Spatial modeling of data with excessive zeros applied to reindeer pellet-group counts

We analyze a real data set pertaining to reindeer fecal pellet-group counts obtained from a survey conducted in a forest area in northern Sweden. In the data set, over 70% of counts are zeros, and there is high spatial correlation. We use conditionally autoregressive random effects for modeling of spatial correlation in a Poisson generalized linear mixed model (GLMM), quasi-Poisson hierarchical generalized linear model (HGLM), zero-inflated Poisson (ZIP), and hurdle models. The quasi-Poisson HGLM allows for both under- and overdispersion with excessive zeros, while the ZIP and hurdle models allow only for overdispersion. In analyzing the real data set, we see that the quasi-Poisson HGLMs can perform better than the other commonly used models, for example, ordinary Poisson HGLMs, spatial ZIP, and spatial hurdle models, and that the underdispersed Poisson HGLMs with spatial correlation fit the reindeer data best. We develop R codes for fitting these models using a unified algorithm for the HGLMs. Spatial count response with an extremely high proportion of zeros, and underdispersion can be successfully modeled using the quasi-Poisson HGLM with spatial random effects.

Ecogeography of roe deer: relation with other ungulates in sympatry

Understanding the spatial distribution of organisms is a central topic in ecology. The European roe deer (Capreolus capreolus) population is in Portugal and Norway at the southwestern and northern edge of its distribution, respectively. Understanding the factors that act on these populations enlightens both local aspects concerning their conservation and wider scale aspects of the species bioclimatic envelope, which is crucial for being better able to predict the impacts of environmental change. The main aim of this thesis was to evaluate roe deer distribution in Portugal and Norway, two countries with contrasting landscapes, seasonality and with different anthropogenic pressure. The interspecific relationship with sympatric ungulates was also analysed. By using pellet group counts, we investigated habitat use of roe deer, identifying the major environmental descriptors, to understand the importance of forest structure, vegetation characteristics, landscape structure and human disturbance on their distribution. The analyses were based on presence – absence data and were carried out at two spatial scales. The results showed that habitat use of roe deer was different across countries. In Portugal, at the local scale, roe deer distribution was positively associated with high density of shrubs, especially heather and brambles, while the presence of red deer had a negative effect on their distribution. At a broad scale, roe deer was negatively associated with spatial heterogeneity, namely mean shape index and made less use of areas close to agricultural fields. In Norway, at the local scale, roe deer made more use of areas with high cover of deciduous trees and patches containing juniper and Vaccinium sp.. At a broad scale, roe deer use patches near edges between fields and forest. In both countries, roe deer make use of areas further away from roads. While in Norway roe deer in both summer and winter are always close to houses, in Portugal they are either far (summer) or indifferent (winter). Anthropogenic disturbance is better tolerated in Norway, where the importance of the critical season seems to be higher. Human disturbance may contribute to roe deer habitat loss in Portugal, while roe deer are able to persist close to humans in managed landscapes in Norway. In fact, some of the differences observed could be more due to the indirect impacts of human exploitation (e.g. presence of free-ranging dogs and hunting regulation) rather than the actual human presence or land-use per se. I conclude that the methodology and tools developed here are readily expandable to address similar questions in different contexts. Wildlife management would benefit greatly from a more holistic/integrative approach and that should include human aspects, as human disturbance is expected to continue increasing.

Ecological assessment of the red deer population in the Lousã Mountain

Durante o último século, as populações de cervídeos têm aumentado substancialmente um pouco por toda a Europa. O veado Cervus elaphus não foi exceção, apresentando atualmente uma ampla distribuição geográfica. Após a quase extinção de todas as populações selvagens desta espécie em Portugal, o número de efetivos de veado e a área de distribuição da espécie têm aumentado significativamente nas últimas décadas. Esta proliferação deveu-se fundamentalmente aos processos de reintrodução implementados em algumas zonas do país, como foi o caso da Serra da Lousã. Dez anos após a reintrodução, a expansão geográfica e demográfica é já uma realidade e a espécie assume um papel relevante tanto do ponto de vista cinegético como turístico. Com o aumento das populações de ungulados, surge a necessidade de aumentar o conhecimento existente sobre estas espécies, particularmente ao nível das estimativas populacionais, do uso e seleção de habitat, do comportamento e da fisiologia das populações. Neste sentido, um dos objetivos foi comparar quatro métodos de contagem de excrementos em termos de estimativa populacional, aplicabilidade e eficiência. Face aos resultados obtidos, o método de transectos lineares com distance sampling revelou-se o mais eficiente, providenciando uma boa precisão num menor tempo. Relativamente ao uso e seleção do habitat, recorrendo a transectos de contagem de excrementos e a observações diretas, verificou-se que o veado seleciona positivamente habitats que lhe proporcionam simultaneamente alimento e refúgio, como é o caso das áreas de ecótono. A preferência por áreas de ecótono evidencia um comportamento adaptativo de maximização de energia, no qual os animais optam por procurar refúgio na proximidade das áreas de alimentação de forma a minimizarem os dispêndios energéticos. Em termos de dinâmica populacional, verificou-se uma relação entre a densidade de veado e o tamanho dos seus grupos, bem como o efeito nos mesmos do coberto vegetal. Contudo, dado o seu alto dimorfismo sexual em termos de tamanho corporal, as preferências de habitat podem também ser em parte responsáveis pela segregação sexual fora da época de reprodução. Face aos resultados obtidos através do método de observação direta de animais, a segregação sexual surge como consequência da interação entre fatores sociais e de habitat, que resultam de diferentes estratégias reprodutivas por parte de ambos os sexos. As diferentes estratégias reprodutivas são também notórias em termos de condição física e imunológica, com os machos a aumentarem a sua condição durante as épocas de primavera e verão de forma a melhorarem a sua performance durante o cio, e as fêmeas a viverem grande parte do ano no limiar da condição física devido ao seu investimento na sobrevivência da sua descendência. Globalmente, o veado apresenta uma boa adaptação à Serra da Lousã e representa um importante recurso natural para esta região. Contudo, para que a proliferação desta população selvagem continue, é necessária a implementação de medidas de gestão adequadas a este ecossistema mediterrâneo.

Renar och vindkraft II : Vindkraft i drift och effekter på renar och renskötsel

Utbyggnaden av vindkraft inom renskötselområdet har ökat markant det senaste decenniet, trots att kunskapen om påverkan av vindkraftsetableringar ännu inte är fullt utredd och dokumenterad. I den här rapporten beskriver vi framförallt hur vindkraftparker i driftsfas påverkar renarna och renskötseln i tre olika områden. I Malå sameby har vi studerat kalvningsområdet kring Storliden och Jokkmokkslidens vindkraftparker. I Vilhelmina Norra sameby har vi studerat vinterbetesområdet kring Stor-Rotlidens vindkraftpark, samt Lögdeålandets betesområde med Gabrielsbergets vindkraftpark som används av Byrkije reinbetesdistrikt från Norge. För att få en helhetsbild av hur renarna använder sitt betesområde är det viktigt att studera renarnas betes- och förflyttningsmönster långsiktigt och över hela deras betesområde och inte bara inom det lokala området nära parken. Det är också viktigt att ta hänsyn till att renarnas betesutnyttjande skiftar från år till år och mellan olika årstider beroende på väderlek och andra yttre förutsättningar. Vi vill också understryka vikten av att kombinera den traditionella kunskapen från renskötarna med vedertagna vetenskapliga analysmetoder för att besvara de frågor som är viktiga för att kunna bedriva en hållbar renskötsel. Vi har undersökt renarnas användning av områdena genom att utföra spillningsinventeringar under åren 2009-2015 (endast i Malå sameby), och genom att följa renar utrustade med GPS-halsband under åren 2005-2015. Datat är insamlat före och under byggfas och under driftsfas (för Gabrielsberget finns GPS-data endast för driftsfasen). Vi har analyserat data genom att utveckla statistiska modeller för val av betesområde för varje område där vi har beräknat hur renarna förhåller sig till vindkraftparksområdet före, under och efter byggnation, och på Gabrielsberget när parken varit avstängd under 40 dagar och under drift vid olika renskötselsituationer. Genom intervjuer, möten och samtal, samt information från Gabrielsbergets vindkraftparks kontrollprogram, har vi tagit del av renskötarnas erfarenheter av hur renarnas beteende, och därmed även renskötseln, påverkats av vindkraftsutbyggnaden i respektive område. Våra resultat visar att renarna både på kalvnings- och på vinterbetesområden påverkas negativt av vindkraftsetableringarna (Tabell a). Renarna undviker att beta i områden där de kan se och/eller höra vindkraftsverken och föredrar att vistas i områden där vindkraftverken är skymda. I kalvningsområdet i Malå ökade användningen av skymda områden med 60 % under driftsfas. I vinterbetesområdet på Gabrielsberget, när renarna utfodrades i parken och kantbevakades intensivt för att stanna i parkområdet under driftsfas, ökade användningen av skymda områden med 13 % jämfört med när de inte var utfodrade och fick ströva mer fritt. Resultaten visar också att renarna minskar sin användning av området nära vindkraftparkerna. I kalvningslandet i Malå minskar renarna sin användning av områden inom 5 km från parkerna med 16-20 %. Vintertid vid Gabrielsbergets vindkraftpark undvek renarna parken med 3 km. Våra resultat visar även att renarnas betesro minskar inom en radie på 4 km från vindkraftparkerna under kalvningsperioden och tiden därefter i jämförelse med perioden före byggfas. Exakta avstånd som renarna påverkas beror på förutsättningarna i respektive område, exempelvis hur topografin ser ut eller om området är begränsat av stängsel eller annan infrastruktur. Förändringarna i habitatutnyttjande i våra studieområden blev tydligare när parkerna var centralt belägna i renarnas betesområde, som i kalvningsområdet i Malå eller i vinterbeteslandet på Gabrielsberget, medan det inte var lika tydliga effekter kring Stor-Rotlidens park, som ligger i utkanten av ett huvudbetesområde. Oftast är snöförhållandena bättre ur betessynpunkt högre upp i terrängen än nere i dalgångarna, på grund av stabilare temperatur, vind som blåser bort snötäcket och mer variation i topografin. Därför kan etablering av vindkraftparker i höglänta områden försämra möjligheten att använda sådana viktiga reservbetesområden under vintrar med i övrigt dåliga snöförhållanden, vilka blir allt vanligare i och med klimatförändringarna. Våra resultat tyder inte direkt på att renarna påverkats negativt under dåliga betesvintrar men fler år av studier behövs för att ytterligare klargöra hur vindkraft påverkar renarna under dessa vintrar. Våra studier har visat att etablering av vindkraft har konsekvenser för renskötseln under både barmarkssäsongen och under vintern, men effekterna förmodas få störst inverkan inom vinterbetesområdet där det är svårt att hitta alternativa betesområden för renarna. Under sommaren är betestillgången oftast mindre begränsad och renarna kan lättare hitta alternativa områden. En direkt konsekvens av Gabrielsbergets vindkraftpark som är placerad mitt i ett vinterbetesområde har blivit att renarna behöver tillskottsutfodras och bevakas intensivare för att de inte ska gå ut ur området. När den naturliga vandringen mellan olika betesområden störs för att renarna undviker att vistas i ett område kan det leda till att den totala tillgången till naturligt bete minskar och att man permanent måste tillskottsutfodra, alternativt minska antalet renar. Annan infrastruktur som vägar och kraftledningar påverkar också renarna. Vid Storliden och Jokkmokksliden och vid Stor-Rotliden där data samlats in innan vindkraftparken uppfördes visar våra resultat att renarna undviker de omkringliggande landsvägarna redan innan parkerna etablerades. Vid Stor-Rotliden ökar dock renarna användningen av områden nära vägarna efter att parken är byggd. På Gabrielsberget, där vi endast har data under drifttiden, är renarna närmare vägarna (även stora vägar som E4) när renskötarna minskar på kantbevakningen för att inte hålla renarna nära parken. Detta ökar naturligtvis risken för trafikolyckor och innebär att renskötarna måste bevaka dessa områden intensivare. Sist i rapporten presenterar vi förslag till åtgärder som kan användas för att underlätta arbetet för renskötseln om det är så att en vindkraftpark redan är byggd. Några exempel på åtgärder som är direkt kopplat till parken är att stänga av vägarna in i vindkraftparken för att förhindra nöjeskörning med skoter och bil under den tiden renarna vistas i området samt tät dialog mellan vindkraftsbolag och sameby angående vinterväghållningen av vägarna till och inom vindkraftparken. Andra mer regionala åtgärder för att förbättra förutsättningarna för renskötselarbetet på andra platser för samebyn, kan vara att sätta stängsel längst större vägar och järnvägar (t.ex. E4:an eller stambanan) i kombination med strategiskt utplacerade ekodukter. Detta för att underlätta och återställa möjligheterna till renarnas fria strövning och renskötarnas flytt av renar mellan olika betesområden.   

Simple Method to Evaluate and to Predict Flash Points of Organic Compounds

Flash points (T(FP)) of organic compounds are calculated from their flash point numbers, N(FP), with the relationship T(FP) = 23.369N(FP)(2/3) + 20.010N(FP)(1/3) + 31.901. In turn, the N(FP) values can be predicted from boiling point numbers (Y(BP)) and functional group counts with the equation N(FP) = 0.974Y(BP) + Sigma(i)n(i)G(i) + 0.095 where G(i) is a functional group-specific contribution to the value of N(FP) and n(i) is the number of such functional groups in the structure. For a data set consisting of 1000 diverse organic compounds, the average absolute deviation between reported and predicted flash points was less than 2.5 K.

Patch selection by wintering white-tailed deer : consequences for eastern hemlock regeneration at local and landscape scales

Tsuga canadensis (eastern hemlock) is a highly shade-tolerant, late-successional, and long-lived conifer species found throughout eastern North America. It is most often found in pure or nearly pure stands, because highly acidic and nutrient poor forest floor conditions are thought to favor T. canadensis regeneration while simultaneously limiting the establishment of some hardwood species with greater nutrient requirements. Once a common species, T. canadensis is currently experiencing widescale declines across its range. The hemlock woolly adelgid (Adelges tsugae) is decimating the population across its eastern distribution. Across the Upper Great Lakes region, where the adelgid is currently being held at bay by cold winter temperatures, T. canadensis has been experiencing failures in regeneration attributed, in part, to herbivory by white-tailed deer (Odocoileus virginianus). Deer utilize T. canadensis stands as winter habitat in areas of high snow depth. Tsuga canadensis, once a major component of these forests, currently exists at just a fraction of its pre-settlement abundance due to historic logging and contemporary forest management practices, and what remains is found in small remnant patches surrounded by second- and third-growth deciduous forests. The deer population across the region, however, is likely double that of pre-European settlement times. In this dissertation I explore the relationship between white-tailed deer use of T. canadensis as winter habitat and the effect this use is having on regeneration and forest succession. For this research I quantified stand composition and structure and abiotic variables of elevation and snow depth in 39 randomly selected T. canadensis stands from across the western Upper Peninsula of Michigan. I also quantified composition and the configuration of the landscapes surrounding these stands. I measured relative deer use of T. canadensis stands as pellet group piles deposited in each stand during each of three consecutive winters, 2005-06, 2006-07, and 2007-08. The results of this research suggest that deer use of T. canadensis stands as winter habitat is influenced primarily by snow depth, elevation, and the composition and configuration of the greater landscapes surrounding these stands. Specifically, stands with more heterogeneous landscapes surrounding them (i.e., a patchy mosaic of conifer, deciduous, and open cover) had higher relative deer use than stands surrounded by homogenous deciduous forest cover. Additionally, the intensity of use and the number of stands used was greater in years with higher average snow depth. Tsuga canadensis regeneration in these stands was negatively associated with deer use and Acer saccharum (sugar maple) basal area. Of the 39 stands, 17 and 22 stands had no T. canadensis regeneration in small and large sapling categories, respectively. Acer saccharum was the most common understory tree species, and the importance of A. saccharum in the understory (stems < 10 cm dbh) of the stands was positively associated with overstory A. saccharum dominance. Tsuga canadensis establishment was associated with high-decay coarse woody debris and moss, and deciduous leaf litter inputs in these stands may be limiting access to these important microsites. Furthermore, A. saccharum is more tolerant to the effects of deer herbivory than T. canadensis, giving A. saccharum a competitive advantage in stands being utilized as winter habitat by deer. My research suggests that limited microsite availability, in conjunction with deer herbivory, may be leading to an erosion in T. canadensis patch stability and an altered successional trajectory toward one of A. saccharum dominance, an alternately stable climax species.

Beluga, Delphinapterus leucas, Group Sizes in Cook Inlet, Alaska, Based on Observer Counts and Aerial Video

Belugas, Delphinapterus leucas, groups were videotaped concurrent to observer counts during annual NMFS aerial surveys of Cook Inlet, Alaska, from 1994 to 2000. The videotapes provided permanent records of whale groups that could be examined and compared to group size estimates ade by aerial observers.Examination of the video recordings resulted in 275 counts of 79 whale groups. The McLaren formula was used to account for whales missed while they were underwater (average correction factor 2.03; SD=0.64). A correction for whales missed due to video resolution was developed by using a second, paired video camera that magnified images relative to the standard video. This analysis showed that some whales were missed either because their image size fell below the resolution of hte standard video recording or because two whales surfaced so close to each other that their images appeared to be one large whale. The correction method that resulted depended on knowing the average whale image size in the videotapes. Image sizes were measured for 2,775 whales from 275 different passes over whale groups. Corrected group sizes were calcualted as the product of the original count from video, the correction factor for whales missed underwater, and the correction factor for whales missed due to video resolution (averaged 1.17; SD=0.06). A regression formula was developed to estimate group sizes from aerial observer counts; independent variables were the aerial counts and an interaction term relative to encounter rate (whales per second during the counting of a group), which were regressed against the respective group sizes as calculated from the videotapes. Significant effects of encounter rate, either positive or negative, were found for several observers. This formula was used to estimate group size when video was not available. The estimated group sizes were used in the annual abundance estimates.

Contents of water, sulphur, total organic and inorganic carbon, XRF counts of Ti, S and Ca and radiocarbon ages of sediment core Co1008 from Skua Lake, Rauer Group, East Antarctica

Limited information on the East Antarctic Ice Sheet (EAIS) geometry during Marine Isotope Stage 3 (MIS 3; 60-25 ka) restricts our understanding of its behaviour during periods of climate and sea level change. Ice sheet models forced by global parameters suggest an expanded EAIS compared to the Holocene during MIS 3, but field evidence from East Antarctic coastal areas contradicts such modelling, and suggests that the ice sheet margins were no more advanced than at present. Here we present a new lake sediment record, and cosmogenic exposure results from bedrock, which confirm that Rauer Group (eastern Prydz Bay) was ice-free for much of MIS 3. We also refine the likely duration of the Last Glacial Maximum (LGM) glaciation in the region. Lacustrine and marine sediments from Rauer Group indicate the penultimate period of ice retreat predates 50 ka. The lacustrine record indicates a change from warmer/wetter conditions to cooler/drier conditions after ca. 35 ka. Substantive ice sheet re-advance, however, may not have occurred until much closer to 20 ka. Contemporary coastal areas were still connected to the sea during MIS 3, restricting the possible extent of grounded ice in Prydz Bay on the continental shelf. In contrast, relative sea levels (RSL) deduced from field evidence indicate an extra ice load averaging several hundred metres thicker ice across the Bay between 45 and 32 ka. Thus, ice must either have been thicker immediately inland (with a steeper ice profile), or there were additional ice domes on the shallow banks of the outer continental shelf. Further work is required to reconcile the differences between empirical evidence of past ice sheet histories, and the history predicted by ice sheet models from far-field temperature and sea level records.

Faster group operations on elliptic curves

This paper improves implementation techniques of Elliptic Curve Cryptography. We introduce new formulae and algorithms for the group law on Jacobi quartic, Jacobi intersection, Edwards, and Hessian curves. The proposed formulae and algorithms can save time in suitable point representations. To support our claims, a cost comparison is made with classic scalar multiplication algorithms using previous and current operation counts. Most notably, the best speeds are obtained from Jacobi quartic curves which provide the fastest timings for most scalar multiplication strategies benefiting from the proposed 12M + 5S + 1D point doubling and 7M + 3S + 1D point addition algorithms. Furthermore, the new addition algorithm provides an efficient way to protect against side channel attacks which are based on simple power analysis (SPA). Keywords: Efficient elliptic curve arithmetic,unified addition, side channel attack.

Literacy assessment that counts : mediating, interpreting and contesting translocal policy in a primary school

In Australia, as in many western education systems over the last two decades, discourses of accountability and performativity have reshaped education policy that has in turn reorganised the work of school leaders and teachers. One of the effects of this reorganisation is increased attention to the production, analysis and display of student achievement data. In this paper we examine in detail a sequence of the production and reading of literacy assessment data in a small Catholic school. Our analysis uses institutional ethnography’s concept of the ‘active text’, the text as occurring in a specific place and time even as it is articulated to social relations beyond its immediate context. Through this process we learn from those involved how their everyday work brings into being formalised, textually authorised processes in a local site that ensure the school meets accountability requirements while enabling teachers to resist standardisation of literacy teaching and assessment.

Focusing on what counts: Using exploratory focus groups to enhance the development of an electronic survey in a mixed-methods research design

This paper describes the use of exploratory focus groups to inform the development of a survey instrument in a sequential phase mixed methods study investigating differences in secondary students’ career choice capability. Five focus groups were conducted with 23 year 10 students in the state of New South Wales (NSW), Australia. Analysis of the focus group data informed the design of the instrument for the second phase of the research project: a large-scale cross-sectional survey. In this paper, we discuss the benefits of using sequential phase mixed method approaches when inquiring into complex phenomena such as human capability.

FOXP3+ regulatory T-cell counts correlate with histological response in Crohn's colitis treated with infliximab

Crohn's disease is a chronic inflammatory bowel disease of unknown aetiology. Mucosal inflammatory dysregulation is likely important, with increased production of pro-inflammatory cytokines, including tumour necrosis factor alpha (TNFα). The chimeric monoclonal antibody, infliximab, inhibits TNFα and promotes intestinal mucosal healing. Despite this, many patients still require surgical intervention. Patients who have undergone colonic resection post-infliximab therapy, show markedly variable morphological response to treatment. FOXP3+ CD4+ regulatory T-cells have been shown to have a protective role in autoimmune/inflammatory diseases and their sequestration to the bowel is found in those treated with infliximab. We examined the immunohistochemical profile of lymphoid aggregates in tissue sections from post-infliximab Crohn's colitis resection specimens, classified as morphological responders or non-responders, defined in relation to the absence/presence of mucosal ulceration and active inflammation, and a control group. Results indicated no significant diffences in CD68-positive cell counts but increased FOXP3-positive (P = 0.02) and CD4-positive (P = 0.05) cell counts in responders versus non-responders. Untreated control scores were similar to non-responders. Although based on small study numbers, our results suggest an association between upregulation of FOXP3+/CD4+ regulatory T-cells and morphological response to infliximab therapy. This represents a possible quantitative methodology for monitoring therapeutic response to infliximab therapy, based on immunohistochemical evaluation of endoscopic biopsy specimens.

'Something That Unites Us All': Understandings of St. Patrick's Day Parades as Representing the Irish National Group

The present study investigates how attendees at national celebratory crowd events-specifically St. Patrick's Day parades-understand the role of such events in representing and uniting the national community. We conducted semi-structured interviews with people who attended St. Patrick's Day parades in either Dublin or Belfast. In year 1, full-length interviews were conducted before and after the events (N=17), and in years 1 and 2, shorter interviews were conducted during the events (year 1 N=170; year 2 N=142). Interview data were analysed using thematic analysis, allowing the identification of three broad themes. Participants reported that (i) the events extend the boundary of the national group, using participation to define who counts as Irish; (ii) the events strategically represent the nature of the national group, maximising positive images and managing stereotypical representations; and (iii) symbolism serves to unify the group but can also disrupt already fragile unity and so must be managed. Overall, this points to a strategic identity dimension to these crowd events. We discuss the implications of these findings for future research in terms of the role of large-scale celebratory events in the strategic representation of everyday social identities.