Conservation value, biodiversity value and methods of assessment in regenerating and human disturbed tropical forest

Although the value of primary forests for biodiversity conservation is well known, the potential biodiversity and conservation value of regenerating forests remains controversial. Many factors likely contribute to this, including: 1. the variable ages of regenerating forests being studied (often dominated by relatively young regenerating forests); 2. the potential for confounding on-going human disturbance (such as logging and hunting); 3. the relatively low number of multi-taxa studies; 4. the lack of studies that directly compare different historic disturbances within the same location; 5. contrasting patterns from different survey methodologies and the paucity of knowledge on the impacts across different vertical levels of rainforest biodiversity (often due to a lack of suitable methodologies available to assess them). We also know relatively little as to how biodiversity is affected by major current impacts, such as unmarked rainforest roads, which contribute to this degradation of habitat and fragmentation. This thesis explores the potential biodiversity value of regenerating rainforests under the best of scenarios and seeks to understand more about the impact of current human disturbance to biodiversity; data comes from case studies from the Manu and Sumaco Biosphere Reserves in the Western Amazon. Specifically, I compare overall biodiversity and conservation value of a best case regenerating rainforest site with a selection of well-studied primary forest sites and with predicted species lists for the region; including a focus on species of key conservation concern. I then investigate the biodiversity of the same study site in reference to different types of historic anthropogenic disturbance. Following this I investigate the impacts to biodiversity from an unmarked rainforest road. In order to understand more about the differential effects of habitat disturbance on arboreal diversity I directly assess how patterns of butterfly biodiversity vary between three vertical strata. Although assessments within the canopy have been made for birds, invertebrates and bats, very few studies have successfully targeted arboreal mammals. I therefore investigate the potential of camera traps for inventorying arboreal mammal species in comparison with traditional methodologies. Finally, in order to investigate the possibility that different survey methodologies might identify different biodiversity patterns in habitat disturbance assessments, I investigate whether two different but commonly used survey methodologies used to assess amphibians, indicate the same or different responses of amphibian biodiversity to historic habitat change by people. The regenerating rainforest study site contained high levels of species richness; both in terms of alpha diversity found in nearby primary forest areas (87% ±3.5) and in terms of predicted primary forest diversity from the region (83% ±6.7). This included 89% (39 out of 44) of the species of high conservation concern predicted for the Manu region. Faunal species richness in once completely cleared regenerating forest was on average 13% (±9.8) lower than historically selectively logged forest. The presence of the small unmarked road significantly altered levels of faunal biodiversity for three taxa, up to and potentially beyond 350m into the forest interior. Most notably, the impact on biodiversity extended to at least 32% of the whole reserve area. The assessment of butterflies across strata showed that different vertical zones within the same rainforest responded differently in areas with different historic human disturbance. A comparison between forest regenerating after selective logging and forest regenerating after complete clearance, showed that there was a 17% greater reduction in canopy species richness in the historically cleared forest compared with the terrestrial community. Comparing arboreal camera traps with traditional ground-based techniques suggests that camera traps are an effective tool for inventorying secretive arboreal rainforest mammal communities and detect a higher number of cryptic species. Finally, the two survey methodologies used to assess amphibian communities identified contrasting biodiversity patterns in a human modified rainforest; one indicated biodiversity differences between forests with different human disturbance histories, whereas the other suggested no differences between forest disturbance types. Overall, in this thesis I find that the conservation and biodiversity value of regenerating and human disturbed tropical forest can potentially contribute to rainforest biodiversity conservation, particularly in the best of circumstances. I also highlight the importance of utilising appropriate study methodologies that to investigate these three-dimensional habitats, and contribute to the development of methodologies to do so. However, care should be taken when using different survey methodologies, which can provide contrasting biodiversity patterns in response to human disturbance.

Data of the molecular dynamics simulations of mutations in the human connexin46 docking interface

The structure of hCx26 derived from the X-ray analysis was used to generate a homology model for hCx46. Interacting connexin molecules were used as starting model for the molecular dynamics (MD) simulation using NAMD and allowed us to predict the dynamic behavior of hCx46wt and the cataract related mutant hCx46N188T as well as two artificial mutants hCx46N188Q and hCx46N188D. Within the 50 ns simulation time the docked complex composed of the mutants dissociate while hCx46wt remains stable. The data indicates that one hCx46 molecule forms 5-7 hydrogen bonds (HBs) with the counterpart connexin of the opposing connexon. These HBs appear essential for a stable docking of the connexons as shown by the simulation of an entire gap junction channel and were lost for all the tested mutants. The data described here are related to the research article entitled "The cataract related mutation N188T in human connexin46 (hCx46) revealed a critical role for residue N188 in the docking process of gap junction channels" (Schadzek et al., 2015) [1].

Beyond human and intellectual capital: Profiling the value of knowledge, skills and experience

The concept of human capital is associated mainly with the Nobel Laureate Gary Becker and, in his usage, has a clear conceptual basis as investment in the costs of formal education. By contrast, this paper suggests that ‘intellectual capital’ is a re-branding of knowledge, skills and experience rather than re-conceptualisation of resource based learning. Becker also chose not to include informal knowledge, skills or experience within his concept of human capital, which remains limited by its constrained premises. This paper submits that both human capital and intellectual capital advocates fail to identify or measure the tacit knowledge and implicit learning which increasingly is recognised as a key to the competitive advantage of organisations. It first focuses on the conceptual basis of claims made for human capital and intellectual capital, outlines limits in their methodology, and contrasts these with insights from theories of tacit knowledge and implicit learning and the central role within them of informal or non-formal skill acquisition. It develops and illustrates instances of interfacing tacit and explicit knowledge before introducing a methodology for profiling the acquisition of knowledge, ability and skills. It does so by introducing the concepts of non-formal learningfrom- work (LfW) and informal learning-from-life (LfL), with evidence from a four country EU case study commissioned within the lifelong learning remit of the Lisbon Agenda.

Zika virus damages the human placental barrier and presents marked fetal neurotropism

An unusually high incidence of microcephaly in newborns has recently been observed in Brazil. There is a temporal association between the increase in cases of microcephaly and the Zika virus (ZIKV) epidemic. Viral RNA has been detected in amniotic fluid samples, placental tissues and newborn and fetal brain tissues. However, much remains to be determined concerning the association between ZIKV infection and fetal malformations. In this study, we provide evidence of the transplacental transmission of ZIKV through the detection of viral proteins and viral RNA in placental tissue samples from expectant mothers infected at different stages of gestation. We observed chronic placentitis (TORCH type) with viral protein detection by immunohistochemistry in Hofbauer cells and some histiocytes in the intervillous spaces. We also demonstrated the neurotropism of the virus via the detection of viral proteins in glial cells and in some endothelial cells and the observation of scattered foci of microcalcifications in the brain tissues. Lesions were mainly located in the white matter. ZIKV RNA was also detected in these tissues by real-time-polymerase chain reaction. We believe that these findings will contribute to the body of knowledge of the mechanisms of ZIKV transmission, interactions between the virus and host cells and viral tropism.

The medico-legal importance of establishing human identity by palatal rugoscopy: evaluation of the immutability and individuality of palatal rugae under the influence of ante mortem orthodontic treatment

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Time since urbanization but not encephalisation is associated with increased tolerance of human proximity in birds

The examination of links between a high degree of encephalisation (i.e., a large brain mass relative to body size) and the capacity of wildlife to inhabit anthropogenic habitats has formed the basis of several recent studies, although typically they have not uncovered any relationship. It, however, remains unclear whether encephalisation is directly related to a species' capacity to develop tolerance to human proximity (i.e., a reduction in response to approaching humans). It is also unknown whether such a relationship is related to the size of specific areas of the brain. Using published data on flight-initiation distance (FID), the distance at which animals flee from an approaching human, we estimate the degree of tolerance of human proximity for 42 bird species by comparing FIDs in urban and rural areas, with relatively high and low exposure to humans, respectively. We used a phylogenetic, comparative approach to analyse the relationship of degree of tolerance, and of FID in urban and rural populations more directly, to relative sizes of whole brains (42 species) and brain components (25 species) for the species, and examine the effect of the year that the bird species was first recorded in an urban area (year of urbanization). We demonstrate an interaction between bird habitat and year of urbanization on FIDs. Urban populations of species that have a longer history of inhabiting urban areas have lower FIDs (i.e., birds that were urbanized earlier are more tolerant), which may suggest local selection for birds with reduced responsiveness to humans in urban areas. The pattern is not seen in rural populations of the same species, providing additional evidence that it is greater exposure to humans that has resulted in this tolerance. While we found that forebrain mass and optic lobe mass are influential positive predictors of FID there was no indication that degree of tolerance itself was related to any brain size metric and hence no support for the idea that urban populations of species with larger brains are better able to habituate to human presence. This suggests that processes other than encephalisation explain the high degree of tolerance evident in urban-dwelling birds.

Assisted reproductive technology – IVF treatment in Ireland: A study of couples with successful outcomes

Human Fertility 17(3):165-9 This article describes the experiences of twelve Irish couples who had successful IVF treatment in Ireland. Irish Medical guidelines specify that IVF may only be used when no other treatment is likely to be effective. This article is based on data drawn from a longitudinal research study by Cotter (2009) which tells the stories of 34 couples who sought fertility treatment. Initially, the women assumed that they would become pregnant when they stopped using contraception. As a couple, it was the ‘right time’ for them to have a child - they were ready, socially and financially. For several months they were patient, hoping it would happen naturally. With envy and some despair they watched as their friends had babies. Infertility came as a shock to most of them. They were reluctant to talk about it to anyone, and over time their anxieties were accompanied by feelings of regret, stigma and social exclusion. They finally sought medical treatment. The latter involved a series of diagnostic treatments, which eventually culminated in IVF which offered them a final chance of having a ‘child of their own’. While IVF can be clinically assessed in terms of cycle success rates, their stories showed treatment as a series of discoveries, as an extensive range of diagnostic tests and procedures helped to reveal to them where their problems might lie. They described their treatments as a series of sequential ‘hurdles’ that they had to overcome, which further strengthened their resolve to try IVF. Much more knowledgeable at that stage, they embraced IVF as a final challenge with single minded dedication while drawing on all their psychological and biological resources to promote a successful outcome. Of the 34 couples who took part in the study, twelve got pregnant. Unfortunately, two children died shortly after birth but eighteen babies survived (see Table I). The findings suggest that health policy should raise awareness of infertility, and advise women to become aware of it just as in the past, when health policy addressed contraception. Increased public knowledge would reduce the stigma attached to the inability to have a baby. In the Irish case, infertility diagnosis should be reviewed with a view to giving eligible couples earlier access to IVF.  

Re-imagining the theology of human sexuality in the Methodist Church: the use of narrative in theological methodology

This thesis proposes the development of a narrative methodology in the British Methodist Church. Such a methodology embraces and communicates both felt experience and critical theological thinking, thus producing and presenting a theology that might have a constructive transformative impact on wider society. In chapter one I explore the ways in which the Church speaks in public, identify some of the challenges it faces, and consider four models of engagement. If the Church is to engage in public discourses then I argue that its words need to be relevant and connect with people’s experiences. To ground the thinking I focus on the context of the British Methodist Church and explore how the Church engages in theological reflection through the lens of its thinking on issues of human sexuality. Chapter two reviews how theological reflection is undertaken in the British Methodist Church. I describe how the Methodist Quadrilateral of Scripture, tradition, reason and experience remains a foundational framework for theological reflection within the Methodist Church and consider the impact of institutional processes and the ways in which the Methodist people actually engage with theological thinking. The third and fourth chapters focus on how the British Methodist Church has produced its theology of human sexuality, giving particular attention to the use of personal and sexual stories in this process. I find that whilst there has been a desire to listen to the stories of the Methodist people, there has not been a corresponding interrogation or analysis of their stories so as to enable robust and constructive theological reflection on these experiences. Using resources from Foucauldian approaches to discourse analysis, I critique key statements and the processes involved in their production, offering an analysis of this body of theological thinking and indicating where possibilities for alternative ways of thinking and acting arise. The proposed methodology draws upon resources from social science methodologies, and in chapter five I look at the use of personal experience and relevant strategies of inquiry that prompt reflection on the hermeneutical process and employ narrative approaches in undertaking, analysing and presenting research. The exploration shows that qualitative research methodologies offer resources and methods of inquiry that could help the Church to engage with personal stories in its theological thinking in a robust, interrogative and imaginative way. In chapter six an examination of story and narrative is undertaken, to show how they have been understood as ways of knowing and how they relate to theological inquiry. Whilst acknowledging some of the limitations of narrative, I indicate how it offers constructive possibilities for theological reflection and could be a means for the British Methodist Church to engage in public discourse. This is explored further in chapter seven, which looks in more detail at how the British Methodist Church has used narrative in its theological thinking, and outlines areas requiring further attention in order for a narrative theological methodology to be developed, namely: attention to the question ‘whose experience?’; investigation of issues of power and the dynamics involved in the process of the production of theological thought; how personal stories and experiences are interrogated and how narrative is constructed; and how narrative might be employed within the Methodist Quadrilateral. The final chapter considers the advantages and limitations of such an approach, whether the development of such a method is possible in the Methodist Church today and its potential for helping the Church to engage in public discourse more effectively. I argue that this methodology can provoke new theological insights and enable new ways of being in the world

The Expanded Human Kallikrein (KLK) gene family : genomic organisation, tissue specific expression and potential functions

The tissue kallikreins are serine proteases encoded by highly conserved multigene families. The rodent kallikrein (KLK) families are particularly large, consisting of 13 26 genes clustered in one chromosomal locus. It has been recently recognised that the human KLK gene family is of a similar size (15 genes) with the identification of another 12 related genes (KLK4-KLK15) within and adjacent to the original human KLK locus (KLK1-3) on chromosome 19q13.4. The structural organisation and size of these new genes is similar to that of other KLK genes except for additional exons encoding 5 or 3 untranslated regions. Moreover, many of these genes have multiple mRNA transcripts, a trait not observed with rodent genes. Unlike all other kallikreins, the KLK4-KLK15 encoded proteases are less related (25–44%) and do not contain a conventional kallikrein loop. Clusters of genes exhibit high prostatic (KLK2-4, KLK15) or pancreatic (KLK6-13) expression, suggesting evolutionary conservation of elements conferring tissue specificity. These genes are also expressed, to varying degrees, in a wider range of tissues suggesting a functional involvement of these newer human kallikrein proteases in a diverse range of physiological processes.