifting. We find evidence for low-angle detachment faults and extensional allochthons in the Bernina nappe similar to those previously described in the Err nappe and explain their role during subsequent reactivation. Our observations reveal a strong control of rift-related structures during the subsequent Alpine reactivation on all scales of the former distal margin. Two zones of intense deformation, referred to as the Albula-Zebru and Lunghin-Mortirolo movement zones, have been reactivated during Alpine deformation and cannot be described as simple monophase faults or shear zones. We propose a tectonic model for the Austroalpine nappe systems that link inherited, rift-related structures with present-day Alpine structures. In conclusion, we believe that apart from the direct regional implications, the results of this paper are of general interest in understanding the control of rift structures during reactivation of distal-rifted margins.

Preclinical evaluation of the immunogenicity of C-type HIV-1-based DNA and NYVAC vaccines in the Balb/C mouse model.

As part of a European initiative (EuroVacc), we report the design, construction, and immunogenicity of two HIV-1 vaccine candidates based on a clade C virus strain (CN54) representing the current major epidemic in Asia and parts of Africa. Open reading frames encoding an artificial 160-kDa GagPolNef (GPN) polyprotein and the external glycoprotein gp120 were fully RNA and codon optimized. A DNA vaccine (DNA-GPN and DNA-gp120, referred to as DNA-C), and a replication-deficient vaccinia virus encoding both reading frames (NYVAC-C), were assessed regarding immunogenicity in Balb/C mice. The intramuscular administration of both plasmid DNA constructs, followed by two booster DNA immunizations, induced substantial T-cell responses against both antigens as well as Env-specific antibodies. Whereas low doses of NYVAC-C failed to induce specific CTL or antibodies, high doses generated cellular as well as humoral immune responses, but these did not reach the levels seen following DNA vaccination. The most potent immune responses were detectable using prime:boost protocols, regardless of whether DNA-C or NYVAC-C was used as the priming or boosting agent. These preclinical findings revealed the immunogenic response triggered by DNA-C and its enhancement by combining it with NYVAC-C, thus complementing the macaque preclinical and human phase I clinical studies of EuroVacc.

Comparison of thermogenic effect of fructose and glucose in normal humans.

After nutrient ingestion there is an increase in energy expenditure that has been referred to as dietary-induced thermogenesis. In the present study we have employed indirect calorimetry to compare the increment in energy expenditure after the ingestion of 75 g of glucose or fructose in 17 healthy volunteers. During the 4 h after glucose ingestion the plasma insulin concentration increased by 33 +/- 4 microU/ml and this was associated with a significant increase in carbohydrate oxidation and decrement in lipid oxidation. Energy expenditure increased by 0.08 +/- 0.01 kcal/min. When fructose was ingested, the plasma insulin concentration increased by only 8 +/- 2 microU/ml vs. glucose. Nonetheless, the increments in carbohydrate oxidation and decrement in lipid oxidation were significantly greater than with glucose. The increment in energy expenditure was also greater with fructose. When the mean increment in plasma insulin concentration after fructose was reproduced using the insulin clamp technique, the increase in carbohydrate oxidation and decrement in lipid oxidation were markedly reduced compared with the fructose-ingestion study; energy expenditure failed to increase above basal levels. To examine the role of the adrenergic nervous system in fructose-induced thermogenesis, fructose ingestion was also performed during beta-adrenergic blockade with propranolol. The increase in energy expenditure during fructose plus propranolol was lower than with fructose ingestion alone. These results indicate that the stimulation of thermogenesis after carbohydrate ingestion is related to an augmentation of cellular metabolism and is not dependent on an increase in the plasma insulin concentration per se.(ABSTRACT TRUNCATED AT 250 WORDS)

Assigning and combining probabilities in single-case studies

There is currently a considerable diversity of quantitative measures available for summarizing the results in single-case studies. Given that the interpretation of some of them is difficult due to the lack of established benchmarks, the current paper proposes an approach for obtaining further numerical evidence on the importance of the results, complementing the substantive criteria, visual analysis, and primary summary measures. This additional evidence consists of obtaining the statistical significance of the outcome when referred to the corresponding sampling distribution. This sampling distribution is formed by the values of the outcomes (expressed as data nonoverlap, R-squared, etc.) in case the intervention is ineffective. The approach proposed here is intended to offer the outcome"s probability of being as extreme when there is no treatment effect without the need for some assumptions that cannot be checked with guarantees. Following this approach, researchers would compare their outcomes to reference values rather than constructing the sampling distributions themselves. The integration of single-case studies is problematic, when different metrics are used across primary studies and not all raw data are available. Via the approach for assigning p values it is possible to combine the results of similar studies regardless of the primary effect size indicator. The alternatives for combining probabilities are discussed in the context of single-case studies pointing out two potentially useful methods one based on a weighted average and the other on the binomial test.

The diagnostic challenge of progressive pseudorheumatoid dysplasia (PPRD): A review of clinical features, radiographic features, and WISP3 mutations in 63 affected individuals.

Progressive pseudorheumatoid dysplasia (PPRD) is a genetic, non-inflammatory arthropathy caused by recessive loss of function mutations in WISP3 (Wnt1-inducible signaling pathway protein 3; MIM 603400), encoding for a signaling protein. The disease is clinically silent at birth and in infancy. It manifests between the age of 3 and 6 years with joint pain and progressive joint stiffness. Affected children are referred to pediatric rheumatologists and orthopedic surgeons; however, signs of inflammation are absent and anti-inflammatory treatment is of little help. Bony enlargement at the interphalangeal joints progresses leading to camptodactyly. Spine involvement develops in late childhood and adolescence leading to short trunk with thoracolumbar kyphosis. Adult height is usually below the 3rd percentile. Radiographic signs are relatively mild. Platyspondyly develops in late childhood and can be the first clue to the diagnosis. Enlargement of the phalangeal metaphyses develops subtly and is usually recognizable by 10 years. The femoral heads are large and the acetabulum forms a distinct "lip" overriding the femoral head. There is a progressive narrowing of all articular spaces as articular cartilage is lost. Medical management of PPRD remains symptomatic and relies on pain medication. Hip joint replacement surgery in early adulthood is effective in reducing pain and maintaining mobility and can be recommended. Subsequent knee joint replacement is a further option. Mutation analysis of WISP3 allowed the confirmation of the diagnosis in 63 out of 64 typical cases in our series. Intronic mutations in WISP3 leading to splicing aberrations can be detected only in cDNA from fibroblasts and therefore a skin biopsy is indicated when genomic analysis fails to reveal mutations in individuals with otherwise typical signs and symptoms. In spite of the first symptoms appearing in early childhood, the diagnosis of PPRD is most often made only in the second decade and affected children often receive unnecessary anti-inflammatory and immunosuppressive treatments. Increasing awareness of PPRD appears to be essential to allow for a timely diagnosis. © 2012 Wiley Periodicals, Inc.

Explaining rapid transitions in the practice of flood risk management

This article draws on empirical material to reflect on what drives rapid change in flood risk management practice, reflecting wider interest in the way that scientific practices make risk landscapes and a specific focus on extreme events as drivers of rapid change. Such events are commonly referred to as a form of creative destruction, ones that reveal both the composition of socioenvironmental assemblages and provide a creative opportunity to remake those assemblages in alternate ways, therefore rapidly changing policy and practice. Drawing on wider thinking in complexity theory, we argue that what happens between events might be as, if not more, important than the events themselves. We use two empirical examples concerned with flood risk management practice: a rapid shift in the dominant technologies used to map flood risk in the United Kingdom and an experimental approach to public participation tested in two different locations, with dramatically different consequences. Both show that the state of the socioenvironmental assemblage in which the events take place matters as much as the magnitude of the events themselves. The periods between rapid changes are not simply periods of discursive consolidation but involve the ongoing mutation of such assemblages, which could either sensitize or desensitize them to rapid change. Understanding these intervening periods matters as much as the events themselves. If events matter, it is because of the ways in which they might bring into sharp focus the coding or framing of a socioenvironmental assemblage in policy or scientific practice irrespective of whether or not those events evolve the assemblage in subtle or more radical ways.

Des faux documents d'identité au renseignement forensique : développement d'une approche systématique et transversale du traitement de la donnée forensique à des fins de renseignement criminel

La fabrication, la distribution et l'usage de fausses pièces d'identité constituent une menace pour la sécurité autant publique que privée. Ces faux documents représentent en effet un catalyseur pour une multitude de formes de criminalité, des plus anodines aux formes les plus graves et organisées. La dimension, la complexité, la faible visibilité, ainsi que les caractères répétitif et évolutif de la fraude aux documents d'identité appellent des réponses nouvelles qui vont au-delà d'une approche traditionnelle au cas par cas ou de la stratégie du tout technologique dont la perspective historique révèle l'échec. Ces nouvelles réponses passent par un renforcement de la capacité de comprendre les problèmes criminels que posent la fraude aux documents d'identité et les phénomènes qui l'animent. Cette compréhension est tout bonnement nécessaire pour permettre d'imaginer, d'évaluer et de décider les solutions et mesures les plus appropriées. Elle requière de développer les capacités d'analyse et la fonction de renseignement criminel qui fondent en particulier les modèles d'action de sécurité les plus récents, tels que l'intelligence-led policing ou le problem-oriented policing par exemple. Dans ce contexte, le travail doctoral adopte une position originale en postulant que les fausses pièces d'identité se conçoivent utilement comme la trace matérielle ou le vestige résultant de l'activité de fabrication ou d'altération d'un document d'identité menée par les faussaires. Sur la base de ce postulat fondamental, il est avancé que l'exploitation scientifique, méthodique et systématique de ces traces au travers d'un processus de renseignement forensique permet de générer des connaissances phénoménologiques sur les formes de criminalité qui fabriquent, diffusent ou utilisent les fausses pièces d'identité, connaissances qui s'intègrent et se mettent avantageusement au service du renseignement criminel. A l'appui de l'épreuve de cette thèse de départ et de l'étude plus générale du renseignement forensique, le travail doctoral propose des définitions et des modèles. Il décrit des nouvelles méthodes de profilage et initie la constitution d'un catalogue de formes d'analyses. Il recourt également à des expérimentations et des études de cas. Les résultats obtenus démontrent que le traitement systématique de la donnée forensique apporte une contribution utile et pertinente pour le renseignement criminel stratégique, opérationnel et tactique, ou encore la criminologie. Combiné aux informations disponibles par ailleurs, le renseignement forensique produit est susceptible de soutenir l'action de sécurité dans ses dimensions répressive, proactive, préventive et de contrôle. En particulier, les méthodes de profilage des fausses pièces d'identité proposées permettent de révéler des tendances au travers de jeux de données étendus, d'analyser des modus operandi ou d'inférer une communauté ou différence de source. Ces méthodes appuient des moyens de détection et de suivi des séries, des problèmes et des phénomènes criminels qui s'intègrent dans le cadre de la veille opérationnelle. Ils permettent de regrouper par problèmes les cas isolés, de mettre en évidence les formes organisées de criminalité qui méritent le plus d'attention, ou de produire des connaissances robustes et inédites qui offrent une perception plus profonde de la criminalité. Le travail discute également les difficultés associées à la gestion de données et d'informations propres à différents niveaux de généralité, ou les difficultés relatives à l'implémentation du processus de renseignement forensique dans la pratique. Ce travail doctoral porte en premier lieu sur les fausses pièces d'identité et leur traitement par les protagonistes de l'action de sécurité. Au travers d'une démarche inductive, il procède également à une généralisation qui souligne que les observations ci-dessus ne valent pas uniquement pour le traitement systématique des fausses pièces d'identité, mais pour celui de tout type de trace dès lors qu'un profil en est extrait. Il ressort de ces travaux une définition et une compréhension plus transversales de la notion et de la fonction de renseignement forensique. The production, distribution and use of false identity documents constitute a threat to both public and private security. Fraudulent documents are a catalyser for a multitude of crimes, from the most trivial to the most serious and organised forms. The dimension, complexity, low visibility as well as the repetitive and evolving character of the production and use of false identity documents call for new solutions that go beyond the traditional case-by-case approach, or the technology-focused strategy whose failure is revealed by the historic perspective. These new solutions require to strengthen the ability to understand crime phenomena and crime problems posed by false identity documents. Such an understanding is pivotal in order to be able to imagine, evaluate and decide on the most appropriate measures and responses. Therefore, analysis capacities and crime intelligence functions, which found the most recent policing models such as intelligence-led policing or problem-oriented policing for instance, have to be developed. In this context, the doctoral research work adopts an original position by postulating that false identity documents can be usefully perceived as the material remnant resulting from the criminal activity undertook by forgers, namely the manufacture or the modification of identity documents. Based on this fundamental postulate, it is proposed that a scientific, methodical and systematic processing of these traces through a forensic intelligence approach can generate phenomenological knowledge on the forms of crime that produce, distribute and use false identity documents. Such knowledge should integrate and serve advantageously crime intelligence efforts. In support of this original thesis and of a more general study of forensic intelligence, the doctoral work proposes definitions and models. It describes new profiling methods and initiates the construction of a catalogue of analysis forms. It also leverages experimentations and case studies. Results demonstrate that the systematic processing of forensic data usefully and relevantly contributes to strategic, tactical and operational crime intelligence, and also to criminology. Combined with alternative information available, forensic intelligence may support policing in its repressive, proactive, preventive and control activities. In particular, the proposed profiling methods enable to reveal trends among extended datasets, to analyse modus operandi, or to infer that false identity documents have a common or different source. These methods support the detection and follow-up of crime series, crime problems and phenomena and therefore contribute to crime monitoring efforts. They enable to link and regroup by problems cases that were previously viewed as isolated, to highlight organised forms of crime which deserve greatest attention, and to elicit robust and novel knowledge offering a deeper perception of crime. The doctoral research work discusses also difficulties associated with the management of data and information relating to different levels of generality, or difficulties associated with the implementation in practice of the forensic intelligence process. The doctoral work focuses primarily on false identity documents and their treatment by policing stakeholders. However, through an inductive process, it makes a generalisation which underlines that observations do not only apply to false identity documents but to any kind of trace as soon as a profile is extracted. A more transversal definition and understanding of the concept and function of forensic intelligence therefore derives from the doctoral work.

Development and application of computational methodologies in qualitative modeling

La présente thèse s'intitule "Développent et Application des Méthodologies Computationnelles pour la Modélisation Qualitative". Elle comprend tous les différents projets que j'ai entrepris en tant que doctorante. Plutôt qu'une mise en oeuvre systématique d'un cadre défini a priori, cette thèse devrait être considérée comme une exploration des méthodes qui peuvent nous aider à déduire le plan de processus regulatoires et de signalisation. Cette exploration a été mue par des questions biologiques concrètes, plutôt que par des investigations théoriques. Bien que tous les projets aient inclus des systèmes divergents (réseaux régulateurs de gènes du cycle cellulaire, réseaux de signalisation de cellules pulmonaires) ainsi que des organismes (levure à fission, levure bourgeonnante, rat, humain), nos objectifs étaient complémentaires et cohérents. Le projet principal de la thèse est la modélisation du réseau de l'initiation de septation (SIN) du S.pombe. La cytokinèse dans la levure à fission est contrôlée par le SIN, un réseau signalant de protéines kinases qui utilise le corps à pôle-fuseau comme échafaudage. Afin de décrire le comportement qualitatif du système et prédire des comportements mutants inconnus, nous avons décidé d'adopter l'approche de la modélisation booléenne. Dans cette thèse, nous présentons la construction d'un modèle booléen étendu du SIN, comprenant la plupart des composantes et des régulateurs du SIN en tant que noeuds individuels et testable expérimentalement. Ce modèle utilise des niveaux d'activité du CDK comme noeuds de contrôle pour la simulation d'évènements du SIN à différents stades du cycle cellulaire. Ce modèle a été optimisé en utilisant des expériences d'un seul "knock-out" avec des effets phénotypiques connus comme set d'entraînement. Il a permis de prédire correctement un set d'évaluation de "knock-out" doubles. De plus, le modèle a fait des prédictions in silico qui ont été validées in vivo, permettant d'obtenir de nouvelles idées de la régulation et l'organisation hiérarchique du SIN. Un autre projet concernant le cycle cellulaire qui fait partie de cette thèse a été la construction d'un modèle qualitatif et minimal de la réciprocité des cyclines dans la S.cerevisiae. Les protéines Clb dans la levure bourgeonnante présentent une activation et une dégradation caractéristique et séquentielle durant le cycle cellulaire, qu'on appelle communément les vagues des Clbs. Cet évènement est coordonné avec la courbe d'activation inverse du Sic1, qui a un rôle inhibitoire dans le système. Pour l'identification des modèles qualitatifs minimaux qui peuvent expliquer ce phénomène, nous avons sélectionné des expériences bien définies et construit tous les modèles minimaux possibles qui, une fois simulés, reproduisent les résultats attendus. Les modèles ont été filtrés en utilisant des simulations ODE qualitatives et standardisées; seules celles qui reproduisaient le phénotype des vagues ont été gardées. L'ensemble des modèles minimaux peut être utilisé pour suggérer des relations regulatoires entre les molécules participant qui peuvent ensuite être testées expérimentalement. Enfin, durant mon doctorat, j'ai participé au SBV Improver Challenge. Le but était de déduire des réseaux spécifiques à des espèces (humain et rat) en utilisant des données de phosphoprotéines, d'expressions des gènes et des cytokines, ainsi qu'un réseau de référence, qui était mis à disposition comme donnée préalable. Notre solution pour ce concours a pris la troisième place. L'approche utilisée est expliquée en détail dans le dernier chapitre de la thèse. -- The present dissertation is entitled "Development and Application of Computational Methodologies in Qualitative Modeling". It encompasses the diverse projects that were undertaken during my time as a PhD student. Instead of a systematic implementation of a framework defined a priori, this thesis should be considered as an exploration of the methods that can help us infer the blueprint of regulatory and signaling processes. This exploration was driven by concrete biological questions, rather than theoretical investigation. Even though the projects involved divergent systems (gene regulatory networks of cell cycle, signaling networks in lung cells), as well as organisms (fission yeast, budding yeast, rat, human), our goals were complementary and coherent. The main project of the thesis is the modeling of the Septation Initiation Network (SIN) in S.pombe. Cytokinesis in fission yeast is controlled by the SIN, a protein kinase signaling network that uses the spindle pole body as scaffold. In order to describe the qualitative behavior of the system and predict unknown mutant behaviors we decided to adopt a Boolean modeling approach. In this thesis, we report the construction of an extended, Boolean model of the SIN, comprising most SIN components and regulators as individual, experimentally testable nodes. The model uses CDK activity levels as control nodes for the simulation of SIN related events in different stages of the cell cycle. The model was optimized using single knock-out experiments of known phenotypic effect as a training set, and was able to correctly predict a double knock-out test set. Moreover, the model has made in silico predictions that have been validated in vivo, providing new insights into the regulation and hierarchical organization of the SIN. Another cell cycle related project that is part of this thesis was to create a qualitative, minimal model of cyclin interplay in S.cerevisiae. CLB proteins in budding yeast present a characteristic, sequential activation and decay during the cell cycle, commonly referred to as Clb waves. This event is coordinated with the inverse activation curve of Sic1, which has an inhibitory role in the system. To generate minimal qualitative models that can explain this phenomenon, we selected well-defined experiments and constructed all possible minimal models that, when simulated, reproduce the expected results. The models were filtered using standardized qualitative ODE simulations; only the ones reproducing the wave-like phenotype were kept. The set of minimal models can be used to suggest regulatory relations among the participating molecules, which will subsequently be tested experimentally. Finally, during my PhD I participated in the SBV Improver Challenge. The goal was to infer species-specific (human and rat) networks, using phosphoprotein, gene expression and cytokine data and a reference network provided as prior knowledge. Our solution to the challenge was selected as in the final chapter of the thesis.

Twenty years of research into Chlamydia-like organisms: a revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae.

Chlamydiae are obligate intracellular bacteria that share a unique but remarkably conserved biphasic developmental cycle that relies on a eukaryotic host cell for survival. Although the phylum was originally thought to only contain one family, the Chlamydiaceae, a total of nine families are now recognized. These so-called Chlamydia-like organisms (CLOs) are also referred to as 'environmental chlamydiae', as many were initially isolated from environmental sources. However, these organisms are also emerging pathogens, as many, such as Parachlamydia sp., Simkania sp. and Waddlia sp., have been associated with human disease, and others, such as Piscichlamydia sp. and Parilichlamydia sp., have been documented in association with diseases in animals. Their strict intracellular nature and the requirement for cell culture have been a confounding factor in characterizing the biology and pathogenicity of CLOs. Nevertheless, the genomes of seven CLO species have now been sequenced, providing new information on their potential ability to adapt to a wide range of hosts. As new isolation and diagnostic methods advance, we are able to further explore the richness of this phylum with further research likely to help define the true pathogenic potential of the CLOs while also providing insight into the origins of the 'traditional' chlamydiae.

Authorship in scientific publications: analysis and recommendations.

In 2008, a Swiss Academies of Arts and Sciences working group chaired by Professor Emilio Bossi issued a "Memorandum on scientific integrity and the handling of misconduct in the scientific context", together with a paper setting out principles and procedures concerning integrity in scientific research. In the Memorandum, unjustified claims of authorship in scientific publications are referred to as a form of scientific misconduct - a view widely shared in other countries. In the Principles and Procedures, the main criteria for legitimate authorship are specified, as well as the associated responsibilities. It is in fact not uncommon for disputes about authorship to arise with regard to publications in fields where research is generally conducted by teams rather than individuals. Such disputes may concern not only the question who is or is not to be listed as an author but also, frequently, the precise sequence of names, if the list is to reflect the various authors' roles and contributions. Subjective assessments of the contributions made by the individual members of a research group may differ substantially. As scientific collaboration - often across national boundaries - is now increasingly common, ensuring appropriate recognition of all parties is a complex matter and, where disagreements arise, it may not be easy to reach a consensus. In addition, customs have changed over the past few decades; for example, the practice of granting "honorary" authorship to an eminent researcher - formerly not unusual - is no longer considered acceptable. It should be borne in mind that the publications list has become by far the most important indicator of a researcher's scientific performance; for this reason, appropriate authorship credit has become a decisive factor in the careers of young researchers, and it needs to be managed and protected accordingly. At the international and national level, certain practices have therefore developed concerning the listing of authors and the obligations of authorship. The Scientific Integrity Committee of the Swiss Academies of Arts and Sciences has collated the relevant principles and regulations and formulated recommendations for authorship in scientific publications. These should help to prevent authorship disputes and offer guidance in the event of conflicts.