Niche, distribution and global change : modeling insights into biogeography and conservation biology Olivier Broennimann

RESUME Les évidences montrant que les changements globaux affectent la biodiversité s'accumulent. Les facteurs les plus influant dans ce processus sont les changements et destructions d'habitat, l'expansion des espèces envahissantes et l'impact des changements climatiques. Une évaluation pertinente de la réponse des espèces face à ces changements est essentielle pour proposer des mesures permettant de réduire le déclin actuel de la biodiversité. La modélisation de la répartition d'espèces basée sur la niche (NBM) est l'un des rares outils permettant cette évaluation. Néanmoins, leur application dans le contexte des changements globaux repose sur des hypothèses restrictives et demande une interprétation critique. Ce travail présente une série d'études de cas investiguant les possibilités et limitations de cette approche pour prédire l'impact des changements globaux. Deux études traitant des menaces sur les espèces rares et en danger d'extinction sont présentées. Les caractéristiques éco-géographiques de 118 plantes avec un haut degré de priorité de conservation sont revues. La prévalence des types de rareté sont analysées en relation avec leur risque d'extinction UICN. La revue souligne l'importance de la conservation à l'échelle régionale. Une évaluation de la rareté à échelle globale peut être trompeuse pour certaine espèces car elle ne tient pas en compte des différents degrés de rareté que présente une espèce à différentes échelles spatiales. La deuxième étude test une approche pour améliorer l'échantillonnage d'espèces rares en incluant des phases itératives de modélisation et d'échantillonnage sur le terrain. L'application de l'approche en biologie de la conservation (illustrée ici par le cas du chardon bleu, Eryngium alpinum), permettrait de réduire le temps et les coûts d'échantillonnage. Deux études sur l'impact des changements climatiques sur la faune et la flore africaine sont présentées. La première étude évalue la sensibilité de 227 mammifères africains face aux climatiques d'ici 2050. Elle montre qu'un nombre important d'espèces pourrait être bientôt en danger d'extinction et que les parcs nationaux africains (principalement ceux situé en milieux xériques) pourraient ne pas remplir leur mandat de protection de la biodiversité dans le futur. La seconde étude modélise l'aire de répartition en 2050 de 975 espèces de plantes endémiques du sud de l'Afrique. L'étude propose l'inclusion de méthodes améliorant la prédiction des risques liés aux changements climatiques. Elle propose également une méthode pour estimer a priori la sensibilité d'une espèce aux changements climatiques à partir de ses propriétés écologiques et des caractéristiques de son aire de répartition. Trois études illustrent l'utilisation des modèles dans l'étude des invasions biologiques. Une première étude relate l'expansion de la laitue sáuvage (Lactuca serriola) vers le nord de l'Europe en lien avec les changements du climat depuis 250 ans. La deuxième étude analyse le potentiel d'invasion de la centaurée tachetée (Centaures maculosa), une mauvaise herbe importée en Amérique du nord vers 1890. L'étude apporte la preuve qu'une espèce envahissante peut occuper une niche climatique différente après introduction sur un autre continent. Les modèles basés sur l'aire native prédisent de manière incorrecte l'entier de l'aire envahie mais permettent de prévoir les aires d'introductions potentielles. Une méthode alternative, incluant la calibration du modèle à partir des deux aires où l'espèce est présente, est proposée pour améliorer les prédictions de l'invasion en Amérique du nord. Je présente finalement une revue de la littérature sur la dynamique de la niche écologique dans le temps et l'espace. Elle synthétise les récents développements théoriques concernant le conservatisme de la niche et propose des solutions pour améliorer la pertinence des prédictions d'impact des changements climatiques et des invasions biologiques. SUMMARY Evidences are accumulating that biodiversity is facing the effects of global change. The most influential drivers of change in ecosystems are land-use change, alien species invasions and climate change impacts. Accurate projections of species' responses to these changes are needed to propose mitigation measures to slow down the on-going erosion of biodiversity. Niche-based models (NBM) currently represent one of the only tools for such projections. However, their application in the context of global changes relies on restrictive assumptions, calling for cautious interpretations. In this thesis I aim to assess the effectiveness and shortcomings of niche-based models for the study of global change impacts on biodiversity through the investigation of specific, unsolved limitations and suggestion of new approaches. Two studies investigating threats to rare and endangered plants are presented. I review the ecogeographic characteristic of 118 endangered plants with high conservation priority in Switzerland. The prevalence of rarity types among plant species is analyzed in relation to IUCN extinction risks. The review underlines the importance of regional vs. global conservation and shows that a global assessment of rarity might be misleading for some species because it can fail to account for different degrees of rarity at a variety of spatial scales. The second study tests a modeling framework including iterative steps of modeling and field surveys to improve the sampling of rare species. The approach is illustrated with a rare alpine plant, Eryngium alpinum and shows promise for complementing conservation practices and reducing sampling costs. Two studies illustrate the impacts of climate change on African taxa. The first one assesses the sensitivity of 277 mammals at African scale to climate change by 2050 in terms of species richness and turnover. It shows that a substantial number of species could be critically endangered in the future. National parks situated in xeric ecosystems are not expected to meet their mandate of protecting current species diversity in the future. The second study model the distribution in 2050 of 975 endemic plant species in southern Africa. The study proposes the inclusion of new methodological insights improving the accuracy and ecological realism of predictions of global changes studies. It also investigates the possibility to estimate a priori the sensitivity of a species to climate change from the geographical distribution and ecological proprieties of the species. Three studies illustrate the application of NBM in the study of biological invasions. The first one investigates the Northwards expansion of Lactuca serriola L. in Europe during the last 250 years in relation with climate changes. In the last two decades, the species could not track climate change due to non climatic influences. A second study analyses the potential invasion extent of spotted knapweed, a European weed first introduced into North America in the 1890s. The study provides one of the first empirical evidence that an invasive species can occupy climatically distinct niche spaces following its introduction into a new area. Models fail to predict the current full extent of the invasion, but correctly predict areas of introduction. An alternative approach, involving the calibration of models with pooled data from both ranges, is proposed to improve predictions of the extent of invasion on models based solely on the native range. I finally present a review on the dynamic nature of ecological niches in space and time. It synthesizes the recent theoretical developments to the niche conservatism issues and proposes solutions to improve confidence in NBM predictions of the impacts of climate change and species invasions on species distributions.

Proportion of out-of-hospital adult non-traumatic cardiac or respiratory arrest among calls for seizure.

OBJECTIVES: To measure the proportion of adult non-traumatic cardiac or respiratory arrest among calls for seizure to an emergency medical dispatch centre and to record whether known epileptic patients present cardiac or respiratory arrest together with seizure. METHODS: This 2-year prospective observational investigation involved the collection of tape recordings of all incoming calls to the emergency medical dispatch centre, in which an out-of-hospital non-traumatic seizure was the chief complaint in patients >18 years, in addition to the paramedics' records of all patients who presented with respiratory or cardiac arrest. The authors also recorded whether the bystander spontaneously mentioned to the dispatcher that the victim was known to have epilepsy. RESULTS: During the 24-month period, the call centre received 561 incoming calls for an out-of-hospital non-traumatic seizure in an adult. Twelve cases were classified as cardiac or respiratory arrest by paramedics. In one case, the caller spontaneously mentioned that the victim had a history of epilepsy. The proportion of cardiac or respiratory arrest among calls for seizure was 2.1%. CONCLUSION: Although these cases are rare, dispatchers should closely monitor seizure patients with the help of bystanders to exclude an out-of-hospital cardiac or respiratory arrest, in which case the dispatcher can offer telephone cardiopulmonary resuscitation advice until the paramedics arrive. Whenever the activity of the centre allows it and no new incoming call is on hold, this can be achieved by staying on the line with the caller or by calling back. A history of epilepsy should not modify the type of monitoring performed by the dispatcher as those patients may also have an arrest together with seizure.

Two Signatures For A New Blood-Based Test For Colorectal Cancer Screening

Background: Detection rates for adenoma and early colorectal cancer (CRC) are unsatisfactory due to low compliance towards invasive screening procedures such as colonoscopy. There is a large unmet screening need calling for an accurate, non-invasive and cost-effective test to screen for early neoplastic and pre-neoplastic lesions. Our goal is to identify effective biomarker combinations to develop a screening test aimed at detecting precancerous lesions and early CRC stages, based on a multigene assay performed on peripheral blood mononuclear cells (PBMC).Methods: A pilot study was conducted on 92 subjects. Colonoscopy revealed 21 CRC, 30 adenomas larger than 1 cm and 41 healthy controls. A panel of 103 biomarkers was selected by two approaches: a candidate gene approach based on literature review and whole transcriptome analysis of a subset of this cohort by Illumina TAG profiling. Blood samples were taken from each patient and PBMC purified. Total RNA was extracted and the 103 biomarkers were tested by multiplex RT-qPCR on the cohort. Different univariate and multivariate statistical methods were applied on the PCR data and 60 biomarkers, with significant p-value (< 0.01) for most of the methods, were selected.Results: The 60 biomarkers are involved in several different biological functions, such as cell adhesion, cell motility, cell signaling, cell proliferation, development and cancer. Two distinct molecular signatures derived from the biomarker combinations were established based on penalized logistic regression to separate patients without lesion from those with CRC or adenoma. These signatures were validated using bootstrapping method, leading to a separation of patients without lesion from those with CRC (Se 67%, Sp 93%, AUC 0.87) and from those with adenoma larger than 1cm (Se 63%, Sp 83%, AUC 0.77). In addition, the organ and disease specificity of these signatures was confirmed by means of patients with other cancer types and inflammatory bowel diseases.Conclusions: The two defined biomarker combinations effectively detect the presence of CRC and adenomas larger than 1 cm with high sensitivity and specificity. A prospective, multicentric, pivotal study is underway in order to validate these results in a larger cohort.

Iowa's frog and toad survey, 1995-2003.

This survey began in response to widespread interest of declines in amphibians. More recently, a comprehensive statewide planning group discovered 44% of Iowa’s herpetofauna (amphibians and reptiles) to be of special concern. In response to these concerns, the Iowa Department of Natural Resources Wildlife Diversity Program (WDP) initiated an auditory survey for calling anurans to determine geographic distributions within the state. This survey has established itself as an extensive, long term monitoring program. This 2005 report is the second edition since the first report of this survey was shared in 1998 by then program biologist Lisa Hemesath. The goals of the survey are to: (1) determine the distributions of Iowa’s anuran species, (2) determine population trends for each species, and (3) promote education about aquatic life by using volunteers to conduct the survey. In addition to Iowa, volunteer-based auditory surveys for frogs and toads are currently being used in the Midwest by Wisconsin, Minnesota, Missouri, and Illinois.

Water planning law and government.

Water planning efforts typically identify problems and needs. But simply calling attention to issues is usually not enough to spur action; the end result of many well-intentioned planning efforts is a report that ends up gathering dust on a shelf. Vague recommendations like “Water conservation measures should be implemented” usually accomplish little by themselves as they don’t assign responsibility to anyone. Success is more likely when an implementation strategy — who can and should do what — is developed as part of the planning process. The more detailed and specific the implementation strategy, the greater the chance that something will actually be done. The question then becomes who has the legal authority or responsibility to do what? Are new laws and programs needed or can existing ones be used to implement the recommendations? ... This document is divided into four main parts. The first, “Carrots and Sticks” looks at two basic approaches — regulatory and non-regulatory — that can be, and are, used to carry out water policy. Both have advantages and disadvantages that need to be considered. The second, “The powers of federal, state and local governments…,” looks at the constitutional powers the federal government and state and local governments have to carry out water policy. An initial look at the U. S. Constitution might suggest the federal government’s regulatory authority over water is limited but, in fact, its powers are very substantial. States have considerable authority to do a number of things but have to be mindful of any federal efforts that might conflict with those state efforts. And local governments can only do those things the state constitution or state legislature says they can do and must conform to any requirements or limitations on those powers that are contained in the enabling acts. Parts three and four examine in more detail the main programs and agencies at the federal level as well as Iowa’s state and local levels and the roles they play in national and state water policy.

Bump time-frequency toolbox: a toolbox for time-frequency oscillatory bursts extraction in electrophysiological signals

Background: oscillatory activity, which can be separated in background and oscillatory burst pattern activities, is supposed to be representative of local synchronies of neural assemblies. Oscillatory burst events should consequently play a specific functional role, distinct from background EEG activity – especially for cognitive tasks (e.g. working memory tasks), binding mechanisms and perceptual dynamics (e.g. visual binding), or in clinical contexts (e.g. effects of brain disorders). However extracting oscillatory events in single trials, with a reliable and consistent method, is not a simple task. Results: in this work we propose a user-friendly stand-alone toolbox, which models in a reasonable time a bump time-frequency model from the wavelet representations of a set of signals. The software is provided with a Matlab toolbox which can compute wavelet representations before calling automatically the stand-alone application. Conclusion: The tool is publicly available as a freeware at the address: http:// www.bsp.brain.riken.jp/bumptoolbox/toolbox_home.html

Food Indicators and Their Relationship with 10 to 12 Year-olds' Subjective Well-Being

This study aimed to test subjective indicators designed to analyze the role food plays in children’s lives, explore children’s personal well-being, and evaluate the relationship between these two phenomena. It was conducted on 371 children aged 10 to 12 by means of a selfadministered questionnaire. Results showed a marked interest in food on the part of children, who consider taste and health the most important indicators when it comes to eating. They demonstrated a high level of personal well-being, measured using Cummins & Lau’s adapted version of the Personal Well- Being Index–School Children (PWI-SC) (2005), overall life satisfaction (OLS) and satisfaction with various life domains (friends, family, sports, food and body). Regression models were conducted to explain satisfaction with food, taking as independent variables the interest children have in food, the importance they give to different reasons for eating, scores from the PWI-SC, OLS and satisfaction with various life domains. In the final model, it was found that OLS, health indicators, satisfaction with health from the PWI-SC and satisfaction with your body contribute to explaining satisfaction with food. The results obtained suggest that satisfaction with food is a relevant indicator in the exploration of children’s subjective well-being, calling into question the widespread belief that these aspects are of exclusive interest to adults. They also seem to reinforce the importance of including food indicators in any study aimed at exploring the well-being of the 10 to 12 year-old population.

Mechanical properties of viral capsids

Viruses are known to tolerate wide ranges of pH and salt conditions and to withstand internal pressures as high as 100 atmospheres. In this paper we investigate the mechanical properties of viral capsids, calling explicit attention to the inhomogeneity of the shells that is inherent to their discrete and polyhedral nature. We calculate the distribution of stress in these capsids and analyze their response to isotropic internal pressure (arising, for instance, from genome confinement and/or osmotic activity). We compare our results with appropriate generalizations of classical (i.e., continuum) elasticity theory. We also examine competing mechanisms for viral shell failure, e.g., in-plane crack formation vs radial bursting. The biological consequences of the special stabilities and stress distributions of viral capsids are also discussed.

Water Planning Law and Government, November 2008

Water planning efforts typically identify problems and needs. But simply calling attention to issues is usually not enough to spur action; the end result of many well-intentioned planning efforts is a report that ends up gathering dust on a shelf. Vague recommendations like “Water conservation measures should be implemented” usually accomplish little by themselves as they don’t assign responsibility to anyone. Success is more likely when an implementation strategy — who can and should do what — is developed as part of the planning process. The more detailed and specific the implementation strategy, the greater the chance that something will actually be done.

Drug interactions with the tyrosine kinase inhibitors imatinib, dasatinib, and nilotinib.

Several cancer treatments are shifting from traditional, time-limited, nonspecific cytotoxic chemotherapy cycles to continuous oral treatment with specific protein-targeted therapies. In this line, imatinib mesylate, a selective tyrosine kinases inhibitor (TKI), has excellent efficacy in the treatment of chronic myeloid leukemia. It has opened the way to the development of additional TKIs against chronic myeloid leukemia, including nilotinib and dasatinib. TKIs are prescribed for prolonged periods, often in patients with comorbidities. Therefore, they are regularly co-administered along with treatments at risk of drug-drug interactions. This aspect has been partially addressed so far, calling for a comprehensive review of the published data. We review here the available evidence and pharmacologic mechanisms of interactions between imatinib, dasatinib, and nilotinib and widely prescribed co-medications, including known inhibitors or inducers of cytochromes P450 or drug transporters. Information is mostly available for imatinib mesylate, well introduced in clinical practice. Several pharmacokinetic aspects yet remain insufficiently investigated for these drugs. Regular updates will be mandatory and so is the prospective reporting of unexpected clinical observations.

Callings in career: A typological approach to essential and optional components

A sense of calling in career is supposed to have positive implications for individuals and organizations but current theoretical development is plagued with incongruent conceptualizations of what does or does not constitute a calling. The present study used cluster analysis to identify essential and optional components of a presence of calling among 407 German undergraduate students from different majors. Three types of calling merged: "negative career self-centered", "pro-social religious", and "positive varied work orientation". All types could be described as vocational identity achieved (high commitment/high self-exploration), high in career confidence and career engagement. Not defining characteristics were centrality of work or religion, endorsement of specific work values, or positivity of core self-evaluations. The results suggest that callings entail intense self-exploration and might be beneficial because they correspond with identity achievement and promote career confidence and engagement while not necessarily having pro-social orientations. Suggestions for future research, theory and practice are suggested.

Behavioral changes in brain-injured critical care adults with different levels of consciousness during nociceptive stimulation: an observational study.

PURPOSE: The primary objective of this study was to describe the frequency of behaviors observed during rest, a non-nociceptive procedure, and a nociceptive procedure in brain-injured intensive care unit (ICU) patients with different levels of consciousness (LOC). Second, it examined the inter-rater reliability and discriminant and concurrent validity of the behavioral checklist used. METHODS: The non-nociceptive procedure involved calling the patient and shaking his/her shoulder. The nociceptive procedure involved turning the patient. The frequency of behaviors was recorded using a behavioral checklist. RESULTS: Patients with absence of movement, or stereotyped flexion or extension responses to a nociceptive stimulus displayed more behaviors during turning (median 5.5, range 0-14) than patients with localized responses (median 4, range 0-10) or able to self-report their pain (median 4, range 0-10). Face flushing, clenched teeth, clenched fist, and tremor were more frequent in patients with absence of movement, or stereotyped responses to a nociceptive stimulus. The reliability of the checklist was supported by a high intra-class correlation coefficient (0.77-0.92), and the internal consistency was acceptable in all three groups (KR 20, 0.71-0.85). Discriminant validity was supported as significantly more behaviors were observed during nociceptive stimulation than at rest. Concurrent validity was confirmed as checklist scores were correlated to the patients' self-reports of pain (r s = 0.53; 95 % CI 0.21-0.75). CONCLUSION: Brain-injured patients reacted significantly more during a nociceptive stimulus and the number of observed behaviors was higher in patients with a stereotyped response.

Peripheral Nerve Neuropathy is Associated with a Glial Reaction in the Gracile Nucleus Associated with a regulation of the GABA transporter GAT-1

Allodynia (pain in response to normally non painful stimulation) and paresthesia (erroneous sensory experience) are two debilitating symptoms of neuropathic pain. These stem, at least partly, from profound changes in the non-nociceptive sensory pathway that comprises large myelinated neuronal afferents terminating in the gracile and cuneate nuclei. Further than neuronal changes, well admitted evidence indicates that glial cells (especially in the spinal cord) are key actors in neuropathic pain, in particular the possible alteration in astrocytic capacity to reuptake neurotransmitters (glutamate and GABA). Yet, the possibility of such a changed astrocytic scavenging capacity remains unexplored in the dorsal column pathway. The present study was therefore undertaken to assess whether peripheral nerve injury (spared nerve injury model, SNI) could trigger a glial reaction, and especially changes in glutamate and GABA transporters, in the gracile nucleus. SNI surgery was performed on male Sprague-Dawley rats. Seven days after surgery, rats were used for immunofluorescence (fixation and brain slicing), western-blot (fresh brain freezing and protein extraction) or GABA reuptake on synaptosomes. We found that SNI results in a profound glial reaction in the ipsilateral gracile nucleus. This reaction was characterized by an enhanced immunolabelling for microglial marker Iba1 as well as astrocytic protein GFAP (further confirmed by western-blot, p <0.05, n = 7). These changes were not observed in sham animals. Immunofluorescence and western-blot analysis shows that the GABA transporter GAT-1 is upregulated in the ipsilateral gracile nucleus (p <0.001; n = 7), with no detectable change in GAT-3 or glutamate transporters EAAT-1 and EAAT-2. Double immunoflurescence shows that GAT-1 and GFAP colocalize within the same cells. Furthermore, the upregulation of GFAP and GAT-1 were shown to occur all along the rostrocaudal axis of the gracile nucleus. Finally, synaptosomes from ipsilateral gracile nucleus show an increased capacity to reuptake GABA. Together, the data presented herein show that glial cells in the gracile nucleus react to neuropathic lesion, in particular through an upregulation of the GABA transporter GAT-1. Hence, this study points to role of an increased GABA transport in the dorsal column nuclei in neuropathic pain, calling attention to GAT-1 as a putative future pharmacological target to treat allodynia and paresthesia.

GPS-paikkatiedonliittäminen matkapuhelinpalveluihin

2000-luvun vaihteessa paikkatietoa hyödyntävistä matkapuhelinpalveluista odotettiin muodostuvan eräs merkittävimmistä kilpailuvalteista eri matkapuhelinoperaattoreiden välillä. Kiinnostusta paikkatietoa hyödyntäviin palveluihin lisäsi kaupallisten sovellusten lisäksi Yhdysvaltojen liittovaltioiden liikenneministeriön säätämä laki, joka velvoittaa paikantamaan yleiseen hätänumeroon soitetut puhelut. Erityisesti laite- ja verkkotoimittajat odottivat tämänluovan heille uusia markkinoita. Markkinoille tuli useita kilpailevia menetelmiä, joilla matkapuhelimia voitiin paikantaa. Suurin osa näistä menetelmistä hyödynsi GSM-verkon signalointia paikannuksen tekemiseen. Samaan aikaan kohonnut matkapuhelinten suorituskyky mahdollisti GPS-vastaanottimien integroinnin matkapuhelimiin ja ensimmäiset tällaiset matkapuhelimet ilmestyivät markkinoille. Matkapuhelinten paikantamiseen liittyvä standardointi on melko hajanaista. ETSI on standardoinut joukon erilaisia menetelmiä, joilla matkapuhelin paikkatieto voidaan selvittää. Nämä standardit eivät kuitenkaan määrittele sitä, kuinka paikkatieto siirretään sitä hyödyntävien palveluiden käyttöön. Paikkatiedonsiirtämiseen ja esittämiseen liittyvässä standardoinnissa eri laite- ja ohjelmistovalmistajat ovat tehneet liittoutumia keskenään ja esitelleet keskenään kilpailevia standardeja ja suosituksia. Tälläkään osa-alueella mikään liittoutuma ei ole saavuttanut määräävää markkina-asemaa. Tässä työssä suunniteltiin ja toteutettiin järjestelmä, jonka avulla voidaan paikantaa sellaisia GSM-päätelaitteita, joihin on integroitu GPS-vastaanotin. Toteutettu järjestelmä liitettiin uudeksi paikannusmenetelmäksi solupaikannuksen rinnalle Sonera Pointer paikannusjärjestelmään. Työn aikana testattiin joukko markkinoilla olleita GSM-puhelimia, joihin oli integroitu GPS-vastaanotin. Matkapuhelinten testauksessa erityinen huomio kiinnittyi siihen, kuinka GPS-paikkatieto saadaan siirrettyä matkapuhelimesta verkossa sijaitsevien sovellusten käyttöön. Toteutetun järjestelmän suunnittelussa täkein lähtökohta oli järjestelmän joustavuus. Standardien hajanaisuus ja osittainen puuttuminen aiheuttivat sen, että järjestelmästä oli tehtävä mahdollisimman helposti laajennettava. Toinen merkittävä suunnitteluun vaikuttanut tekijä oli operaattoririippumattomuus, koska Sonera Pointer järjestelmää oli tarkoitus myydä myös muille matkapuhelinoperaattoreille.