Reconstruction of the recent history of a large deep prealpine lake (Lake Bourget, France) using subfossil chironomids, diatoms, and organic matter analysis: towards the definition of a lake-specific reference state

This paper presents the recent history of a large prealpine lake (Lake Bourget) using chironomids, diatoms and organic matter analysis, and deals with the ability of paleolimnological approach to define an ecological reference state for the lake in the sense of the European Framework Directive. The study at low resolution of subfossil chironomids in a 4-m-long core shows the remarkable stability over the last 2.5 kyrs of the profundal community dominated by a Micropsectra-association until the beginning of the twentieth century, when oxyphilous taxa disappeared. Focusing on this key recent period, a high resolution and multiproxy study of two short cores reveals a progressive evolution of the lake's ecological state. Until AD 1880, Lake Bourget showed low organic matter content in the deep sediments (TOC less than 1%) and a well-oxygenated hypolimnion that allowed the development of a profundal oxyphilous chironomid fauna (Micropsectra-association). Diatom communities were characteristic of oligotrophic conditions. Around AD 1880, a slight increase in the TOC was the first sign of changes in lake conditions. This was followed by a first limited decline in oligotrophic diatom taxa and the disappearance of two oxyphilous chironomid taxa at the beginning of the twentieth century. The 1940s were a major turning point in recent lake history. Diatom assemblages and accumulation of well preserved planktonic organic matter in the sediment provide evidence of strong eutrophication. The absence of profundal chironomid communities reveals permanent hypolimnetic anoxia. From AD 1995 to 2006, the diatom assemblages suggest a reduction in nutrients, and a return to mesotrophic conditions, a result of improved wastewater management. However, no change in hypolimnion benthic conditions has been shown by either the organic matter or the subfossil chironomid profundal community. Our results emphasize the relevance of the paleolimnological approach for the assessment of reference conditions for modern lakes. Before AD 1900, the profundal Micropsectra-association and the Cyclotella dominated diatom community can be considered as the Lake Bourget reference community, which reflects the reference ecological state of the lake.

PDZ domain-binding motif regulates cardiomyocyte compartment-specific NaV1.5 channel expression and function.

BACKGROUND: Sodium channel NaV1.5 underlies cardiac excitability and conduction. The last 3 residues of NaV1.5 (Ser-Ile-Val) constitute a PDZ domain-binding motif that interacts with PDZ proteins such as syntrophins and SAP97 at different locations within the cardiomyocyte, thus defining distinct pools of NaV1.5 multiprotein complexes. Here, we explored the in vivo and clinical impact of this motif through characterization of mutant mice and genetic screening of patients. METHODS AND RESULTS: To investigate in vivo the regulatory role of this motif, we generated knock-in mice lacking the SIV domain (ΔSIV). ΔSIV mice displayed reduced NaV1.5 expression and sodium current (INa), specifically at the lateral myocyte membrane, whereas NaV1.5 expression and INa at the intercalated disks were unaffected. Optical mapping of ΔSIV hearts revealed that ventricular conduction velocity was preferentially decreased in the transversal direction to myocardial fiber orientation, leading to increased anisotropy of ventricular conduction. Internalization of wild-type and ΔSIV channels was unchanged in HEK293 cells. However, the proteasome inhibitor MG132 rescued ΔSIV INa, suggesting that the SIV motif is important for regulation of NaV1.5 degradation. A missense mutation within the SIV motif (p.V2016M) was identified in a patient with Brugada syndrome. The mutation decreased NaV1.5 cell surface expression and INa when expressed in HEK293 cells. CONCLUSIONS: Our results demonstrate the in vivo significance of the PDZ domain-binding motif in the correct expression of NaV1.5 at the lateral cardiomyocyte membrane and underline the functional role of lateral NaV1.5 in ventricular conduction. Furthermore, we reveal a clinical relevance of the SIV motif in cardiac disease.

Transcriptome analysis of intraspecific competition in Arabidopsis thaliana reveals organ-specific signatures related to nutrient acquisition and general stress response pathways.

ABSTRACT: BACKGROUND: Plants are sessile and therefore have to perceive and adjust to changes in their environment. The presence of neighbours leads to a competitive situation where resources and space will be limited. Complex adaptive responses to such situation are poorly understood at the molecular level. RESULTS: Using microarrays, we analysed whole-genome expression changes in Arabidopsis thaliana plants subjected to intraspecific competition. The leaf and root transcriptome was strongly altered by competition. Differentially expressed genes were enriched in genes involved in nutrient deficiency (mainly N, P, K), perception of light quality, and responses to abiotic and biotic stresses. Interestingly, performance of the generalist insect Spodoptera littoralis on densely grown plants was significantly reduced, suggesting that plants under competition display enhanced resistance to herbivory. CONCLUSIONS: This study provides a comprehensive list of genes whose expression is affected by intraspecific competition in Arabidopsis. The outcome is a unique response that involves genes related to light, nutrient deficiency, abiotic stress, and defence responses.

Nuclear translocation and DNA recognition signals colocalized within the bZIP domain of cyclic adenosine 3',5'-monophosphate response element-binding protein CREB.

CREB is a cAMP-responsive nuclear DNA-binding protein that binds to cAMP response elements and stimulates gene transcription upon activation of the cAMP signalling pathway. The protein consists of an amino-terminal transcriptional transactivation domain and a carboxyl-terminal DNA-binding domain (bZIP domain) comprised of a basic region and a leucine zipper involved in DNA recognition and dimerization, respectively. Recently, we discovered a testis-specific transcript of CREB that contains an alternatively spliced exon encoding multiple stop codons. CREB encoded by this transcript is a truncated protein lacking the bZIP domain. We postulated that the antigen detected by CREB antiserum in the cytoplasm of germinal cells is the truncated CREB that must also lack its nuclear translocation signal (NTS). To test this hypothesis we prepared multiple expression plasmids encoding carboxyl-terminal deletions of CREB and transiently expressed them in COS-1 cells. By Western immunoblot analysis as well as immunocytochemistry of transfected cells, we show that CREB proteins truncated to amino acid 286 or shorter are sequestered in the cytoplasm, whereas a CREB of 295 amino acids is translocated into the nucleus. Chimeric CREBs containing a heterologous NTS fused to the first 248 or 261 amino acids of CREB are able to drive the translocation of the protein into the nucleus. Thus, the nine amino acids in the basic region involved in DNA recognition between positions 287 and 295 (RRKKKEYVK) of CREB contain the NTS. Further, mutation of the lysine at position 290 in CREB to an asparagine diminishes nuclear translocation of the protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Mycobacterium tuberculosis subverts innate immunity to evade specific effectors.

The macrophage is the niche of the intracellular pathogen Mycobacterium tuberculosis. Induction of macrophage apoptosis by CD4(+) or CD8(+) T cells is accompanied by reduced bacterial counts, potentially defining a host defense mechanism. We have already established that M. tuberculosis-infected primary human macrophages have a reduced susceptibility to Fas ligand (FasL)-induced apoptosis. To study the mechanisms by which M. tuberculosis prevents apoptotic signaling, we have generated a cell culture system based on PMA- and IFN-gamma-differentiated THP-1 cells recapitulating the properties of primary macrophages. In these cells, nucleotide-binding oligomerization domain 2 or TLR2 agonists and mycobacterial infection protected macrophages from apoptosis and resulted in NF-kappaB nuclear translocation associated with up-regulation of the antiapoptotic cellular FLIP. Transduction of a receptor-interacting protein-2 dominant-negative construct showed that nucleotide-binding oligomerization domain 2 is not involved in protection in the mycobacterial infection system. In contrast, both a dominant-negative construct of the MyD88 adaptor and an NF-kappaB inhibitor abrogated the protection against FasL-mediated apoptosis, showing the implication of TLR2-mediated activation of NF-kappaB in apoptosis protection in infected macrophages. The apoptosis resistance of infected macrophages might be considered as an immune escape mechanism, whereby M. tuberculosis subverts innate immunity signaling to protect its host cell against FasL(+)-specific cytotoxic lymphocytes.

Aetiologies of pulseless electrical activity in out-of-hospital cardiac arrests:A retrospective study and analysis of specific causes

Background: Pulseless electrical activity (PEA) cardiac arrest is defined as a cardiac arrest (CA) presenting with a residual organized electrical activity on the electrocardiogram. In the last decades, the incidence of PEA has regularly increased, compared to other types of CA like ventricular fibrillation or pulseless ventricular tachycardia. PEA is frequently induced by reversible conditions. The "4 (or 5) H" & "4 (or 5) T" are proposed as a mnemonic to asses for Hypoxia, Hypovolemia, Hypo- /Hyperkalaemia, Hypothermia, Thrombosis (cardiac or pulmonary), cardiac Tamponade, Toxins, and Tension pneumothorax. Other pathologies (intracranial haemorrhage, severe sepsis, myocardial contraction dysfunction) have been identified as potential causes for PEA, but their respective probability and frequencies are unclear and they are not yet included into the resuscitation guidelines. The aim of this study was to analyse the aetiologies of PEA out-of-hospital CA, in order to evaluate the relative frequencies of each cause and therefore to improve the management of patients suffering a PEA cardiac arrest. Method: This retrospective study was based on data routinely and prospectively collected for each PEMS intervention. All adult patients treated from January 1st 2002 to December 2012 31st by the PEMS for out-of-hospital cardiac arrest, with PEA as the first recorded rhythm, and admitted to the emergency department (ED) of the Lausanne University Hospital were included. The aetiologies of PEA cardiac arrest were classified into subgroups, based on the classical H&T's classification, supplemented by four other subgroups analysis: trauma, intra-cranial haemorrhage (ICH), non-ischemic cardiomyopathy (NIC) and undetermined cause. Results: 1866 OHCA were treated by the PEMS. PEA was the first recorded rhythm in 240 adult patients (13.8 %). After exclusion of 96 patients, 144 patients with a PEA cardiac arrest admitted to the ED were included in the analysis. The mean age was 63.8 ± 20.0 years, 58.3% were men and the survival rate at 48 hours was 29%. 32 different causes of OHCA PEA were established for 119 patients. For 25 patients (17.4 %), we were unable to attribute a specific cause for the PEA cardiac arrest. Hypoxia (23.6 %), acute coronary syndrome (12.5%) and trauma (12.5 %) were the three most frequent causes. Pulmonary embolism, Hypovolemia, Intoxication and Hyperkaliemia occurs in less than 10% of the cases (7.6 %, 5.6 %, 3.5%, respectively 2.1 %). Non ischemic cardiomyopathy and intra-cranial haemorrhage occur in 8.3 % and 6.9 %, respectively. Conclusions: According to our results, intra-cranial haemorrhage and non-ischemic cardiomyopathy represent noticeable causes of PEA in OHCA, with a prevalence equalling or exceeding the frequency of classical 4 H's and 4 T's aetiologies. These two pathologies are potentially accessible to simple diagnostic procedures (native CT-scan or echocardiography) and should be included into the 4 H's and 4 T's mnemonic.

O6-Methylguanine-DNA methyltransferase protein expression by immunohistochemistry in brain and non-brain systemic tumours: systematic review and meta-analysis of correlation with methylation-specific polymerase chain reaction

Background: The DNA repair protein O6-Methylguanine-DNA methyltransferase (MGMT) confers resistance to alkylating agents. Several methods have been applied to its analysis, with methylation-specific polymerase chain reaction (MSP) the most commonly used for promoter methylation study, while immunohistochemistry (IHC) has become the most frequently used for the detection of MGMT protein expression. Agreement on the best and most reliable technique for evaluating MGMT status remains unsettled. The aim of this study was to perform a systematic review and meta-analysis of the correlation between IHC and MSP. Methods A computer-aided search of MEDLINE (1950-October 2009), EBSCO (1966-October 2009) and EMBASE (1974-October 2009) was performed for relevant publications. Studies meeting inclusion criteria were those comparing MGMT protein expression by IHC with MGMT promoter methylation by MSP in the same cohort of patients. Methodological quality was assessed by using the QUADAS and STARD instruments. Previously published guidelines were followed for meta-analysis performance. Results Of 254 studies identified as eligible for full-text review, 52 (20.5%) met the inclusion criteria. The review showed that results of MGMT protein expression by IHC are not in close agreement with those obtained with MSP. Moreover, type of tumour (primary brain tumour vs others) was an independent covariate of accuracy estimates in the meta-regression analysis beyond the cut-off value. Conclusions Protein expression assessed by IHC alone fails to reflect the promoter methylation status of MGMT. Thus, in attempts at clinical diagnosis the two methods seem to select different groups of patients and should not be used interchangeably.

Expanding the Customer Relationship Management scope to the non-profit organizations : an analysis focused on the e-university domain

Peer-reviewed

Utilization of a Time Domain Simulator in the Technical and Economic Analysis of a Wind Turbine Electric Drive Train

The amount of installed wind power has been growing exponentially during the past ten years. As wind turbines have become a significant source of electrical energy, the interactions between the turbines and the electric power network need to be studied more thoroughly than before. Especially, the behavior of the turbines in fault situations is of prime importance; simply disconnecting all wind turbines from the network during a voltage drop is no longer acceptable, since this would contribute to a total network collapse. These requirements have been a contributor to the increased role of simulations in the study and design of the electric drive train of a wind turbine. When planning a wind power investment, the selection of the site and the turbine are crucial for the economic feasibility of the installation. Economic feasibility, on the other hand, is the factor that determines whether or not investment in wind power will continue, contributing to green electricity production and reduction of emissions. In the selection of the installation site and the turbine (siting and site matching), the properties of the electric drive train of the planned turbine have so far been generally not been taken into account. Additionally, although the loss minimization of some of the individual components of the drive train has been studied, the drive train as a whole has received less attention. Furthermore, as a wind turbine will typically operate at a power level lower than the nominal most of the time, efficiency analysis in the nominal operating point is not sufficient. This doctoral dissertation attempts to combine the two aforementioned areas of interest by studying the applicability of time domain simulations in the analysis of the economicfeasibility of a wind turbine. The utilization of a general-purpose time domain simulator, otherwise applied to the study of network interactions and control systems, in the economic analysis of the wind energy conversion system is studied. The main benefits of the simulation-based method over traditional methods based on analytic calculation of losses include the ability to reuse and recombine existing models, the ability to analyze interactions between the components and subsystems in the electric drive train (something which is impossible when considering different subsystems as independent blocks, as is commonly done in theanalytical calculation of efficiencies), the ability to analyze in a rather straightforward manner the effect of selections other than physical components, for example control algorithms, and the ability to verify assumptions of the effects of a particular design change on the efficiency of the whole system. Based on the work, it can be concluded that differences between two configurations can be seen in the economic performance with only minor modifications to the simulation models used in the network interaction and control method study. This eliminates the need ofdeveloping analytic expressions for losses and enables the study of the system as a whole instead of modeling it as series connection of independent blocks with no lossinterdependencies. Three example cases (site matching, component selection, control principle selection) are provided to illustrate the usage of the approach and analyze its performance.

Be-Fe coupled method for the analysis of 3D elastodynamic problems in the time domain

By coupling the Boundary Element Method (BEM) and the Finite Element Method (FEM) an algorithm that combines the advantages of both numerical processes is developed. The main aim of the work concerns the time domain analysis of general three-dimensional wave propagation problems in elastic media. In addition, mathematical and numerical aspects of the related BE-, FE- and BE/FE-formulations are discussed. The coupling algorithm allows investigations of elastodynamic problems with a BE- and a FE-subdomain. In order to observe the performance of the coupling algorithm two problems are solved and their results compared to other numerical solutions.

A frequency-domain pseudo-force method for dynamic structural analysis nonlinear systems and nonproportional damping

A frequency-domain method for nonlinear analysis of structural systems with viscous, hysteretic, nonproportional and frequency-dependent damping is presented. The nonlinear effects and nonproportional damping are considered through pseudo-force terms. The modal coordinates uncoupled equations are iteratively solved. The treatment of initial conditions in the frequency domain which is necessary for the treatment of the uncoupled equations is initially adressed.

A Well Stated Time Domain Integral Representation for Elastodynamic Analysis and Applications

This article discusses three possible ways to derive time domain boundary integral representations for elastodynamics. This discussion points out possible difficulties found when using those formulations to deal with practical applications. The discussion points out recommendations to select the convenient integral representation to deal with elastodynamic problems and opens the possibility of deriving simplified schemes. The proper way to take into account initial conditions applied to the body is an interesting topict shown. It illustrates the main differences between the discussed boundary integral representation expressions, their singularities and possible numerical problems. The correct way to use collocation points outside the analyzed domain is carefully described. Some applications are shown at the end of the paper, in order to demonstrate the capabilities of the technique when properly used.

Target audience analysis in cyber domain

This thesis aims to find an effective way of conducting a target audience analysis (TAA) in cyber domain. There are two main focal points that are addressed; the nature of the cyber domain and the method of the TAA. Of the cyber domain the object is to find the opportunities, restrictions and caveats that result from its digital and temporal nature. This is the environment in which the TAA method is examined in this study. As the TAA is an important step of any psychological operation and critical to its success, the method used must cover all the main aspects affecting the choice of a proper target audience. The first part of the research was done by sending an open-ended questionnaire to operators in the field of information warfare both in Finland and abroad. As the results were inconclusive, the research was completed by assessing the applicability of United States Army Joint Publication FM 3-05.301 in the cyber domain via a theory-based content analysis. FM 3- 05.301 was chosen because it presents a complete method of the TAA process. The findings were tested against the results of the questionnaire and new scientific research in the field of psychology. The cyber domain was found to be “fast and vast”, volatile and uncontrollable. Although governed by laws to some extent, the cyber domain is unpredictable by nature and not controllable to reasonable amount. The anonymity and lack of verification often present in the digital channels mean that anyone can have an opinion, and any message sent may change or even be counterproductive to the original purpose. The TAA method of the FM 3-05.301 is applicable in the cyber domain, although some parts of the method are outdated and thus suggested to be updated if used in that environment. The target audience categories of step two of the process were replaced by new groups that exist in the digital environment. The accessibility assessment (step eight) was also redefined, as in the digital media the mere existence of a written text is typically not enough to convey the intended message to the target audience. The scientific studies made in computer sciences and both in psychology and sociology about the behavior of people in social media (and overall in cyber domain) call for a more extensive remake of the TAA process. This falls, however, out of the scope of this work. It is thus suggested that further research should be carried out in search of computer-assisted methods and a more thorough TAA process, utilizing the latest discoveries of human behavior. ---------------------------------------------------------------------------------------------------------------------------------- Tämän opinnäytetyön tavoitteena on löytää tehokas tapa kohdeyleisöanalyysin tekemiseksi kybertoimintaympäristössä. Työssä keskitytään kahteen ilmiöön: kybertoimintaympäristön luonteeseen ja kohdeyleisöanalyysin metodiin. Kybertoimintaympäristön osalta tavoitteena on löytää sen digitaalisesta ja ajallisesta luonteesta juontuvat mahdollisuudet, rajoitteet ja sudenkuopat. Tämä on se ympäristö jossa kohdeyleisöanalyysiä tarkastellaan tässä työssä. Koska kohdeyleisöanalyysi kuuluu olennaisena osana jokaiseen psykologiseen operaatioon ja on onnistumisen kannalta kriittinen tekijä, käytettävän metodin tulee pitää sisällään kaikki oikean kohdeyleisön valinnan kannalta merkittävät osa-alueet. Tutkimuksen ensimmäisessä vaiheessa lähetettiin avoin kysely informaatiosodankäynnin ammattilaisille Suomessa ja ulkomailla. Koska kyselyn tulokset eivät olleet riittäviä johtopäätösten tekemiseksi, tutkimusta jatkettiin tarkastelemalla Yhdysvaltojen armeijan kenttäohjesäännön FM 3-05.301 soveltuvuutta kybertoimintaympäristössä käytettäväksi teorialähtöisen sisällönanalyysin avulla. FM 3-05.301 valittiin koska se sisältää kokonaisvaltaisen kohdeyleisöanalyysiprosessin. Havaintoja verrattiin kyselytutkimuksen tuloksiin ja psykologian uusiin tutkimuksiin. Kybertoimintaympäristö on tulosten perusteella nopea ja valtava, jatkuvasti muuttuva ja kontrolloimaton. Vaikkakin lait hallitsevat kybertoimintaympäristöä jossakin määrin, on se silti luonteeltaan ennakoimaton eikä sitä voida luotettavasti hallita. Digitaalisilla kanavilla usein läsnäoleva nimettömyys ja tiedon tarkastamisen mahdottomuus tarkoittavat että kenellä tahansa voi olla mielipide asioista, ja mikä tahansa viesti voi muuttua, jopa alkuperäiseen tarkoitukseen nähden vastakkaiseksi. FM 3-05.301:n metodi toimii kybertoimintaympäristössä, vaikkakin jotkin osa-alueet ovat vanhentuneita ja siksi ne esitetään päivitettäväksi mikäli metodia käytetään kyseisessä ympäristössä. Kohdan kaksi kohdeyleisökategoriat korvattiin uusilla, digitaalisessa ympäristössä esiintyvillä ryhmillä. Lähestyttävyyden arviointi (kohta 8) muotoiltiin myös uudestaan, koska digitaalisessa mediassa pelkkä tekstin läsnäolo ei sellaisenaan tyypillisesti vielä riitä halutun viestin välittämiseen kohdeyleisölle. Tietotekniikan edistyminen ja psykologian sekä sosiologian aloilla tehty tieteellinen tutkimus ihmisten käyttäytymisestä sosiaalisessa mediassa (ja yleensä kybertoimintaympäristössä) mahdollistavat koko kohdeyleisöanalyysiprosessin uudelleenrakentamisen. Tässä työssä sitä kuitenkaan ei voida tehdä. Siksi esitetäänkin että lisätutkimusta tulisi tehdä sekä tietokoneavusteisten prosessien että vielä syvällisempien kohdeyleisöanalyysien osalta, käyttäen hyväksi viimeisimpiä ihmisen käyttäytymiseen liittyviä tutkimustuloksia.