Self-potential investigations of a gravel bar in a restored river corridor

Self-potentials (SP) are sensitive to water fluxes and concentration gradients in both saturated and unsaturated geological media, but quantitative interpretations of SP field data may often be hindered by the superposition of different source contributions and time-varying electrode potentials. Self-potential mapping and close to two months of SP monitoring on a gravel bar were performed to investigate the origins of SP signals at a restored river section of the Thur River in northeastern Switzerland. The SP mapping and subsequent inversion of the data indicate that the SP sources are mainly located in the upper few meters in regions of soil cover rather than bare gravel. Wavelet analyses of the time-series indicate a strong, but non-linear influence of water table and water content variations, as well as rainfall intensity on the recorded SP signals. Modeling of the SP response with respect to an increase in the water table elevation and precipitation indicate that the distribution of soil properties in the vadose zone has a very strong influence. We conclude that the observed SP responses on the gravel bar are more complicated than previously proposed semi-empiric relationships between SP signals and hydraulic head or the thickness of the vadose zone. We suggest that future SP monitoring in restored river corridors should either focus on quantifying vadose zone processes by installing vertical profiles of closely spaced SP electrodes or by installing the electrodes within the river to avoid signals arising from vadose zone processes and time-varying electrochemical conditions in the vicinity of the electrodes.

A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL

Background: Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improvement of this trait through artificial selection. Moreover, the relative contributions of additive, dominant and epistatic QTL to the genetic variance of pig prolificacy remain to be defined. In this work, we have undertaken this issue by performing one-dimensional and bi-dimensional genome scans for number of piglets born alive (NBA) and total number of piglets born (TNB) in a three generation Iberian by Meishan F2 intercross. Results: The one-dimensional genome scan for NBA and TNB revealed the existence of two genome-wide highly significant QTL located on SSC13 (P < 0.001) and SSC17 (P < 0.01) with effects on both traits. This relative paucity of significant results contrasted very strongly with the wide array of highly significant epistatic QTL that emerged in the bi-dimensional genome-wide scan analysis. As much as 18 epistatic QTL were found for NBA (four at P < 0.01 and five at P < 0.05) and TNB (three at P < 0.01 and six at P < 0.05), respectively. These epistatic QTL were distributed in multiple genomic regions, which covered 13 of the 18 pig autosomes, and they had small individual effects that ranged between 3 to 4% of the phenotypic variance. Different patterns of interactions (a × a, a × d, d × a and d × d) were found amongst the epistatic QTL pairs identified in the current work.Conclusions: The complex inheritance of prolificacy traits in pigs has been evidenced by identifying multiple additive (SSC13 and SSC17), dominant and epistatic QTL in an Iberian × Meishan F2 intercross. Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.

Characterization of the ligand-binding site of the serotonin 5-HT3 receptor: the role of glutamate residues 97, 224, AND 235.

Ligand-gated ion channels of the Cys loop family are receptors for small amine-containing neurotransmitters. Charged amino acids are strongly conserved in the ligand-binding domain of these receptor proteins. To investigate the role of particular residues in ligand binding of the serotonin 5-HT3AS receptor (5-HT3R), glutamate amino acid residues at three different positions, Glu97, Glu224, and Glu235, in the extracellular N-terminal domain were substituted with aspartate and glutamine using site-directed mutagenesis. Wild type and mutant receptor proteins were expressed in HEK293 cells and analyzed by electrophysiology, radioligand binding, fluorescence measurements, and immunochemistry. A structural model of the ligand-binding domain of the 5-HT3R based on the acetylcholine binding protein revealed the position of the mutated amino acids. Our results demonstrate that mutations of Glu97, distant from the ligand-binding site, had little effect on the receptor, whereas mutations Glu224 and Glu235, close to the predicted binding site, are indeed important for ligand binding. Mutations E224Q, E224D, and E235Q decreased EC50 and Kd values 5-20-fold, whereas E235D was functionally expressed at a low level and had a more than 100-fold increased EC50 value. Comparison of the fluorescence properties of a fluorescein-labeled antagonist upon binding to wild type 5-HT3R and E235Q, allowed us to localize Glu235 within a distance of 1 nm around the ligand-binding site, as proposed by our model.

Renal effects of adenosine A1-receptor blockade with 8-cyclopentyl-1,3-dipropylxanthine in hypoxemic newborn rabbits.

The key role of intrarenal adenosine in mediating the hypoxemic acute renal insufficiency in newborn rabbits has been well demonstrated using the nonspecific adenosine antagonist theophylline. The present study was designed to define the role of adenosine A1 receptors during systemic hypoxemia by using the specific A1-receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine (DPCPX). Renal function parameters were assessed in 31 anesthetized and mechanically ventilated newborn rabbits. In normoxia, DPCPX infusion induced a significant increase in diuresis (+44%) and GFR (+19%), despite a significant decrease in renal blood flow (RBF) (-22%) and an increase in renal vascular resistance (RVR) (+37%). In hypoxemic conditions, diuresis (-19%), GFR (-26%), and RBF (-35%) were decreased, whereas RVR increased (+33%). DPCPX administration hindered the hypoxemia-induced decrease in GFR and diuresis. However, RBF was still significantly decreased (-27%), whereas RVR increased (+22%). In all groups, the filtration fraction increased significantly. The overall results support the hypothesis that, in physiologic conditions, intrarenal adenosine plays a key role in regulating glomerular filtration in the neonatal period through preferential A1-mediated afferent vasoconstriction. During a hypoxemic stress, the A1-specific antagonist DPCPX only partially prevented the hypoxemia-induced changes, as illustrated by the elevated RVR and drop in RBF. These findings imply that the contribution of intrarenal adenosine to the acute adverse effects of hypoxemia might not be solely mediated via the A1 receptor.

Rehabilitation of Concrete Pavements Utilizing Rebblization and Crack and Seat Methods, June 2005

Deterioration in portland cement concrete (PCC) pavements can occur due to distresses caused by a combination of traffic loads and weather conditions. Hot mix asphalt (HMA) overlay is the most commonly used rehabilitation technique for such deteriorated PCC pavements. However, the performance of these HMA overlaid pavements is hindered due to the occurrence of reflective cracking, resulting in significant reduction of pavement serviceability. Various fractured slab techniques, including rubblization, crack and seat, and break and seat are used to minimize reflective cracking by reducing the slab action. However, the design of structural overlay thickness for cracked and seated and rubblized pavements is difficult as the resulting structure is neither a “true” rigid pavement nor a “true” flexible pavement. Existing design methodologies use the empirical procedures based on the AASHO Road Test conducted in 1961. But, the AASHO Road Test did not employ any fractured slab technique, and there are numerous limitations associated with extrapolating its results to HMA overlay thickness design for fractured PCC pavements. The main objective of this project is to develop a mechanistic-empirical (ME) design approach for the HMA overlay thickness design for fractured PCC pavements. In this design procedure, failure criteria such as the tensile strain at the bottom of HMA layer and the vertical compressive strain on the surface of subgrade are used to consider HMA fatigue and subgrade rutting, respectively. The developed ME design system is also implemented in a Visual Basic computer program. A partial validation of the design method with reference to an instrumented trial project (IA-141, Polk County) in Iowa is provided in this report. Tensile strain values at the bottom of the HMA layer collected from the FWD testing at this project site are in agreement with the results obtained from the developed computer program.

Kaupungin ja maaseudun vuorovaikutus alueellisessa kehittämispolitiikassa

In Finland, European Union membership and economic globalisation have changed the position of regions from closed territorial systems to nodes of open international networks. The increasing complexity of cities as globalised knowledge centres and functionally specialised and diversified rural areas, and on the other hand growing disparities between prosperous urban cores and lagging peripheral areas are also essential features in contemporary regional development. These trends have produced new needs to promote mutual dialogue between cities and the countryside in western market economies. Urban-rural interaction is an idea which was developed in the late 1990s within regional policy to pull together these new challenges to regional development and handle cities and the countryside as a whole. The aim of my study is to conceptualise the idea of urban-rural interaction, explain the phenomenon theoretically, clarify past and present urban and rural development and analyse regional policies from the interaction angle. The ultimate purpose is to illustrate the existence and nature of particular interaction policy in a globalising society. The general method is discourse analysis, which I use in three cases: Central Finland, South-Ostrobothnia and South-West Finland. Theoretically I have a two-dimensional approach. On the first hand I use World-System theory to explain how the global economy is moulding urban and rural structures at the regional level. On the other hand I use regime theory to explain local political actions and practises between cities and the countryside under the overlapping pressures deriving from reformulated regional structures and policies.

Adaptation to globalisation in Finland has been carried out by strengthening urban centres. The stress in regional policy has been in urban development. The development of the countryside has mostly been implemented by a separate rural policy. At the end of the 1990s and early 2000s Finnish cities have actually shown themselves to be competitive in global markets. The drawbacks of the new growth centre policy have been the sparse network of prosperous cities and their weak spreading effects, which have hindered comprehensive regional development. Tensions between urban and rural areas have also deepened. In this situation the interaction policy is used as a way of balancing development and moderate conflicts within the regions. From this point of view urban-rural interaction can be seen as a way of tackling the challenges of globalisation.

On the other hand the results emphasise that actors involved in regional development still believe, although the hegemonic discourse is on urban policy, that there are opportunities to stimulate progress in the countryside as well. In the situation where regional authorities control development resources, rural development can be successful only if rural actors manage to establish fruitful relationships with their urban partners. This is also the weakness of the programme-based regional policy. If rural municipalities or other actors are for any reason incapable of building development regimes with cities, the offers of interaction policy will be useless.

The problem of the interaction policy is that the focus and methods of it have so far been rather underdeveloped. In order to improve the efficiency of the interaction policy, further research should concentrate on the social processes which define the position of cities and the countryside as partners of interaction, and practises which promote or prohibit the possibilities of developing the interaction policy. The efforts to define different contents of urban-rural interaction or promote interaction projects should not have such an important role in the future as they have had so far. Instead, the focus of interaction policy should be on questions such as how to manage the political tensions between town and country and how to create a positive atmosphere for regional policy where the needs of urban and rural development are promoted equally.

Viral-mediated overexpression of mutant huntingtin to model HD in various species.

Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by an expansion of CAG repeats in the huntingtin (Htt) gene. Despite intensive efforts devoted to investigating the mechanisms of its pathogenesis, effective treatments for this devastating disease remain unavailable. The lack of suitable models recapitulating the entire spectrum of the degenerative process has severely hindered the identification and validation of therapeutic strategies. The discovery that the degeneration in HD is caused by a mutation in a single gene has offered new opportunities to develop experimental models of HD, ranging from in vitro models to transgenic primates. However, recent advances in viral-vector technology provide promising alternatives based on the direct transfer of genes to selected sub-regions of the brain. Rodent studies have shown that overexpression of mutant human Htt in the striatum using adeno-associated virus or lentivirus vectors induces progressive neurodegeneration, which resembles that seen in HD. This article highlights progress made in modeling HD using viral vector gene transfer. We describe data obtained with of this highly flexible approach for the targeted overexpression of a disease-causing gene. The ability to deliver mutant Htt to specific tissues has opened pathological processes to experimental analysis and allowed targeted therapeutic development in rodent and primate pre-clinical models.

Biana: a software framework for compiling biological interactions and analyzing networks

Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.Results: We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.Conclusions: BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

The molecular basis of social behavior: models, methods and advances.

Elucidating the molecular and neural basis of complex social behaviors such as communal living, division of labor and warfare requires model organisms that exhibit these multi-faceted behavioral phenotypes. Social insects, such as ants, bees, wasps and termites, are attractive models to address this problem, with rich ecological and ethological foundations. However, their atypical systems of reproduction have hindered application of classical genetic approaches. In this review, we discuss how recent advances in social insect genomics, transcriptomics, and functional manipulations have enhanced our ability to observe and perturb gene expression, physiology and behavior in these species. Such developments begin to provide an integrated view of the molecular and cellular underpinnings of complex social behavior.

Regulation of phosphate starvation responses in plants: signaling players and cross-talks.

Phosphate (Pi) availability is a major factor limiting growth, development, and productivity of plants. In both ecological and agricultural contexts, plants often grow in soils with low soluble phosphate content. Plants respond to this situation by a series of developmental and metabolic adaptations that are aimed at increasing the acquisition of this vital nutrient from the soil, as well as to sustain plant growth and survival. The development of a comprehensive understanding of how plants sense phosphate deficiency and coordinate the responses via signaling pathways has become of major interest, and a number of signaling players and networks have begun to surface for the regulation of the phosphate-deficiency response. In practice, application of such knowledge to improve plant Pi nutrition is hindered by complex cross-talks, which are emerging in the face of new data, such as the coordination of the phosphate-deficiency signaling networks with those involved with hormones, photo-assimilates (sugar), as well as with the homeostasis of other ions, such as iron. In this review, we focus on these cross-talks and on recent progress in discovering new signaling players involved in the Pi-starvation responses, such as proteins having SPX domains.

Oviposition behavior and performance aspects of Ascia monuste (Godart, 1919) (Lepidoptera, Pieridae) on kale (Brassica oleracea var. acephala)

Host part selection by ovipositing females of Ascia monuste (Godart, 1919) (Lepidoptera, Pieridae) on kale (Brassica oleracea var. acephala) was determined in greenhouse and field. Performance of offspring (larval period, efficiency of food utilization, number of eggs/female and others) was investigated under laboratory conditions. In the field, the number of A. monuste egg clutches on the apical and medium parts of kale leaves was greater than on the basal part. In greenhouse, A. monuste exhibited a strong preference for the apical part of kale leaves for ovipositing. The best results on food utilization indices, pupal mass and female wing size were obtained with the leaf apical part. This part of kale leaves exhibited the highest nitrogen and protein concentration and the smallest water content, when compared to the other leaf parts. However, the apical part of the leaves seems not to provide ovipositing females with enough protection against birds, making them easy preys in the field. We suggest that good relationship between oviposition preference and performance of offspring was hindered by predation in field conditions.

Calceology : an introduction to North Western European archaeological leather footwear (Neolithic period to c. AD 1600)

Calceology is the study of recovered archaeological leather footwear and is comprised of conservation, documentation and identification of leather shoe components and shoe styles. Recovered leather shoes are complex artefacts that present technical, stylistic and personal information about the culture and people that used them. The current method in calceological research for typology and chronology is by comparison with parallel examples, though its use poses problems by an absence of basic definitions and the lack of a taxonomic hierarchy. The research findings of the primary cutting patterns, used for making all leather footwear, are integrated with the named style method and the Goubitz notation, resulting in a combined methodology as a basis for typological organisation for recovered footwear and a chronology for named shoe styles. The history of calceological research is examined in chapter two and is accompanied by a review of methodological problems as seen in the literature. Through the examination of various documentation and research techniques used during the history of calceological studies, the reasons why a standard typology and methodology failed to develop are investigated. The variety and continual invention of a new research method for each publication of a recovered leather assemblage hindered the development of a single standard methodology. Chapter three covers the initial research with the database through which the primary cutting patterns were identified and the named styles were defined. The chronological span of each named style was established through iterative cross-site sedation and named style comparisons. The technical interpretation of the primary cutting patterns' consistent use is due to constraints imposed by the leather and the forms needed to cover the foot. Basic parts of the shoe patterns and the foot are defined, plus terms provided for identifying the key points for pattern making. Chapter four presents the seventeen primary cutting patterns and their sub-types, these are divided into three main groups: six integral soled patterns, four hybrid soled patterns and seven separately soled patterns. Descriptions of the letter codes, pattern layout, construction principle, closing seam placement and list of sub-types are included in the descriptions of each primary cutting pattern. The named shoe styles and their relative chronology are presented in chapter five. Nomenclature for the named styles is based on the find location of the first published example plus the primary cutting pattern code letter. The named styles are presented in chronological order from Prehistory through to the late 16th century. Short descriptions of the named styles are given and illustrated with examples of recovered archaeological leather footwear, reconstructions of archaeological shoes and iconographical sources. Chapter six presents documentation of recovered archaeological leather using the Goubitz notation, an inventory and description of style elements and fastening methods used for defining named shoe styles, technical information about sole/upper constructions and the consequences created by the use of lasts and sewing forms for style identification and fastening placement in relation to the instep point. The chapter concludes with further technical information about the implications for researchers about shoemaking, pattern making and reconstructive archaeology. The conclusion restates the original research question of why a group of primary cutting patterns appear to have been used consistently throughout the European archaeological record. The quantitative and qualitative results from the database show the use of these patterns but it is the properties of the leather that imposes the use of the primary cutting patterns. The combined methodology of primary pattern identification, named style and artefact registration provides a framework for calceological research.

Delayed diagnosis of acute ischemic stroke in children - a registry-based study in Switzerland.

QUESTIONS UNDER STUDY/PRINCIPLES: After arterial ischemic stroke (AIS) an early diagnosis helps preserve treatment options that are no longer available later. Paediatric AIS is difficult to diagnose and often the time to diagnosis exceeds the time window of 6 hours defined for thrombolysis in adults. We investigated the delay from the onset of symptoms to AIS diagnosis in children and potential contributing factors. METHODS: We included children with AIS below 16 years from the population-based Swiss Neuropaediatric Stroke Registry (2000-2006). We evaluated the time between initial medical evaluation for stroke signs/symptoms and diagnosis, risk factors, co-morbidities and imaging findings. RESULTS: A total of 91 children (61 boys), with a median age of 5.3 years (range: 0.2-16.2), were included. The time to diagnosis (by neuro-imaging) was <6 hours in 32 (35%), 6-12 hours in 23 (25%), 12-24 hours in 15 (16%) and >24 hours in 21 (23%) children. Of 74 children not hospitalised when the stroke occurred, 42% had adequate outpatient management. Delays in diagnosis were attributed to: parents/caregivers (n = 20), physicians of first referral (n = 5) and tertiary care hospitals (n = 8). A co-morbidity hindered timely diagnosis in eight children. No other factors were associated with delay to diagnosis. A total of 17 children were inpatients at AIS onset. CONCLUSIONS: One-third of children with AIS were diagnosed within six hours. Diagnostic delay was predominately caused by insufficient recognition of stroke symptoms. Increased public and expert awareness and immediate access to diagnostic imaging are essential. The ability of parents/caregivers and health professionals to recognise stroke symptoms in a child needs to be improved.

Condiciones bio-oceanográficas en San José, islas Lobos de Afuera, Perú. 2010

En este estudio se muestra la variabilidad oceanográfica que se presenta en Lambayeque. Se evidenció con la generación del evento frío La Niña, después que se registrara el arribo de ondas Kelvin hacia la costa desde fines del 2009, lo que se llegó a considerar como la ocurrencia de un evento El Niño de intensidad moderada. Esta situación propició que los recursos pesqueros se ausentaran de sus áreas habituales de pesca, sumado a la presencia de oleajes anómalos y fuertes vientos que dificultaron las faenas de pesca. Durante el 2010, la Extensión Sur de la Corriente de Cromwell (ESCC) se presentó moderadamente fortalecida en marzo, evidenciada por la relativa alta concentración de oxígeno disuelto en las áreas más profundas de San José, situación inusual para la época en la zona. La proyección de la ESCC se vio intensificada en abril, pero comenzó a debilitarse en junio hasta ausentarse en noviembre, como se puede deducir de los valores de oxígeno encontrados cerca del fondo durante las prospecciones realizadas.

De Novo Assembly of the Pneumocystis jirovecii Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient.

ABSTRACT Pneumocystis jirovecii is a fungus that causes severe pneumonia in immunocompromised patients. However, its study is hindered by the lack of an in vitro culture method. We report here the genome of P. jirovecii that was obtained from a single bronchoalveolar lavage fluid specimen from a patient. The major challenge was the in silico sorting of the reads from a mixture representing the different organisms of the lung microbiome. This genome lacks virulence factors and most amino acid biosynthesis enzymes and presents reduced GC content and size. Together with epidemiological observations, these features suggest that P. jirovecii is an obligate parasite specialized in the colonization of human lungs, which causes disease only in immune-deficient individuals. This genome sequence will boost research on this deadly pathogen. IMPORTANCE Pneumocystis pneumonia is a major cause of mortality in patients with impaired immune systems. The availability of the P. jirovecii genome sequence allows new analyses to be performed which open avenues to solve critical issues for this deadly human disease. The most important ones are (i) identification of nutritional supplements for development of culture in vitro, which is still lacking 100 years after discovery of the pathogen; (ii) identification of new targets for development of new drugs, given the paucity of present treatments and emerging resistance; and (iii) identification of targets for development of vaccines.