Folkbiology doesn’t come from Folkpsychology: evidence from Yukatek Maya in cross-cultural perspective

Nearly all psychological research on basic cognitive processes of category formation and reasoning uses sample populations associated with large research institutions in technologically-advanced societies. Lopsided attention to a select participant pool risks biasing interpretation, no matter how large the sample or how statistically reliable the results. The experiments in this article address this limitation. Earlier research with urban-USA children suggests that biological concepts are (1) thoroughly enmeshed with their notions of naive psychology, and (2) strikingly human-centered. Thus, if children are to develop a causally appropriate model of biology, in which humans are seen as simply one animal among many, they must undergo fundamental conceptual change. Such change supposedly occurs between 7 and 10 years of age, when the human-centered view is discarded. The experiments reported here with Yukatek Maya speakers challenge the empirical generality and theoretical importance of these claims. Part 1 shows that young Maya children do not anthropocentrically interpret the biological world. The anthropocentric bias of American children appears to owe to a lack of cultural familiarity with non-human biological kinds, not to initial causal understanding of folkbiology as such. Part 2 shows that by age of 4-5 (the earliest age tested in this regard) Yukatek Maya children employ a concept of innate species potential or underlying essence much as urban American children seem to, namely, as an inferential framework for understanding the affiliation of an organism to a biological species, and for projecting known and unknown biological properties to organisms in the face of uncertainty. Together, these experiments indicate that folkpsychology cannot be the initial source of folkbiology. They also underscore the possibility of a species-wide and domain-specific basis for acquiring knowledge about the living world that is constrained and modified but not caused or created by prior nonbiological thinking and subsequent cultural experience.

Animal maiming, intimacy and the politics of shared life: the bestial and the beastly in eighteenth- and early nineteenth-century England

The everyday lives of many farm workers in eighteenth- and early nineteenth-century England were intricately and often intimately bound with the lives of animals, the ebb and flow of human life being inseparable from that of animal life. Farmyards, fields, folds as well as barns and stables were all spaces where animals transcended being the mere instruments of capital to instead being obvious co-constituents of the rhythms of existence. Living and working in such close proximity meant that the ‘species barrier’ was crossed and intimacies developed in everyday agricultural practices. Still, the relationship was based upon, if not reducible to, the workings of capital: the animal enrolled as a form of embodied capital, the labourer engaged by the farmer to act upon the animal. And in such relationships intimacies are mirrored by violences: the keeping captive, slaughter, and – occasionally – abuse. In this formative period in which the discourses and policies that continue to inform animal welfare were first formulated, the declining economic and material fortunes of farm workers when juxtaposed to farm animals’ fortune as increasingly ‘cosseted capital’ gave a particular charge to these abuses. Farm animals, and especially horses and cattle, so it is shown, were subjected to a series of violences. Many cases of animal maiming parodied tenderness in their brutality, whilst other attacks on the sexual organs of animals represented complex statements about the ways in which agrarian capitalism regulated all culture. Analysing the changing relationship between humans and animals therefore also helps us to better understand how capitalism mediates – and is mediated by – the non-human as well as the human, and how it defines cultural relations.

Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis

We genotyped 2,861 cases of primary biliary cirrhosis (PBC) from the UK PBC Consortium and 8,514 UK population controls across 196,524 variants within 186 known autoimmune risk loci. We identified 3 loci newly associated with PBC (at P <5 × 10(-8)), increasing the number of known susceptibility loci to 25. The most associated variant at 19p12 is a low-frequency nonsynonymous SNP in TYK2, further implicating JAK-STAT and cytokine signaling in disease pathogenesis. An additional five loci contained nonsynonymous variants in high linkage disequilibrium (LD; r(2) > 0.8) with the most associated variant at the locus. We found multiple independent common, low-frequency and rare variant association signals at five loci. Of the 26 independent non-human leukocyte antigen (HLA) signals tagged on the Immunochip, 15 have SNPs in B-lymphoblastoid open chromatin regions in high LD (r(2) > 0.8) with the most associated variant. This study shows how data from dense fine-mapping arrays coupled with functional genomic data can be used to identify candidate causal variants for functional follow-up.

Measles immune suppression:lessons from the Macaque Model

Measles remains a significant childhood disease, and is associated with a transient immune suppression. Paradoxically, measles virus (MV) infection also induces robust MV-specific immune responses. Current hypotheses for the mechanism underlying measles immune suppression focus on functional impairment of lymphocytes or antigen-presenting cells, caused by infection with or exposure to MV. We have generated stable recombinant MVs that express enhanced green fluorescent protein, and remain virulent in non-human primates. By performing a comprehensive study of virological, immunological, hematological and histopathological observations made in animals euthanized at different time points after MV infection, we developed a model explaining measles immune suppression which fits with the "measles paradox". Here we show that MV preferentially infects CD45RA - memory T-lymphocytes and follicular B-lymphocytes, resulting in high infection levels in these populations. After the peak of viremia MV-infected lymphocytes were cleared within days, followed by immune activation and lymph node enlargement. During this period tuberculin-specific T-lymphocyte responses disappeared, whilst strong MV-specific T-lymphocyte responses emerged. Histopathological analysis of lymphoid tissues showed lymphocyte depletion in the B- and T-cell areas in the absence of apoptotic cells, paralleled by infiltration of T-lymphocytes into B-cell follicles and reappearance of proliferating cells. Our findings indicate an immune-mediated clearance of MV-infected CD45RA - memory T-lymphocytes and follicular B-lymphocytes, which causes temporary immunological amnesia. The rapid oligoclonal expansion of MV-specific lymphocytes and bystander cells masks this depletion, explaining the short duration of measles lymphopenia yet long duration of immune suppression. © 2012 de Vries et al.

Defining the molecular basis for the first potent and selective orthosteric agonists of the FFA2 free fatty acid receptor

FFA2 is a G protein-coupled receptor that responds to short chain fatty acids (SCFAs) and has generated interest as a therapeutic target for metabolic and inflammatory conditions. However, definition of its functions has been slowed by a dearth of selective ligands that can distinguish it from the closely related FFA3. At present, the only selective ligands described for FFA2 suffer from either poor potency, altered signaling due to allosteric modes of action, or a lack of function at non-human orthologs of the receptor. To address the need for novel selective ligands, we synthesized two compounds potentially having FFA2 activity and examined the molecular basis of their function. These compounds were confirmed to be potent and selective FFA2 agonists that interact with the orthosteric binding site. A combination of ligand structure-activity relationship, pharmacological analysis, homology modeling, species ortholog comparisons and mutagenesis studies were then employed to define the molecular basis of selectivity and function of these ligands. From this, we identified key residues within both extracellular loop 2 (ECL2) and the transmembrane domain (TM) regions of FFA2 critical for ligand function. One of these ligands was active with reasonable potency at rodent orthologs of FFA2 and demonstrated the role of FFA2 in the regulation of lipolysis in murine 3T3-L1 adipocytes. Together, these findings describe the first potent and selective FFA2 orthosteric agonists and demonstrate key aspects of ligand interaction within the orthosteric binding site of FFA2 that will be invaluable in future ligand development at this receptor.

Morphometric analysis of corneal endothelial giant cells in normal and traumatized corneas

Corneal endothelial cells from normal and traumatized human, primate, cat and rabbit eyes were studied by specular microscopy. Morphometric analysis was performed on micrographs of corneal endothelium using a semi-automated image analysis system. The results showed that under normal conditions the corneal endothelium of all four species exhibit major morphological similarities (mean cell areas: human 317 +/- 32 microns 2, primate 246 +/- 22 microns2, cat 357 +/- 25 microns 2, rabbit 308 +/- 35 microns 2). The normal corneal endothelium in man was found to be more polymegethous than that of the other species. Trauma to cat, primate and human corneas resulted in a long-term reduction in endothelial cell density and enhanced polymegethism. In contrast, the reparative response of the rabbit ensured the reformation of an essentially normal monolayer following injury. Endothelial giant cells were a normal inclusion in the rabbit corneal endothelium but were only significant in cat, primate and man following trauma. The presence of corneal endothelial giant cells in amitotic corneas may therefore represent a compensatory response in the absence of mitotic potential.

Invention and uninvention in nuclear weapons politics

If there is one uncontroversial point in nuclear weapons politics it is that uninventing nuclear weapons is impossible. This article seeks to make this claim controversial by showing that it is premised on attenuated understandings of invention and the status of objects operative through familiar but problematic conceptual dualisms. The claimed impossibility of uninvention is an assertion that invention is irreversible. Drawing on “new materialism” this article produces a different understanding of invention, reinvention, and uninvention as ontologically similar practices of techno-political invention. On the basis of empirical material on the invention and re-invention of nuclear weapons, and an in-depth ethnography of laboratories inventing a portable radiation detector, both the process of invention and the “objects” themselves (weapons and detectors) are shown to be fragile and not wholly irreversible processes of assembling diverse actors (human and non-human) and provisionally stabilizing their relations. Nuclear weapons cannot be uninvented! Why not?

Does subjective rating reflect behavioural coding? Personality in 2 month-old dog puppies: An open-field test and adjective-based questionnaire

A number of studies have recently investigated personality traits in non-human species, with the dog gaining popularity as a subject species for research in this area. Recent research has shown the consistency of personality traits across both context and time for adult dogs, both when using questionnaire based methods of investigation and behavioural analyses of the dogs' behaviour. However, only a few studies have assessed the correspondence between these two methods, with results varying considerably across studies. Furthermore, most studies have focused on adult dogs, despite the fact that an understanding of personality traits in young puppies may be important for research focusing on the genetic basis of personality traits. In the current study, we sought to evaluate the correspondence between a questionnaire based method and the in depth analyses of the behaviour of 2-month old puppies in an open-field test in which a number of both social and non-social stimuli were presented to the subjects. We further evaluated consistency of traits over time by re-testing a subset of puppies. The correspondence between methods was high and test-retest consistency (for the main trait) was also good using both evaluation methods. Results showed clear factors referring to the two main personality traits 'extroversion,' (i.e. the enthusiastic, exuberant approach to the stimuli) and 'neuroticism,' (i.e. the more cautious and fearful approach to the stimuli), potentially similar to the shyness-boldness dimension found in previous studies. Furthermore, both methods identified an 'amicability' dimension, expressing the positive interactions the pups directed at the humans stranger, and a 'reservedness' dimension which identified pups who largely chose not to interact with the stimuli, and were defined as quiet and not nosey in the questionnaire.

Killing animals: sociology, species relations and institutionalized violence

Influential voices have argued for a sociology which acknowledges the way we are co-constituted with a range of non-human species as part of the condition of life on this planet. Despite this, sociology has generally retained a conception of the social that is centred on the human. This paper argues for the inclusion of non-human animals in sociological agendas, focusing on the emerging field of the sociology of violence. It examines the institutions and processes through which non-human animals are subjected to different forms of violence, most notably, mass killing.The practice of killing animals is routine,normative,institutionalized and globalized.The scale of killing is historically unprecedented and the numbers killed are enormous. The paper argues that this killing of non-humans raises questions around inequal- ities and intersectionality, human relations with other species, the embedding of violence in everyday practices and links between micro and macro analyses. These are questions with which the new sociology of violence might engage.

A ética como criação de qualidade de vida : o apreço pela vida como pilar de sustentação da acção humana

Relatório da Prática de Ensino Supervisionada, Mestrado em Ensino da Filosofia, Universidade de Lisboa, 2011

Rhetorical Topographies of Post-Earthquake L'Aquila: Locality, Activism, and Citizenship Engagement

Thesis (Ph.D.)--University of Washington, 2014

IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms.

Integração de um sistema de gestão de informação clínica hospitalar numa unidade de cuidados continuados

O crescimento da população idosa impõe o desenvolvimento de serviços de qualidade orientados para as necessidades comuns desta faixa etária. A área dos cuidados continuados corresponde a um segmento em crescimento com um forte potencial de desenvolvimento no que concerne ao domínio dos sistemas de informação (SI). O presente trabalho pressupõe o acompanhamento do processo de integração de um SI de uma Unidade Hospitalar (UH) numa Unidade de Cuidados Continuados (UCC) para idosos. A análise envolveu o recurso à Teoria Actor-network (ANT), enquanto posicionamento teórico de relevo para o desenvolvimento de SI. Esta teoria coloca, equitativamente, em destaque os factores humano e não humano como concorrentes para o sucesso no desenvolvimento de um SI. O processo em destaque neste trabalho envolveu a análise compreensiva dos SI das unidades de saúde envolvidas; monitorização e descrição do processo de integração do SI de inspiração hospitalar na UCC; avaliação do resultado final; estabelecimento de requisitos fundamentais para o desenho de um SI adaptado a uma organização prestadora de cuidados continuados a idosos. Estas etapas foram desenvolvidas tendo por base a concretização de 3 ciclos, integradores dos conceitos da ANT com o processo de Engenharia de Requisitos: Ciclo 1 - análise do sistema sócio-técnico; Ciclo 2 – desenho do novo sistema sócio-técnico; Ciclo 3 – transformação da rede sócio-técnica. A metodologia inerente ao processo envolveu a análise documental, realização de notas de campo, entrevista e questionário. Os requisitos são apresentados através da conceptualização de um SI denominado Gestão de Cuidados Residenciais (GCR). Conclui-se, que para que um SI resulte com eficácia, eficiência e efetividade para uma organização, deverá revelar-se adaptado ao propósito e missão da organização em causa, sob pena de induzir fragilidade ao ciclo operacional e ao modelo de gestão de informação.

Bioprocess design of canine adenovirus vectors for gene therapy applications

The potential of human adenovirus vectors as vehicles for gene transfer with clinical applications in vaccination, cancer treatment and in many monogenic and acquired diseases has been demonstrated in several studies and clinical trials. However, the clinical use of these vectors can be limited by pre-existing humoral and cellular anti-capsid immunity. One way to circumvent this bottleneck while keeping the advantages of using adenovirus vectors is using non-human viruses such as Canine Adenovirus type 2 (CAV-2). Moreover, CAV-2 vectors present attractive features to develop potential treatment of neurodegenerative and ocular disorders. While the interest in CAV-2 vectors increases, scalable and robust production processes are required to meet the need for preclinical and possibly clinical uses.(...)

Construction of bovine adenovirus type 3 E1 and E3, substitution plasmids and the sequencing analysis of DNA pol and pTP /

The relative ease to concentrate and purify adenoviruses, their well characterized mid-sized genome, and the ability to delete non-essential regions from their genome to accommodate foreign gene, made adenoviruses a suitable candidate for the construction of vectors. The use of adenoviral vectors in gene therapy, vaccination, and as a general vector system for expressing foreign genes have been documented for some time. In this study, the objective was to rescue a BAV3 E1 or E3 recombinant vector carrying the kanamycin resistant gene, a dominant selectable marker with useful applications in studying vectored gene expression in mammalian cells. To accomplish the objective of this study, more information about BAV3 DNA sequences was required in order to make the manipulation of the virus genome accessible. Therefore, sequencing of the BAV3 genome from 1 1 .7% to 30.8% was carried out. Analysis of the determined sequences revealed the primary structure of important viral gene products coded by E2 including BAV3 DNA pol and precursor to terminal protein. Comparative analysis of these proteins with their counterparts from human and non human adenoviruses revealed important insights as to the evolutionary lineage of BAV3. In order to insert the kanamycin resistance gene in either E1 or E3, it was necessary to delete BAV3 sequences to accommodate the foreign gene so as not to exceed the limit of the packaging capacity of the virus. To construct a recombinant BAV3 in which a foreign gene was inserted in the deleted E1 region, an E1 shuttle vector was constructed. This involved the deletion from the viral sequences a region between 1.3% to 9% and inserting the kanamycin resistance gene to replace the deletion. The E1 shuttle vector contained the left (0%- 53.9%) segment of the genome and was expected to generate BAV3 recombinants that can be grown and propagated in cells that can complement the missing E1 functions. To construct a similar shuttle vector for E3 deletion, DNA sequences extending from 78.9% to 82.5% (1281 bp) were deleted from within the E3 region that had been cloned into a plasmid vector. The deleted region corresponds to those that have been shown to be non-essential for viral replication in cell culture. The resulting plasmid was used to construct another recombinant plasmid with BAV3 DNA sequences extending from 37.1% to 100% and with a deletion of E3 sequences that were replaced by kanamycin resistance gene. This shuttle plasmid was used in cotransfections with digested viral DNA in an attempt to rescue a recombinant BAV3 carrying the kanamycin resistance gene to replace the deleted E3. In spite of repeated attempts of transfection, El or E3 recombinant BAV3 were not isolated. It seems that other approaches should be applied to make a final conclusion on BAV3 infectivity.