A common ancestor DNA motif for invertebrate and vertebrate hormone response elements.

The ecdysone-responsive DNA sequence of the Drosophila hsp27 gene promoter contains four direct and inverted repeats reminiscent of those that compose the vertebrate palindromic estrogen response element (ERE) and the thyroid hormone/retinoic acid response element (TRE/RRE). Interestingly, a 3 bp substitution in the wild-type Hsp27 ecdysone response element (EcdRE) increases both its similarity with the vertebrate ERE and TRE/RRE and its capacity to confer ecdysone responsiveness to a heterologous promoter. Remarkably, increasing the spacing between the inverted repeats of this strong EcdRE by two nucleotides converts it into an ERE. Inversely, decreasing the spacing between the two inverted repeats of the vertebrate consensus palindromic ERE, from three to one nucleotide, converts it into a functional EcdRE. Thus, the only difference between an invertebrate EcdRE and a vertebrate palindromic ERE or TRE/RRE is in the spacing between the conserved inverted repeated motifs forming these palindromic HREs. The finding that the sequence motif 5'-GGTCA-3' present in the vertebrate ERE and TRE/RRE is also a functionally important characteristic of an invertebrate HRE, suggests that a common ancestor regulatory DNA sequence gave rise to all HREs known so far. We discuss the possibility that this progenitor motif is the GGTCA sequence.

Time consistent Pareto solutions in common access resource gameswith asymmetric players

In the analysis of equilibrium policies in a di erential game, if agents have different time preference rates, the cooperative (Pareto optimum) solution obtained by applying the Pontryagin's Maximum Principle becomes time inconsistent. In this work we derive a set of dynamic programming equations (in discrete and continuous time) whose solutions are time consistent equilibrium rules for N-player cooperative di erential games in which agents di er in their instantaneous utility functions and also in their discount rates of time preference. The results are applied to the study of a cake-eating problem describing the management of a common property exhaustible natural resource. The extension of the results to a simple common property renewable natural resource model in in nite horizon is also discussed.

A tailored approach for the treatment of indirect inguinal hernia in adults--an old problem revisited.

A patent processus vaginalis peritonei (PPV) presents typically as an indirect hernia with an intact inguinal canal floor during childhood. Little is known however about PPV in adults and its best treatment. A cohort study included all consecutive patients admitted for ambulatory open hernia repair. In patients with a PPV, demographics, hernia characteristics, and outcome were prospectively assessed. Annulorrhaphy was the treatment of choice in patients with an internal inguinal ring diameter of < 30 mm. Between 1998 and 2006, 92 PPVs (two bilateral) were diagnosed in 676 open hernia repairs (incidence of 14%). Eighty nine of the 90 patients were males, the median age was 34 years (range: 17-85). A PPV was right-sided in 67% and partially obliterated in 66%. Forty-one patients had an annulorrhaphy and 51 patients had a tension-free mesh repair. The median operation time was significantly shorter in the annulorrhaphy group (38 vs. 48 min, P <.0001). In a median follow-up period of 56 months (27-128), both groups did not differ concerning recurrence (1/41 vs. 2/51), chronic pain (3/41 vs. 4/51), and hypoesthesia (5/41 vs. 9/51). There was however a clear trend to less neuropathic symptoms in favor of annulorrhaphy (0/41 vs. 5/51, P < 0.066). PPV occurs in 14% of adults undergoing hernia repair. In selected patients, annulorrhaphy takes less time and is associated with equally low recurrence but less potential for neuropathic symptoms.

Pattern recognition ecological niche models fit to presence-only and presence-absence data

1. Identifying the boundary of a species' niche from observational and environmental data is a common problem in ecology and conservation biology and a variety of techniques have been developed or applied to model niches and predict distributions. Here, we examine the performance of some pattern-recognition methods as ecological niche models (ENMs). Particularly, one-class pattern recognition is a flexible and seldom used methodology for modelling ecological niches and distributions from presence-only data. The development of one-class methods that perform comparably to two-class methods (for presence/absence data) would remove modelling decisions about sampling pseudo-absences or background data points when absence points are unavailable. 2. We studied nine methods for one-class classification and seven methods for two-class classification (five common to both), all primarily used in pattern recognition and therefore not common in species distribution and ecological niche modelling, across a set of 106 mountain plant species for which presence-absence data was available. We assessed accuracy using standard metrics and compared trade-offs in omission and commission errors between classification groups as well as effects of prevalence and spatial autocorrelation on accuracy. 3. One-class models fit to presence-only data were comparable to two-class models fit to presence-absence data when performance was evaluated with a measure weighting omission and commission errors equally. One-class models were superior for reducing omission errors (i.e. yielding higher sensitivity), and two-classes models were superior for reducing commission errors (i.e. yielding higher specificity). For these methods, spatial autocorrelation was only influential when prevalence was low. 4. These results differ from previous efforts to evaluate alternative modelling approaches to build ENM and are particularly noteworthy because data are from exhaustively sampled populations minimizing false absence records. Accurate, transferable models of species' ecological niches and distributions are needed to advance ecological research and are crucial for effective environmental planning and conservation; the pattern-recognition approaches studied here show good potential for future modelling studies. This study also provides an introduction to promising methods for ecological modelling inherited from the pattern-recognition discipline.

Cultured epithelial autografts in the management of burn injuries: a review of the literature

Introduction. The management of large burn victims has significantly improved in the last decades. Specifically autologous cultured keratinocytes (CEA) overcame the problem of limited donor sites in severely burned patients. Several studies testing CEA's in their burn centers give mixed results on the general outcomes of burn patients. Methods. A review of publications with a minimum of 15 patients per study using CEA for the management of severe burn injury from 1989 until 2011 were recruited by using an online database including Medline, Pub Med and the archives of the medical library of the CHUV in Lausanne. Results. 18 studies with a total of 977 patients were included into this review. Most of the studies did not specify if CEA's were grafted alone or in combination with split thickness skin grafts (STSG) although most of the patients seemed to have received both methodologies in reviewed studies. The mean TBSA per study ranged from 33% to 78% in patients that were grafted with CEA's. Here no common minimum TBSA making a patient eligible for CEA grafting could be found. The definition of the "take rate" is not standardized and varied largely from 26% to 73%. Mortality and hospitalization time could not be shown to correlate with CEA use in all of the studies. As late complications, some authors described the fragility of the CEA regenerated skin. Conclusion. Since the healing of large burn victims demands for a variety of different surgical and non-surgical treatment strategies and the final outcome mainly depends on the burned surface as well as the general health condition of the patient, no definitive conclusion could be drawn from the use of CEA's of reviewed studies. From our own experience, we know that selected patients significantly profit from CEA grafts although cost efficiency or the reduction of mortality cannot be demonstrated on this particular cases.

Errors in palliative care: kinds, causes, and consequences: a pilot survey of experiences and attitudes of palliative care professionals.

Abstract Background: Medical errors have recently been recognized as a relevant concern in public health, and increasing research efforts have been made to find ways of improving patient safety. In palliative care, however, studies on errors are scant. Objective: Our aim was to gather pilot data concerning experiences and attitudes of palliative care professionals on this topic. Methods: We developed a questionnaire, which consists of questions on relevance, estimated frequency, kinds and severity of errors, their causes and consequences, and the way palliative care professionals handle them. The questionnaire was sent to all specialist palliative care institutions in the region of Bavaria, Germany (n=168; inhabitants 12.5 million) reaching a response rate of 42% (n=70). Results: Errors in palliative care were regarded as a highly relevant problem (median 8 on a 10-point numeric rating scale). Most respondents experienced a moderate frequency of errors (1-10 per 100 patients). Errors in communication were estimated to be more common than those in symptom control. The causes most often mentioned were deficits in communication or organization. Moral and psychological problems for the person committing the error were seen as more frequent than consequences for the patient. Ninety percent of respondents declared that they disclose errors to the harmed patient. For 78% of the professionals, the issue was not a part of their professional training. Conclusion: Professionals acknowledge errors-in particular errors in communication-to be a common and relevant problem in palliative care, one that has, however, been neglected in training and research.

Dynamics of ammonium and pH in the solution of soils with different salinity levels, growing irrigated rice

Rice in Rio Grande do Sul State is grown mostly under flooding, which induces a series of chemical, physical and biological changes in the root environment. These changes, combined with the presence of rice plants, affect the availability of exchangeable ammonium (NH4+) and pH of soil solution, whereas the dynamics of both variables can be influenced by soil salinity, a common problem in the coastal region. This study was conducted to evaluate the dynamics of exchangeable NH4+ and pH in the soil solution, and their relation in the solution of Albaqualf soils with different salinity levels, under rice. Four field experiments were conducted with soils with exchangeable Na percentage (ESP) of 5.6, 9.0, 21.2, and 32.7 %. Prior to flooding, soil solution collectors were installed at depths of 5, 10 and 20 cm. The soil solution was collected weekly, from 7 to 91 days after flooding (DAF), to analyze exchangeable NH4+ and pH in the samples. Plant tissue was sampled 77 DAF, to determine N uptake and estimate the contribution of other N forms to rice nutrition. The content of exchangeable NH4+ decreased over time at all sites and depths, with a more pronounced reduction in soils with lower salinity levels, reaching values close to zero. A possible contribution of non-exchangeable NH4+ forms and N from soil organic matter to rice nutrition was observed. Soil pH decreased with time in soils with ESP 5.6 and 9.0 %, being positively correlated with the decreasing NH4+ levels at these sites.

Effect of swine residue rates on corn, common bean, soybean and wheat yield

Swine residue (SR) applied as nutrient source of crops such as corn, bean, soybean and wheat, besides representing an environmental-friendly way of disposing of organic waste resulting from swine production, may significantly increase grain yields, replacing mineral fertilizer. The objective was to evaluate the effect of SR rates on corn, common bean, soybean and wheat yields from 2002 to 2007, in comparison with mineral fertilizer. The experiment was carried out at the Instituto Agronômico do Paraná - IAPAR, Pato Branco, PR and consisted of increasing SR rates (0, 15, 30, 45, and 60 m³ ha-1) and one treatment with mineral fertilizer (NPK 4-30-10), using 250 kg ha-1 for bean and 300 kg ha-1 for corn, soybean and wheat. Also, in the treatment with mineral fertilizer, 60, 120 and 90 kg ha-1 N was applied as topdressing to bean, corn and wheat, respectively. There were significant increases of grain yield in all evaluated years and crops with increasing SR rates, especially in the grass species under study. Also, with increasing SR rates applied every six months, K, P, Ca and Mg were accumulated in the soil and the pH increased. The application of 60 m³ ha-1 SR increased yields and exceeded the yield obtained with the recommended mineral fertilizer, indicating this amount as adequate for these crops.

Pathologies mimicking deep venous thrombosis of the legs : pictorial review of US findings : P27

Purpose: Precise diagnosis of DVT of the legs is a challenging problem, not only in front of suspicion of PE, but also in all status of leg pain, warmth and swelling. Clinical diagnosis has a low accuracy and further investigations are mandatory in order to diagnose DVT. Amongst the possible investigations, US has a high specificity and a good NPV. However, many pathologies unrelated to the veins may mimic the signs and symptoms of DVT and have to be recognized in order to make the correct diagnosis. The purpose of this paper is to review the results of the US investigations of the legs performed in our Department during the last three years for a suspicion of DVT and describe alternative diagnoses mimicking DVT. Methods and materials: Through a RIS-based search, we retrospectively reviewed all the cases of US of the legs performed in our Department between January 2006 and December 2008 for a suspicion of DVT. We selected the cases of positive findings unrelated to the veins and illustrated these findings with characteristic images. Results: 419 US of the legs were performed between December 2006 and December 2008 for a suspicion of DVT. Among these, 75 were positive for DVT, and 79 for alternative diagnosis. The most common alternative diagnosis was edema of the legs (31%), followed by hematoma (23%). Other findings were Baker cysts (13%), cellulitis (10%) and lymphoceles (5%). Rare diagnoses were arterio-venous malformations, pseudoaneurysms, pelvic masses, necrosing fasciitis, intramuscular abscesses, subcutaneous seromas, sarcoma and ganglion cysts. Conclusion: A greater knowledge of the US appearance of the pathologies mimicking DVT may help to make the correct diagnosis, avoiding further expensive investigations or inappropriate anticoagulant therapy.

Effects of common origin and common rearing environment on variance in ectoparasite load and phenotype of nestling Alpine swifts

Knowledge of the quantitative genetics of resistance to parasitism is key to appraise host evolutionary responses to parasite selection. Here, we studied effects of common origin (i.e. genetic and pre-hatching parental effects) and common rearing environment (i.e. post-hatching parental effects and other environment effects) on variance in ectoparasite load in nestling Alpine swifts (Apus melba). This colonial bird is intensely parasitized by blood sucking louse-flies that impair nestling development and survival. By cross-fostering half of the hatchlings between pairs of nests, we show strong significant effect of common rearing environment on variance (90.7% in 2002 and 90.9% in 2003) in the number of louse-flies per nestling and no significant effect of common origin on variance in the number of louse-flies per nestling. In contrast, significant effects of common origin were found for all the nestling morphological traits (i.e. body mass, wing length, tail length, fork length and sternum length) under investigation. Hence, our study suggests that genetic and pre-hatching parental effects play little role in the distribution of parasites among nestling Alpine swifts, and thus that nestlings have only limited scope for evolutionary responses against parasites. Our results highlight the need to take into consideration environmental factors, including the evolution of post-hatching parental effects such as nest sanitation, in our understanding of host-parasite relationships.

Radiological detection of dissolved cocaine

Introduction: Smuggling dissolved drugs, especially cocaine, in bottled liquids is a problem at borders nowadays. Common fluoroscopy of packages at the border cannot detect contaminated liquids. To find a dissolved drug, an immunological test using a drug-test panel has to be performed. This means that a control sample of the cargo must be opened to perform the test. As it is not possible to open all boxes, and as smugglers hide the drugcontaining boxes between regularly filled boxes, contaminated cargos can be overlooked. Investigators sometimes cannot perform the drug-test panel because they try not to arouse the smugglers' suspicion in order to follow the cargo and to find the recipient. Aims: The objective of our studies was to define non-invasive examination techniques to investigate cargos that are suspicions to contain dissolved cocaine without leaving traces on the samples. We examined vessels containing cocaine by radiological cross-section techniques such as multidetector computed tomography (MDCT) and magnetic resonance spectroscopy (MRS). Methods: In a previous study, we examined bottles of wine containing dissolved cocaine in different quantities using an MDCT unit. To distinguish between bottles containing red wine and those where cocaine was solved in the wine, cross sectional 2D-images have been reconstructed and the absorption of X-rays was quantified by measuring the mean density of the liquid inside the bottles. In our new study, we investigated phantoms containing cocaine dissolved in water with or without ethanol as well as cocaine dissolved in different sorts of commercially available wine by the use of a clinical magnetic resonance unit (3 tesla). To find out if dissolved cocaine could be detected, magnetic resonance spectroscopy (1H MRS) was performed. Results: By using a MDCT-unit and measuring the mean attenuation of X-rays, it is possible to distinguish weather substances are dissolved in a liquid or not, if a comparative liquid without any solutions is available. The increase of the mean density indicates the presence of dissolved substances without the possibility to identify the substance. By using magnetic resonance spectroscopy, dissolved cocaine can be clearly identified because it produces distinctive resonances in the spectrum. In contrast to MDCT, this technique shows a high sensitivity (detection of 1 mM cocaine in wine). Conclusions: Cross-sectional imaging techniques such as MDCT and MRS appropriated to examine cargos that are suspicious to contain dissolved cocaine. They allow to perform non-invasive investigations without leaving any trace on the cargo. While an MDCT scan can detect dissolved substances in liquids, identification of cocaine can be obtained by MR-spectroscopy. Acknowledgment: This work was supported by the Centre d'Imagerie BioMédicale (CIBM) of the University of Lausanne (UNIL), the Swiss Federal Institute of Technology Lausanne (EPFL), the University of Geneva (UniGe), the Centre Hospitalier Universitaire Vaudois (CHUV), the Hôpitaux Universitaire de Genève (HUG) and the Leenaards and the Jeantet Foundations.

Advanced Kernel Methods For Remote Sensing Image Classification

Résumé Suite aux recentes avancées technologiques, les archives d'images digitales ont connu une croissance qualitative et quantitative sans précédent. Malgré les énormes possibilités qu'elles offrent, ces avancées posent de nouvelles questions quant au traitement des masses de données saisies. Cette question est à la base de cette Thèse: les problèmes de traitement d'information digitale à très haute résolution spatiale et/ou spectrale y sont considérés en recourant à des approches d'apprentissage statistique, les méthodes à noyau. Cette Thèse étudie des problèmes de classification d'images, c'est à dire de catégorisation de pixels en un nombre réduit de classes refletant les propriétés spectrales et contextuelles des objets qu'elles représentent. L'accent est mis sur l'efficience des algorithmes, ainsi que sur leur simplicité, de manière à augmenter leur potentiel d'implementation pour les utilisateurs. De plus, le défi de cette Thèse est de rester proche des problèmes concrets des utilisateurs d'images satellite sans pour autant perdre de vue l'intéret des méthodes proposées pour le milieu du machine learning dont elles sont issues. En ce sens, ce travail joue la carte de la transdisciplinarité en maintenant un lien fort entre les deux sciences dans tous les développements proposés. Quatre modèles sont proposés: le premier répond au problème de la haute dimensionalité et de la redondance des données par un modèle optimisant les performances en classification en s'adaptant aux particularités de l'image. Ceci est rendu possible par un système de ranking des variables (les bandes) qui est optimisé en même temps que le modèle de base: ce faisant, seules les variables importantes pour résoudre le problème sont utilisées par le classifieur. Le manque d'information étiquétée et l'incertitude quant à sa pertinence pour le problème sont à la source des deux modèles suivants, basés respectivement sur l'apprentissage actif et les méthodes semi-supervisées: le premier permet d'améliorer la qualité d'un ensemble d'entraînement par interaction directe entre l'utilisateur et la machine, alors que le deuxième utilise les pixels non étiquetés pour améliorer la description des données disponibles et la robustesse du modèle. Enfin, le dernier modèle proposé considère la question plus théorique de la structure entre les outputs: l'intègration de cette source d'information, jusqu'à présent jamais considérée en télédétection, ouvre des nouveaux défis de recherche. Advanced kernel methods for remote sensing image classification Devis Tuia Institut de Géomatique et d'Analyse du Risque September 2009 Abstract The technical developments in recent years have brought the quantity and quality of digital information to an unprecedented level, as enormous archives of satellite images are available to the users. However, even if these advances open more and more possibilities in the use of digital imagery, they also rise several problems of storage and treatment. The latter is considered in this Thesis: the processing of very high spatial and spectral resolution images is treated with approaches based on data-driven algorithms relying on kernel methods. In particular, the problem of image classification, i.e. the categorization of the image's pixels into a reduced number of classes reflecting spectral and contextual properties, is studied through the different models presented. The accent is put on algorithmic efficiency and the simplicity of the approaches proposed, to avoid too complex models that would not be used by users. The major challenge of the Thesis is to remain close to concrete remote sensing problems, without losing the methodological interest from the machine learning viewpoint: in this sense, this work aims at building a bridge between the machine learning and remote sensing communities and all the models proposed have been developed keeping in mind the need for such a synergy. Four models are proposed: first, an adaptive model learning the relevant image features has been proposed to solve the problem of high dimensionality and collinearity of the image features. This model provides automatically an accurate classifier and a ranking of the relevance of the single features. The scarcity and unreliability of labeled. information were the common root of the second and third models proposed: when confronted to such problems, the user can either construct the labeled set iteratively by direct interaction with the machine or use the unlabeled data to increase robustness and quality of the description of data. Both solutions have been explored resulting into two methodological contributions, based respectively on active learning and semisupervised learning. Finally, the more theoretical issue of structured outputs has been considered in the last model, which, by integrating outputs similarity into a model, opens new challenges and opportunities for remote sensing image processing.

Do riverine barriers, history or introgression shape the genetic structuring of a common shrew (Sorex araneus) population?

The common shrew (Sorex araneus) is subdivided into numerous chromosome races. The Valais and Cordon chromosome races meet and hybridize at a mountain river in Les Houches (French Alps). Significant genetic structuring was recently reported among populations found on the Valais side of this hybrid zone. In this paper, a phylogenetic analysis and partial Mantel tests are used to investigate the patterns and causes of this structuring. A total of 185 shrews were trapped at 12 localities. All individuals were typed for nine microsatellite loci. Although several mountain rivers are found in the study area, riverine barriers do not have a significant influence on gene flow. Partial Mantel tests show that our result is caused by the influence of the hybrid zone with the Cordon race. The geographical patterns of this structuring are discussed in the context of the contact zone, which appears to extend up to a group of two rivers. The glacier they originate from is known to have cut the Arve valley as recently as 1818. The recent history of this glacier, its moraine and possibly rivers, may therefore be linked to the history of this hybrid zone.

Ligamentous and tendinous anatomy of the intermetacarpal and common carpometacarpal joints: evaluation with MR imaging and MR arthrography.

PURPOSE: The purpose of this work was to demonstrate the normal ligamentous and tendinous anatomy of the intermetacarpal (IMC) and common carpometacarpal (CCMC) joints with MRI and MR arthrography. METHOD: MR images of 22 wrists derived from fresh human cadavers were obtained before and after arthrography. The MR imaging features of the ligaments and tendons about the CCMC and IMC joints and the joints themselves were analyzed in a randomized fashion and correlated with those seen on anatomic sections. RESULTS: Six CCMC ligaments were visualized. The dorsal and palmar CCMC ligaments and the pisometacarpal ligament were best visualized in the sagittal plane. The radial and ulnar CCMC collateral ligaments and the capito-third metacarpal ligament were best visualized in the coronal plane. Three main IMC ligaments were observed: a dorsal and a palmar ligament and an interosseous ligament complex. All three ligaments were best visualized in the axial plane. Four tendinous insertions to the metacarpal bases were evident. CONCLUSION: The anatomy of the ligaments and tendinous insertions about the second to fifth IMC and the CCMC joints is well demonstrated by MR imaging and MR arthrography. MR arthrography does not significantly improve the visualization of these complex structures.

Subclass problem-dependent design for error-correcting output codes

A common way to model multiclass classification problems is by means of Error-Correcting Output Codes (ECOCs). Given a multiclass problem, the ECOC technique designs a code word for each class, where each position of the code identifies the membership of the class for a given binary problem. A classification decision is obtained by assigning the label of the class with the closest code. One of the main requirements of the ECOC design is that the base classifier is capable of splitting each subgroup of classes from each binary problem. However, we cannot guarantee that a linear classifier model convex regions. Furthermore, nonlinear classifiers also fail to manage some type of surfaces. In this paper, we present a novel strategy to model multiclass classification problems using subclass information in the ECOC framework. Complex problems are solved by splitting the original set of classes into subclasses and embedding the binary problems in a problem-dependent ECOC design. Experimental results show that the proposed splitting procedure yields a better performance when the class overlap or the distribution of the training objects conceal the decision boundaries for the base classifier. The results are even more significant when one has a sufficiently large training size.