Numerical simulation of post-flame oxidation of hydrocarbons in spark ignition engines

About 50-90 percent of the hydrocarbons that escape combustion during flame passage in spark-ignition engine operation are oxidized in the cylinder before leaving the system. The process involves the transport of unreacted fuel from cold walls towards the hotter burned gas regions and subsequent reaction. In order to understand controlling factors in the process, a transient one-dimensional reactive-diffusive model has been formulated for simulating the oxidation processes taking place in the reactive layer between hot burned gases and cold unreacted air/fuel mixture, with initial and boundary conditions provided by the emergence of hydrocarbons from the piston top land crevice. Energy and species conservation equations are solved for the entire process, using a detailed chemical kinetic mechanism for propane. Simulation results show that the post-flame oxidation process takes place within a reactive layer where intermediate hydrocarbon products are formed at temperatures above 1100-1200 K, followed by a carbon monoxide conversion region closer to the hot burned gases. Model results show that most of hydrocarbons leaving the crevice are completely oxidized inside the cylinder. The largest contribution of remaining hydrocarbons are those leaving the crevice at temperatures below 1400 K. The largest fraction of non-fuel (intermediate) hydrocarbons results from hydrocarbons leaving the crevice when core temperatures are around 1400 K Copyright © 1997 Society of Automotive Engineers, Inc.

Use of "entertainment" chimpanzees in commercials distorts public perception regarding their conservation status.

Chimpanzees (Pan troglodytes) are often used in movies, commercials and print advertisements with the intention of eliciting a humorous response from audiences. The portrayal of chimpanzees in unnatural, human-like situations may have a negative effect on the public's understanding of their endangered status in the wild while making them appear as suitable pets. Alternatively, media content that elicits a positive emotional response toward chimpanzees may increase the public's commitment to chimpanzee conservation. To test these competing hypotheses, participants (n = 165) watched a series of commercials in an experiment framed as a marketing study. Imbedded within the same series of commercials was one of three chimpanzee videos. Participants either watched 1) a chimpanzee conservation commercial, 2) commercials containing "entertainment" chimpanzees or 3) control footage of the natural behavior of wild chimpanzees. Results from a post-viewing questionnaire reveal that participants who watched the conservation message understood that chimpanzees were endangered and unsuitable as pets at higher levels than those viewing the control footage. Meanwhile participants watching commercials with entertainment chimpanzees showed a decrease in understanding relative to those watching the control footage. In addition, when participants were given the opportunity to donate part of their earnings from the experiment to a conservation charity, donations were least frequent in the group watching commercials with entertainment chimpanzees. Control questions show that participants did not detect the purpose of the study. These results firmly support the hypothesis that use of entertainment chimpanzees in the popular media negatively distorts the public's perception and hinders chimpanzee conservation efforts.

Place and Special Places: Innovations in Conservation Practice in Northern Ireland

The sense of place that relates human beings to their environment is under threat from the rising tide of placelessness which can result from potentially positive forces such as urban regeneration as well as negative ones such as incremental degradation. The concept of sense of place, and the need to protect and enhance special places, has underpinned UK conservation legislation and policy in the post-war era. In Northern Ireland, due to its distinctive settlement tradition, its troubled political circumstances and its centralised administrative system, a unique hierarchy of special places has evolved, involving areas of townscape and village character as well as conventional conservation areas. For the first time a comprehensive comparative survey of the townscape quality of most of these areas has been carried out in order to test the hypothesis that too many conservation area designations may devalue the conservation coinage. It also assesses the contribution that areas of townscape character can make in this situation, as potential conservation areas or as second-level local amenity designations. Its findings support the initial hypothesis: assessment of townscape quality on the basis of consistent criteria demonstrates a decline in the quality of more recent conservation area designations, and hence some devaluation of the coinage. However, the need for local discretion in the protection of local amenity supports the concept of areas of townscape and village character as an additional and distinct designation. This contradicts recent policy recommendations from the Northern Ireland Planning Commission and contains valuable lessons for conservation policy and practice in other parts of the UK.

Phylogeographic structure of brown trout (Salmo trutta) in Britain and Ireland: glacial refugia, post-glacial colonisation, and origins of sympatric populations

The phylogeographical structure of brown trout Salmo trutta in Britain and Ireland was studied using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of four mitochondrial DNA segments (16S/ND1, ND5/6, COXIII/ND5 and ND5/12S). Analysis of 3636 individuals from 83 sites-morphotypes revealed a total of 25 haplotypes. These haplotypes were nested in seven two-step clades. Although there was a clear geographical patterning to the occurrence of derived clades, admixture among ancestral clades was extensive throughout the studied area. A relevant feature of the data was that some populations contained mixtures of highly divergent clades. This type II phylogeographic pattern is uncommon in nature. Clade intermixing is likely to have taken place during earlier interglacials as well as since the Last Glacial Maximum. The anadromous life history of many S. trutta populations has probably also contributed to clade mixing. Based on the data presented here and published data, postglacial colonization of Britain and Ireland most likely involved S. trutta from at least five potential glacial refuges. Probable locations for such refugia were: south of England-western France, east of the Baltic Sea, western Ireland, Celtic Sea and North Sea. Ferox S. trutta, as defined by their longevity, late maturation and piscivory, exhibited a strong association with a particular clade indicating that they share a common ancestor. Current evidence indicates that the Lough Melvin gillaroo S. trutta and sonaghen S. trutta sympatric types diverged prior to colonization of Lough Melvin and, although limited gene flow has occurred since secondary contact, they have remained largely reproductively isolated due to inlet and outlet river spawning segregation. Gillaroo S. trutta may reflect descendents of a previously more widespread lineage that has declined due to habitat alterations particularly affecting outlet rivers. The mosaic-like distribution of mtDNA lineages means that conservation prioritization in Britain and Ireland should be based on the biological characteristics of local populations rather than solely on evolutionary lineages.

Post-release GPS tracking of hand-reared Irish hare Lepus timidus hibernicus leverets, Slemish, Co. Antrim, Northern Ireland.

Animal rescue centres release large numbers of captive-bred, rehabilitated or translocated animals into the wild annually but little is known about their post-release survival and behaviour. We developed a novel and innovative coupling of traditional radio-tags with new GPS loggers to track hand-reared Irish hare Lepus timidus hibernicus leverets after release into the wild. Cyanoacrylate SuperGlue® proved a poor fixative with two out of three leverets managing to detach their tags within 24 hours. Nevertheless, a total of 2,505 GPS locations were recorded every 60 seconds for one leveret over three nights (approx. 835 per night). The leveret dispersed

Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size ('size shifts'), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.

Origin of British and Irish mammals: disparate post-glacial colonisation and species introductions

Global climate changes during the Quaternary reveal much about broader evolutionary effects of environmental change. Detailed regional studies reveal how evolutionary lineages and novel communities and ecosystems, emerge through glacial bottlenecks or from refugia. There have been significant advances in benthic imaging and dating, particularly with respect to the movements of the British (Scottish) and Irish ice sheets and associated changes in sea level during and after the Last Glacial Maximum (LGM). Ireland has been isolated as an island for approximately twice as long as Britain with no evidence of any substantial, enduring land bridge between these islands after ca 15 kya. Recent biogeographical studies show that Britain's mammal community is akin to those of southern parts of Scandinavia, The Netherlands and Belgium, but the much lower mammal species richness of Ireland is unique and needs explanation. Here, we consider physiographic, archaeological, phylogeographical i.e. molecular genetic, and biological evidence comprising ecological, behavioural and morphological data, to review how mammal species recolonized western Europe after the LGM with emphasis on Britain and, in particular, Ireland. We focus on why these close neighbours had such different mammal fauna in the early Holocene, the stability of ecosystems after LGM subject to climate change and later species introductions.

There is general concordance of archaeological and molecular genetic evidence where data allow some insight into history after the LGM. Phylogeography reveals the process of recolonization, e.g. with respect to source of colonizers and anthropogenic influence, whilst archaeological data reveal timing more precisely through carbon dating and stratigraphy. More representative samples and improved calibration of the ‘molecular clock’ will lead to further insights with regards to the influence of successive glaciations. Species showing greatest morphological, behavioural and ecological divergence in Ireland in comparison to Britain and continental Europe, were also those which arrived in Ireland very early in the Holocene either with or without the assistance of people. Cold tolerant mammal species recolonized quickly after LGM but disappeared, potentially as a result of a short period of rapid warming. Other early arrivals were less cold tolerant and succumbed to the colder conditions during the Younger Dryas or shortly after the start of the Holocene (11.5 kya), or the area of suitable habitat was insufficient to sustain a viable population especially in larger species. Late Pleistocene mammals in Ireland were restricted to those able to colonize up to ca 15 kya, probably originating from adjacent areas of unglaciated Britain and land now below sea level, to the south and west (of Ireland). These few, early colonizers retain genetic diversity which dates from before the LGM. Late Pleistocene Ireland, therefore, had a much depleted complement of mammal species in comparison to Britain.

Mammal species, colonising predominantly from southeast and east Europe occupied west Europe only as far as Britain between ca 15 and 8 kya, were excluded from Ireland by the Irish and Celtic Seas. Smaller species in particular failed to colonise Ireland. Britain being isolated as an island from ca. 8 kya has similar species richness and composition to adjacent lowland areas of northwest continental Europe and its mammals almost all show strongest genetic affinity to populations in neighbouring continental Europe with a few retaining genotypes associated with earlier, western lineages.

The role of people in the deliberate introduction of mammal species and distinct genotypes is much more significant with regards to Ireland than Britain reflecting the larger species richness of the latter and its more enduring land link with continental Europe. The prime motivation of early people in moving mammals was likely to be resource driven but also potentially cultural; as elsewhere, people exploring uninhabited places introduced species for food and the materials they required to survive. It is possible that the process of introduction of mammals to Ireland commenced during the Mesolithic and accelerated with Neolithic people. Irish populations of these long established, introduced species show some unique genetic variation whilst retaining traces of their origins principally from Britain but in some cases, Scandinavia and Iberia. It is of particular interest that they may retain genetic forms now absent from their source populations. Further species introductions, during the Bronze and late Iron Ages, and Viking and Norman invasions, follow the same pattern but lack the time for genetic divergence from their source populations. Accidental introductions of commensal species show considerable genetic diversity based on numerous translocations along the eastern Atlantic coastline. More recent accidental and deliberate introductions are characterised by a lack of genetic diversity other than that explicable by more than one introduction.

The substantial advances in understanding the postglacial origins and genetic diversity of British and Irish mammals, the role of early people in species translocations, and determination of species that are more recently introduced, should inform policy decisions with regards to species and genetic conservation. Conservation should prioritise early, naturally recolonizing species and those brought in by early people reflecting their long association with these islands. These early arrivals in Britain and Ireland and associated islands show genetic diversity that may be of value in mitigating anthropogenic climate change across Europe. In contrast, more recent introductions are likely to disturb ecosystems greatly, lead to loss of diversity and should be controlled. This challenge is more severe in Ireland where the number and proportion of invasive species from the 19th century to the present has been greater than in Britain.

Recreational shore fishing in southern Portugal: biological and socio-economic aspects and perspectives for management

Although overfishing is a concern for many fish stocks, it was for a long time only associated with commercial fishing exploitation, with less or no attention being given to the recreational fisheries. Recent research has shown however that the impact of recreational fishing on particular species can be considerable, and that the recreational harvest needs to be taken into account if fisheries are to be accurately assessed and effectively managed. In Portugal, the first recreational fishing regulations were only recently implemented. However, mirroring other European countries, regulations lacked scientific support, and specific knowledge of the activity was limited to a few studies with limited coverage. This thesis aimed to characterize the biological and socioeconomic aspects of the recreational shore angling activity in southern Portugal, to investigate whether the regulations in place were adequate and effective, and to provide recommendations for improved management and conservation of the inshore fisheries resources. A combined aerial-roving survey was conducted to gather data on fishing effort, catch, fishing trips and socioeconomic aspects (including anglers’ perceptions of regulations) of the recreational angling activity. The analysis of anglers’ catches suggested that compliance with daily bag limits was high, with less than 0.5% of creels exceeding the 10 kg angler-1 day-1 bag limit. Overall, 11.5% of the retained fishes were undersized, but non-compliance with minimum size limits was found to be high for some species (e.g. seabass, 73% undersized). In terms of the impact of recreational shore angling, the total estimated catches corresponded to less than 1% of the commercial landings for the same period (shared species). However, shore angling catches for white sea bream (Diplodus sargus) were found to be considerable, corresponding to 65% of the commercial landings (39.4% of total catch). In terms of anglers’ perceptions about the recreational fishing regulations in Portugal, the present study has shown that the majority of anglers accepted the existence of some kind of SRF regulations, but in general there was a partial or total disagreement with the recreational fishing restrictions recently put in place. Most anglers perceived themselves as not being involved in the decision-making process and claimed that some restrictions lacked a meaningful rationale (e.g. prohibition of fishing from piers/jetties). Fishers’ awareness with regard to specific aspects of the restrictions (such as the rationale for minimum size limits) was found to be very limited. During the same period, catches from sport fishing competitions were examined to test for differences with the recreational activity in terms of catches, and evaluate long term trends in catch and mean size of fish. Catches of the sport fishing competitions were found to be different from those observed for recreational fishing, being dominated by different species (e.g. garfish, mullets), and suggesting different fishing strategies of the the two types of anglers. High percentages of undersized fish were observed to be captured (and retained) during the competitions (in particular seabass, with 100% undersized), probably as a result of a single allowable minimum size (AMS) of 15 cm for all species in use in competitions. Lastly, catch and release fishing experiments were carried out to assess post-release mortality of three recreationally important species: two banded sea bream Diplodus vulgaris; black sea bream Spondyliosoma cantharus; and gilthead sea bream Sparus aurata. Post-release mortalities were found to be low (0-12%). The main predictor of mortality for Sparus aurata was anatomical hooking location, with 63% of the fishes that died being deeply hooked. The results support the release of fish, either from mandatory (e.g. minimum landing sizes) or voluntary practices. In summary, this thesis has demonstrated that the impact of recreational fishing for particular species is significant and needs to be taken into account for more effective management and stock assessment purposes. It has also highlighted several management issues that should be addressed in order to promote more adequate regulations in the future and prevent noncompliance issues. A periodic monitoring of the recreational fishing activity including all fishing modes (i.e. spear fishing, boat, and shore angling) would also be beneficial to ensure a timely knowledge on the global recreational fishing activity and support future management actions.

Biochemistry of grape berries: post-genomics approaches to uncover the effects of water deficits on ripening

Dissertation presented to obtain the Ph.D degree in Biochemistry, Plant Physiology

L'efecte de la gestió forestal post-incendi sobre l'avifauna i la dispersió de llavors per ocells frugívors

The objective of this thesis is to analyze the effect of the transformation in the habitat that postfire salvage logging supposes on birds in Mediterranean pine forests, at different levels: species, community and ecosystem, focusing on the bird-mediated seed dispersal process. Salvage logging with commercial purposes is the main factor that determines the species composition after a fire, with the substitution of forest birds by open-habitat species, some of which hold an unfavourable conservation status in Europe. On the other hand, wood debris piles built by non-profitable burnt wood favour the presence of seed disperser frugivorous birds, and these structures show more seed dispersal than other microhabitats, and a higher abundance of bird-dispersed plants, so that it is recommendable to build them in managed burned forests.

Post-abscission, pre-dispersal seeds of Digitalis purpurea remain in a developmental state that is not terminated by desiccation ex planta

Seed quality may be compromised if seeds are harvested before natural dispersal (shedding). It has been shown previously that slow or delayed drying can increase potential quality compared with immediate rapid drying. This study set out to investigate whether or not there is a critical moisture content, below which drying terminates maturation events for seeds harvested after mass maturity but before dispersal. Seeds of foxglove (Digitalis purpurea) in the post-abscission pre-dispersal phase were held at between 15 and 95 % RH for 4 or 8 d, with or without re-hydration to 95 % RH for a further 4 d, before drying to equilibrium at 15 % RH. In addition, dry seeds were primed for 48 h at -1 MPa. Subsequent seed longevity was assessed at 60 % RH and 45 degrees C. Rate of germination and longevity were improved by holding seeds at a wide range of humidities after harvest. Longevity was further improved by re-hydration at 95 % RH. Priming improved the longevity of the seeds dried immediately after harvest, but not of those first held at 95 % RH for 8 d prior to drying. Maturation continued ex planta in these post-abscission, pre-dispersal seeds of D. purpurea dried at 15-80 % RH at a rate correlated positively with RH (cf. ageing of mature seeds). Subsequent re-hydration at 95 % RH enabled a further improvement in quality. Priming seeds initially stored air-dry for 3 months also allowed maturation events to resume. However, once individual seeds within the population had reached maximum longevity, priming had a negative impact on their subsequent survival.

Drying method influences the development of germinability, dessication tolerance and subsequent longevity of immature seeds of sumauma (Ceiba pentandra (L.) Gaertn. [Bombacaceae])

The ability to germinate, tolerate desiccation and survive in air-dry storage was investigated during early seed development in planta and subsequent ex planta maturation of sumauma (Ceiba pentandra). Immature fruits were collected on three different dates (i.e. from about 5 days before until 7 days after mass maturity). Immature fresh seeds were not able to germinate. Fruits or seeds were subjected immediately after each collection to three different drying treatments with progressively slower rates of dessication: (i) seeds were extracted from the fruits and dried immediately; (ii) fruits were dried in a thin layer; (iii) fruits were dried in a tied polyethylene bag (with 10 holes of 1cm diameter). Drying was in a room maintained at 25 degrees C +/- 3 degrees C and 65%+/- 5% r.h. For treatment (i) the seeds were dried for 6 days in order to reduce moisture content to around 13% ( +/- 2%) moisture content. For treatments (ii) and (iii) the fruits were subjected to different periods of drying depending upon collection date. The results of these post-collection treatments showed generally that the more immature the seeds the slower the rate of drying that is required to improve ability to germinate, ability to tolerate desiccation and potential longevity, but at the third harvest, 7 days after mass maturity, the intermediate drying rate treatment was the most beneficial. Thus post fruit collection treatments can be modified depending upon the stage of seed development in order to provide good to high quality seeds of sumauma when collection has to be made at a site with difficult access at less than ideal times. The results are relevant to seed collection practices for both forestry and ex situ plant biodiversity conservation.

Post-dispersal seed predation of non-target weeds in arable crops

Field experiments were conducted to quantify the natural levels of post-dispersal seed predation of arable weed species in spring barley and to identify the main groups of seed predators. Four arable weed species were investigated that were of high biodiversity value, yet of low to moderate competitive ability with the crop. These were Chenopodium album, Sinapis arvensis, Stellaria media and Polygonum aviculare. Exclusion treatments were used to allow selective access to dishes of seeds by different predator groups. Seed predation was highest early in the season, followed by a gradual decline in predation over the summer for all species. All species were taken by invertebrates. The activity of two phytophagous carabid genera showed significant correlations with seed predation levels. However, in general carabid activity was not related to seed predation and this is discussed in terms of the mainly polyphagous nature of many Carabid species that utilized the seed resource early in the season, but then switched to carnivory as prey populations increased. The potential relevance of post-dispersal seed predation to the development of weed management systems that maximize biological control through conservation and optimize herbicide use, is discussed.

Post-dispersal seed predation of non-target weeds in arable crops

Field experiments were conducted to quantify the natural levels of post-dispersal seed predation of arable weed species in spring barley and to identify the main groups of seed predators. Four arable weed species were investigated that were of high biodiversity value, yet of low to moderate competitive ability with the crop. These were Chenopodium album, Sinapis arvensis, Stellaria media and Polygonum aviculare. Exclusion treatments were used to allow selective access to dishes of seeds by different predator groups. Seed predation was highest early in the season, followed by a gradual decline in predation over the summer for all species. All species were taken by invertebrates. The activity of two phytophagous carabid genera showed significant correlations with seed predation levels. However, in general carabid activity was not related to seed predation and this is discussed in terms of the mainly polyphagous nature of many Carabid species that utilized the seed resource early in the season, but then switched to carnivory as prey populations increased. The potential relevance of post-dispersal seed predation to the development of weed management systems that maximize biological control through conservation and optimize herbicide use, is discussed.

Analysis of wave phenomena in a morphogenetic mechanochemical model and an application to post-fertilization waves on eggs

Wave solutions to a mechanochemical model for cytoskeletal activity are studied and the results applied to the waves of chemical and mechanical activity that sweep over an egg shortly after fertilization. The model takes into account the calcium-controlled presence of actively contractile units in the cytoplasm, and consists of a viscoelastic force equilibrium equation and a conservation equation for calcium. Using piecewise linear caricatures, we obtain analytic solutions for travelling waves on a strip and demonstrate uiat the full nonlinear system behaves as predicted by the analytic solutions. The equations are solved on a sphere and the numerical results are similar to the analytic solutions. We indicate how the speed of the waves can be used as a diagnostic tool with which the chemical reactivity of the egg surface can be measured.