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1.
This discussion is a rejoinder to Drid Williams' discussion of the article “Church Festivals and the Visualization of Identity in Collingwood Bay, Papua New Guinea” [Hermkens 2007 2007 Church Festivals and the Visualization of Identity in Collingwood Bay, Papua New Guinea . Visual Anthropology , 20 ( 5 ): 347364 .[Taylor & Francis Online] [Google Scholar]].  相似文献   

2.
3.

Background

Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors.

Methods

In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families.

Results

We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database.

Conclusions

Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement.
  相似文献   

4.
Abstract

Gypsy, Roma or traveller minorities remain a group that is still homogenized as the ‘other’11. There are an estimated 12 million Gypsy people across Europe, with the majority residing in Central and Eastern Europe. ‘Roma’ is the European institutional preferred umbrella term, but it is often rejected by activists and at a local level because many groups still identify as ‘Gypsies’ (Gay y Blasco 2002 Gay Y Blasco, Paloma 2002Gypsy/Gypsy diasporas: A comparative perspective’, Social Anthropology, vol. 10, no. 2, pp. 17388[Crossref] [Google Scholar]; Mayall 2004 Mayall, David 2004 Gypsy Identities 1500–2000: From Egipcyans and Moon-men to the Ethnic Romany, London: Routledge[Crossref] [Google Scholar]; Szuhay 2005 Szuhay, Péter 2005The self-definitions of Roma ethnic groups and their perceptions of other Roma groups’, in Kemény István (ed.), Roma of Hungary, New York: Columbia University Press, pp. 23746 [Google Scholar]). In this article I use ‘Gypsy’ as a translation of the Hungarian word cigány as this is how the participants self-identified.. The European imagination continues to be entrenched in the spectacle of their difference – images of weddings, musicians, funerals and fights are fascinating and are thus prioritized. But what would happen if the cameras were given to these people themselves? What if they became the image-makers? This article examines how ethnic studies might contribute to breaking the mould of the exoticized Gypsy through self-representations. The study here formed part of an ethnographic project among primary school pupils in Hungary. Using the photo elicitation method, children were given disposable cameras producing 451 photographs that then formed the basis of interviews. The results reveal very few indicators that could be described as significantly or distinctively divided into ‘Gypsy’ or ‘non-Gypsy’ identifications, questioning the status of difference in discourses around such minorities.  相似文献   

5.
Shelter dogs are typically cared for by staff and volunteers. At the Boston location of the Massachusetts Society for the Prevention of Cruelty to Animals, prior to 2009, any member of the public who was older than 16 years of age and attended 1 orientation could walk dogs available for adoption. There was no systematic method of training volunteers or staff to walk unruly, strong, or fearful dogs, nor was there any organized system of enrichment in the form of in-kennel or out-of-kennel training for the population of 20 to 40 dogs in the shelter. Using the Dick and Carey (1996 Dick, W., &; Carey, L. (1996). The systematic design of instruction. New York, NY: Harper Collins. [Google Scholar]) model of instructional design, a curriculum called “Safewalk” was devised and implemented. Safewalk created a hierarchical training system for volunteers. After training was implemented, outcomes and lengths of stay were then compared for dogs for the 3 years before and 4 years after Safewalk. Changes in adoption rates for pit bull-type dogs and non-pit bulls were significantly improved, and length of stay for non-pit bulls was significantly decreased. Other components of shelter life for dogs and people were also improved.  相似文献   

6.
Pluripotent stem cells, including induced pluripotent and embryonic stem cells (ESCs), have less developed mitochondria than somatic cells and, therefore, rely more heavily on glycolysis for energy production.1-3 Zhang J, Nuebel E, Daley GQ, Koehler CM, Teitell MA. Metabolic regulation in pluripotent stem cells during reprogramming and self-renewal. Cell Stem Cell 2012; 11:589-95; PMID:23122286; http://dx.doi.org/10.1016/j.stem.2012.10.005 Vessoni AT, Muotri AR, Okamoto OK. Autophagy in stem cell maintenance and differentiation. Stem Cells Dev 2012; 21:513-20; PMID:22066548; http://dx.doi.org/10.1089/scd.2011.0526 Suhr ST, Chang EA, Tjong J, Alcasid N, Perkins GA, Goissis MD, Ellisman MH, Perez GI, Cibelli JB. Mitochondrial rejuvenation after induced pluripotency. PLoS One 2010; 5:e14095; PMID:21124794; http://dx.doi.org/10.1371/journal.pone.0014095  However, how mitochondrial homeostasis matches the demands of nuclear reprogramming and regulates pluripotency in ESCs is largely unknown. Here, we identified ATG3-dependent autophagy as an executor for both mitochondrial remodeling during somatic cell reprogramming and mitochondrial homeostasis regulation in ESCs. Dysfunctional autophagy by Atg3 deletion inhibited mitochondrial removal during pluripotency induction, resulting in decreased reprogramming efficiency and accumulation of abnormal mitochondria in established iPSCs. In Atg3 null mouse ESCs, accumulation of aberrant mitochondria was accompanied by enhanced ROS generation, defective ATP production and attenuated pluripotency gene expression, leading to abnormal self-renewal and differentiation. These defects were rescued by reacquisition of wild-type but not lipidation-deficient Atg3 expression. Taken together, our findings highlight a critical role of ATG3-dependent autophagy for mitochondrial homeostasis regulation in both pluripotency acquirement and maintenance.  相似文献   

7.
Accurately determining the proper captive environment for apes requires adequately assessing the psychological similarities between apes and humans. Scientists currently believe apes lack mental complexity (Millikan, 2006 Millikan, R. G. 2006. “Styles of rationality”. In Rational animals?, Edited by: Hurley, S. and Nudds, M. 117126. Oxford, , England: Oxford University Press.. [Crossref] [Google Scholar]), raising questions concerning the evolution of human culture from ape-like societies (Tomasello, 1999 Tomasello, M. 1999. The cultural origins of human cognition, Cambridge, , MA: Harvard University Press..  [Google Scholar]). A long-term cultural study with bonobos suggests less intellectual divergence from humans than currently postulated (Savage-Rumbaugh, 2005 Savage-Rumbaugh, E. S. 2005. “Individual differences in language competencies in apes resulting from unique rearing conditions imposed by different first epistemologies”. In Symbol use and symbolic representation, Edited by: Namy, L. L. 199219. Mahwah, , NJ: Lawrence Erlbaum Associates, Inc..  [Google Scholar]). Because humans view apes as mentally limited, some current captive environments may appear idyllic while offering only an illusion of appropriate care, derived from a simplistic view of what apes are, rather than what they might be. This perception of apes determines their handling, which determines their mental development, which perpetuates the prevailing perception. Only breaking this cycle will allow the current perception of apes to change. Their usual captive environment limits any demonstration of culture. However, the bonobo study reveals what ape culture can become, which should affect future welfare considerations for at least those species genetically close to humans (bonobos and chimpanzees). Development of a languaged bonobo culture allows these nonhuman animals to provide their own responses regarding adequate ape welfare.  相似文献   

8.
Abstract

In his recent article in Ethnic and Racial Studies, entitled ‘Curbing Kurdish ethno-nationalism in Turkey’, (Sarigil 2010 Sarigil, Zeki. 2010. Curbing Kurdish ethno-nationalism in Turkey: an empirical assessment of pro-Islamic and socio-economic approaches. Ethnic and Racial Studies, 33(3): 53353. [Taylor &; Francis Online], [Web of Science ®] [Google Scholar]) tests two rival hypotheses regarding Kurdish ethno-nationalism in Turkey and, using data from the World Values Survey (WVS), finds that socio-economic status (levels of income and education) better explains the individual roots of Kurdish ethno-nationalism in Turkey than does religiousness. In this paper, I offer both a methodological critique of Sarigil's research and a replication of his model with a more appropriate sample. I first argue that Sarigil's research design lacks internal validity because it studies Kurdish nationalism within a sample that predominantly consists of Turks, which invalidates his findings. I then replicate and expand Sarigil's model within a specific sample of Kurdish-speaking people in Turkey. The results show dramatic changes. Religiosity and political satisfaction seem to be better predictors of support for Kurdish ethno-nationalism in Turkey than do socio-economic factors.  相似文献   

9.
《Animal biotechnology》2013,24(1):97-112

Developed countries are not immune from serious food-borne diseases, and the source is often the intestine of cattle, sheep and poultry livestock. Outbreaks of Escherichia coli 0157, most recently killing people in Ontario, and of salmonella and shigella food poisoning especially during summer months, remind us of the seriousness of the problem. Thus, there is renewed interest in alternative approaches to antibiotics to control bacterial diseases, both in humans and veterinary medicine.3-4 Whatley, B. T. 1987. “A ‘Natural’ Answer to Antibiotics.”. In InBooker T. Whatley's Handbook on How to Make $100,000 Farming 25 Acres: With Special Plans for Prospering on 10 to 200 Acres Edited by: DeVault, G. 137139. Cramer, C. 1990. Healthy Livestock with Fewer Drugs. The New Farm, 12: 2330.   Consumers are believed to be concerned not only about bacterial pathogens being in meat, but also that residues of antibiotics may also be present. The trend to “natural” farming without exposure to chemicals, pesticides and herbicides could be one reason for increased interest in probiotics for livestock farming.  相似文献   

10.
The ratios of d- versus l-amino acids can be used to infer the sources and composition of sedimentary organic matter. Such inferences, however, rely on knowing the rates at which amino acids in sedimentary organic matter racemize abiotically between the d- and the l-forms. Based on a heating experiment, we report kinetic parameters for racemization of aspartic acid, glutamic acid, serine, and alanine in bulk sediment from Aarhus Bay, Denmark, taken from the surface, 30 cm, and 340 cm depth below seafloor. Extrapolation to a typical cold deep sea sediment temperature of 3°C suggests racemization rate constants of 0.50×10−5–11×10−5 yr−1. These results can be used in conjunction with measurements of sediment age to predict the ratio of d:l amino acids due solely to abiotic racemization of the source material, deviations from which can indicate the abundance and turnover of active microbial populations.  相似文献   

11.
Bacteria may change their behavior depending on the population density. Here we study a dynamical model in which cells of radius $R$ within a diffusive medium communicate with each other via diffusion of a signalling substance produced by the cells. The model consists of an initial boundary value problem for a parabolic PDE describing the exterior concentration $u$ of the signalling substance, coupled with $N$ ODEs for the masses $a_i$ of the substance within each cell. We show that for small $R$ the model can be approximated by a hierarchy of models, namely first a system of $N$ coupled delay ODEs, and in a second step by $N$ coupled ODEs. We give some illustrations of the dynamics of the approximate model.  相似文献   

12.
We identified active isoforms of the chimeric anti-GD2 antibody, ch14.18, a recombinant antibody produced in Chinese hamster ovary cells, which is already used in clinical trials.1,2,3 Ladenstein R, Weixler S, Baykan B, Bleeke M, Kunert R, Katinger D, Pribill I, Glander P, Bauer S, Pistoia V, et al. Ch14.18 antibody produced in CHO cells in relapsed or refractory Stage 4 neuroblastoma patients: a SIOPEN Phase 1 study. MAbs 2013; 5:801-9; PMID:23924804; http://dx.doi.org/10.4161/mabs.25215 Desai AV, Fox E, Smith LM, Lim AP, Maris JM, Balis FM. Pharmacokinetics of the chimeric anti-GD2 antibody, ch14.18, in children with high-risk neuroblastoma. Cancer Chemother Pharmacol 2014; 74:1047-55; PMID:25212536; http://dx.doi.org/10.1007/s00280-014-2575-9 Siebert N, Eger C, Seidel D, Jüttner M, Zumpe M, Wegner D, Kietz S, Ehlert K, Veal GJ, Siegmund W, et al. Pharmacokinetics and pharmacodynamics of ch14.18/CHO in relapsed/refractory high-risk neuroblastoma patients treated by long-term infusion in combination with IL-2. MAbs 2016; 8:604-16; PMID:26785755; http://dx.doi.org/10.1080/19420862.2015.1130196  We separated the antibody by high resolution ion-exchange chromatography with linear pH gradient elution into acidic, main and basic charge variants on a preparative scale yielding enough material for an in-depth study of the sources and the effects of microheterogeneity. The binding affinity of the charge variants toward the antigen and various cell surface receptors was studied by Biacore. Effector functions were evaluated using cellular assays for antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity. Basic charge variants showed increased binding to cell surface receptor FcγRIIIa, which plays a major role in regulating effector functions. Furthermore, increased binding of the basic fractions to the neonatal receptor was observed. As this receptor mediates the prolonged half-life of IgG in human serum, this data may well hint at an increased serum half-life of these basic variants compared to their more acidic counterparts. Different glycoform patterns, C-terminal lysine clipping and N-terminal pyroglutamate formation were identified as the main structural sources for the observed isoform pattern. Potential differences in structural stability between individual charge variant fractions by nano differential scanning calorimetry could not been detected. Our in-vitro data suggests that the connection between microheterogeneity and the biological activity of recombinant antibody therapeutics deserves more attention than commonly accepted.  相似文献   

13.
Genome-wide association studies (GWAS) have revealed numerous genomic 'hits' associated with complex phenotypes. In most cases these hits, along with surrogate genetic variation as measure by numerous single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium, are not in coding genes making assignment of functionality or causality intractable. Here we propose that fine-mapping along with the matching of risk SNPs at chromatin biofeatures lessen this complexity by reducing the number of candidate functional/causal SNPs. For example, we show here that only on average 2 SNPs per prostate cancer risk locus are likely candidates for functionality/causality; we further propose that this manageable number should be taken forward in mechanistic studies. The candidate SNPs can be looked up for each prostate cancer risk region in 2 recent publications in 20151,2 Han Y, Hazelett DJ, Wiklund F, Schumacher FR, Stram DO, Berndt SI, Wang Z, Rand KA, Hoover RN, Machiela MJ, et al. Integration of Multiethnic Fine-mapping and Genomic Annotation to Prioritize Candidate Functional SNPs at Prostate Cancer Susceptibility Regions. Hum Mol Genet 2015; 24(19):560318. Amin Al Olama A, Dadaev T, Hazelett DJ, Li Q, Leongamornlert D, Saunders EJ, Stephens S, Cieza-Borrella C, Whitmore I, Benlloch Garcia S, et al. Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans. Hum Mol Genet 2015; 24(19):5589602.  from our groups.  相似文献   

14.
15.
Effect of oxygen tension on l-lysine, l-threonine and l-isoleucine accumulation was investigated. Sufficient supply of oxygen to satisfy the cell’s oxygen demand was essential for the maximum production in each fermentation. The dissolved oxygen level must be controlled at greater than 0.01 atm in every fermentation, and the optimum redox potentials of culture media were above ?170 mV in l-lysine and l-threonine and above ?180 mV in l-isoleucine fermentations. The maximum concentrations of the products were 45.5 mg/ml for l-lysine, 10.3 mg/ml for l-threonine and 15.1 mg/ml for l-isoleucine. The degree of the inhibition due to oxygen limitation was slight in the fermentative production of l-lysine, l-threonine and l-isoleucine, whose biosynthesis is initiated with l-aspartic acid, in contrast to the accumulation of l-proline, l-glutamine and l-arginine, which is biosynthesized by way of l-glutamic acid.  相似文献   

16.
Quorum sensing is a wide-spread mode of cell–cell communication among bacteria in which cells release a signalling substance at a low rate. The concentration of this substance allows the bacteria to gain information about population size or spatial confinement. We consider a model for \(N\) cells which communicate with each other via a signalling substance in a diffusive medium with a background flow. The model consists of an initial boundary value problem for a parabolic PDE describing the exterior concentration \(u\) of the signalling substance, coupled with \(N\) ODEs for the masses \(a_i\) of the substance within each cell. The cells are balls of radius \(R\) in \(\mathbb {R} ^3\) , and under some scaling assumptions we formally derive an effective system of \(N\) ODEs describing the behaviour of the cells. The reduced system is then used to study the effect of flow on communication in general, and in particular for a number of geometric configurations.  相似文献   

17.
Hana Popelka 《Autophagy》2017,13(3):449-451
Atg13 is an essential subunit of the Atg1 autophagy initiation complex in yeast and its mammalian counterpart, ATG13, is indispensable for autophagy induction by the ULK1 complex. The N terminus of the protein folds into a HORMA domain, an architecture that has been revealed by crystallography.1-4 Jao CC, Ragusa MJ, Stanley RE, Hurley JH. A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy. P Natl Acad Sci USA 2013; 110:5486-91; PMID:23509291; http://dx.doi.org/10.1073/pnas.1220306110 Suzuki SW, Yamamoto H, Oikawa Y, Kondo-Kakuta C, Kimura Y, Hirano H, Ohsumi Y. Atg13 HORMA domain recruits Atg9 vesicles during autophagosome formation. P Natl Acad Sci USA 2015; 112:3350-5; PMID:25737544; http://dx.doi.org/10.1073/pnas.1421092112 Suzuki H, Kaizuka T, Mizushima NNoda NN. Structure of the Atg101-Atg13 complex reveals essential roles of Atg101 in autophagy initiation. Nat Struct Mol Biol 2015; 22:572-81; PMID:26030876; http://dx.doi.org/10.1038/nsmb.3036 Qi SQ, Kim DJ, Stjepanovic G, Hurley JH. Structure of the human Atg13-Atg101 HORMA heterodimer: An interaction hub within the Ulk1 complex. Structure 2015; 23:1848-57; PMID:26299944; http://dx.doi.org/10.1016/j.str.2015.07.011  In human cells, the ATG13 HORMA domain interacts directly with ATG14, a subunit of the class III phosphatidylinositol 3-kinase complex.5 Park JM, Jung CH, Seo M, Otto NM, Grunwald D, Kim KH, Moriarity B, Kim YM, Starker C, Nho RS, et al. The Ulk1 complex mediates mTORC1 signaling to the autophagy initiation machinery via binding and phosphorylating Atg14. Autophagy 2016; 12:547-64; PMID:27046250; http://dx.doi.org/10.1080/15548627.2016.1140293[Taylor & Francis Online], [Web of Science ®] [Google Scholar] In budding yeast, the HORMA domain of Atg13 recruits Atg14, but a direct interaction remains to be proven.1 Jao CC, Ragusa MJ, Stanley RE, Hurley JH. A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy. P Natl Acad Sci USA 2013; 110:5486-91; PMID:23509291; http://dx.doi.org/10.1073/pnas.1220306110[Crossref], [PubMed], [Web of Science ®] [Google Scholar] The amino acid sequence that follows the HORMA domain does not adopt any 3-dimensional structure on its own; therefore, it is termed an intrinsically disordered region (IDR). Here we discuss the results of 2 recent studies in light of previous reports on Atg13 from yeast. Together, they yield an insight into the molecular mechanism for the function of this intriguing protein, and reveal why Atg13, as well as the mammalian homolog ATG13, cannot have a structurally rigid architecture.  相似文献   

18.
In this article I discuss how visual anthropology methods are advancing in a present-day environment where applied, activist, public and interdisciplinary anthropologies are increasingly central. In earlier work [Pink 2004 Pink , Sarah 2004 Applied Visual Anthropology, a guest edited issue of Visual Anthropology Review, 20(1) . [Google Scholar], 2006 2006 The Future of Visual Anthropology: Engaging the Senses . Oxford : Routledge . [Google Scholar], 2007a 2007a Visual Interventions: Applied Visual Anthropology . Oxford : Berghahn . [Google Scholar]] I outlined the field of an applied visual anthropology, and discussed the potential of visual methods and media in the production of a public anthropology [Pink 2006 2006 The Future of Visual Anthropology: Engaging the Senses . Oxford : Routledge . [Google Scholar]]. Here I build on this to suggest how recent visual anthropology practices might both contribute to and resolve issues relating to contemporary debates in applied and public anthropology and the relationship between scholarly research and social intervention.  相似文献   

19.
Assessing risks involves developing predictive mathematical models, using interpretations of data that are based on scientific assumptions or theories and knowledge of how the data were created. The predictions are used for developing strategies that affect many people in society. Often, it is sufficient that the models that are used are justifiable by a well-accepted set of assumptions or theories, reflecting the state-of-the art science at the time. However, this does not ensure that the “best” decision would be made, nor does it ensure that the decision processes would be fair by ensuring that concerned and affected individuals would be able to participate, effectively presenting arguments on their own behalf. Because of these concerns, procedures of risk analysis, including the management of the process, have been written about, for example, in a National Research Council (NRC 1996 NRC. 1996. Understanding Risk, Informing Decisions in a Democratic Society, Washington, DC, , USA: National Academy Press.  [Google Scholar]) publication, with the intention of getting stakeholders (interested participants) more involved in the risk analysis process. This publication suggests that Risk Characterization be expanded to include an active participation of stakeholders. Such an expansion would affect the risk assessor's approach toward science compared to the present approach, as implied in the seminal NRC (1983) NRC (National Research Council). 1983. Risk Assessment in the Federal Government: Managing the Process, Washington, DC, , USA: National Academy Press.  [Google Scholar] publication. Both of these NRC publications have had great influence on the development of risk analysis management and policy in the United States and elsewhere. Subsequent risk assessment guidance documents have generally relied heavily on these publications, but have focused mainly on managerial attitudes (or policy) toward the uncertainty that is inherent in risk assessment and in communicating to the public the risk assessment conclusions and decisions made from them. Subsequent documents have not, unlike NRC (1996) NRC. 1996. Understanding Risk, Informing Decisions in a Democratic Society, Washington, DC, , USA: National Academy Press.  [Google Scholar], focused on the risk assessors' attitude toward science inference that would better help ensure that risk assessments contain the type of information that could be used to empower stakeholders. Thus, in this Perspective article I focus on the two NRC “foundation documents,” identifying and contrasting two types of approaches toward science, one narrow and the other expansive. The latter approach is designed to increase stakeholders' involvement more than the former. The features of the expansive approach include a contemplative method toward science, where the risk assessor does not express opinions or take a stand regarding the scientific material, but rather considers many possibilities, presents discussions that include direct challenges to assumptions, and uses falsification principles for excluding theories.  相似文献   

20.
Authors and scholars published within Arts Education Policy Review have been diligent to investigate various topics surrounding music educator preparation, mentoring, retention, as well as avenues for continued professional development and growth. Linda Darling-Hammond and Robert Rothman, along with various chapter authors, address education reform on an international level within Teaching in the Flat World: Learning from High-Performing Systems (2015 Rothman, R., & Darling-Hammond, L. (2015). Teaching quality initiatives in the United States. In L. Darling-Hammond & R. Rothman (Eds.), Teaching in the flat world: Learning from high-performing systems (pp. 627). New York, NY: Teachers College Press. [Google Scholar]). The purpose of this article is to examine the recommendations presented by Darling-Hammond, Rothman, and colleagues through the lens of music education research and policy review. Specific areas of focus include: (a) recruitment and rigor of teacher education programs, (b) alternative routes into the teaching profession, (c) teacher induction and new teacher support, (d) career advancement and professional development support, and (e) teacher evaluation.  相似文献   

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